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Schloßhauer JL, Tholen L, Körner A, Kubick S, Chatzopoulou S, Hönow A, Zemella A. Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2α. Synth Syst Biotechnol 2024; 9:416-424. [PMID: 38601208 PMCID: PMC11004649 DOI: 10.1016/j.synbio.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/12/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024] Open
Abstract
Chinese hamster ovary (CHO) cells are crucial in biopharmaceutical production due to their scalability and capacity for human-like post-translational modifications. However, toxic proteins and membrane proteins are often difficult-to-express in living cells. Alternatively, cell-free protein synthesis can be employed. This study explores innovative strategies for enhancing the production of challenging proteins through the modification of CHO cells by investigating both, cell-based and cell-free approaches. A major result in our study involves the integration of a mutant eIF2 translation initiation factor and T7 RNA polymerase into CHO cell lysates for cell-free protein synthesis. This resulted in elevated yields, while eliminating the necessity for exogenous additions during cell-free production, thereby substantially enhancing efficiency. Additionally, we explore the potential of the Rosa26 genomic site for the integration of T7 RNA polymerase and cell-based tetracycline-controlled protein expression. These findings provide promising advancements in bioproduction technologies, offering flexibility to switch between cell-free and cell-based protein production as needed.
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Affiliation(s)
- Jeffrey L. Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Lena Tholen
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
| | - Alexander Körner
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus –Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Sofia Chatzopoulou
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
| | - Anja Hönow
- New/era/mabs GmbH, August-Bebel-Str. 89, 14482, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
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Pennati A, Jakobi M, Zeng F, Ciampa L, Rothbächer U. Optimizing CRISPR/Cas9 approaches in the polymorphic tunicate Ciona intestinalis. Dev Biol 2024; 510:31-39. [PMID: 38490564 DOI: 10.1016/j.ydbio.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
CRISPR/Cas9 became a powerful tool for genetic engineering and in vivo knockout also in the invertebrate chordate Ciona intestinalis. Ciona (ascidians, tunicates) is an important model organism because it shares developmental features with the vertebrates, considered the sister group of tunicates, and offers outstanding experimental advantages: a compact genome and an invariant developmental cell lineage that, combined with electroporation mediated transgenesis allows for precise and cell type specific targeting in vivo. A high polymorphism and the mosaic expression of electroporated constructs, however, often hamper the efficient CRISPR knockout, and an optimization in Ciona is desirable. Furthermore, seasonality and artificial maintenance settings can profit from in vitro approaches that would save on animals. Here we present improvements for the CRISPR/Cas9 protocol in silico, in vitro and in vivo. Firstly, in designing sgRNAs, prior sequencing of target genomic regions from experimental animals and alignment with reference genomes of C. robusta and C. intestinalis render a correction possible of subspecies polymorphisms. Ideally, the screening for efficient and non-polymorphic sgRNAs will generate a database compatible for worldwide Ciona populations. Secondly, we challenged in vitro assays for sgRNA validation towards reduced in vivo experimentation and report their suitability but also overefficiency concerning mismatch tolerance. Thirdly, when comparing Cas9 with Cas9:Geminin, thought to synchronize editing and homology-direct repair, we could indeed increase the in vivo efficiency and notably the access to an early expressed gene. Finally, for in vivo CRISPR, genotyping by next generation sequencing (NGS) ex vivo streamlined the definition of efficient single guides. Double CRISPR then generates large deletions and reliable phenotypic excision effects. Overall, while these improvements render CRISPR more efficient in Ciona, they are useful when newly establishing the technique and very transferable to CRISPR in other organisms.
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Affiliation(s)
- Alessandro Pennati
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Miloš Jakobi
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Fan Zeng
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Luca Ciampa
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Ute Rothbächer
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria.
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Lei X, Cao S, Liu T, Wu Y, Yu S. Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection. Talanta 2024; 271:125663. [PMID: 38232570 DOI: 10.1016/j.talanta.2024.125663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.
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Affiliation(s)
- Xueying Lei
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Shengnan Cao
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Tao Liu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Yongjun Wu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Songcheng Yu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China.
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Nathans JF, Ayers JL, Shendure J, Simpson CL. Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin. J Invest Dermatol 2024; 144:936-949. [PMID: 38643988 PMCID: PMC11034889 DOI: 10.1016/j.jid.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 04/23/2024]
Abstract
The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.
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Affiliation(s)
- Jenny F Nathans
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jessica L Ayers
- Molecular Medicine and Mechanisms of Disease PhD Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Dermatology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Cory L Simpson
- Department of Dermatology, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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Sun S, Han X, Jin R, Jiao J, Wang J, Niu S, Yang Z, Wu D, Wang Y. Generation of CRISPR-edited birch plants without DNA integration using Agrobacterium-mediated transformation technology. Plant Sci 2024; 342:112029. [PMID: 38354755 DOI: 10.1016/j.plantsci.2024.112029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
CRISPR/Cas9 system has emerged as a powerful tool in genome editing; however, generation of CRISPR-edited DNA-free plants is still challenging. In this study, Betula platyphylla (birch) was used to build a method to generate CRISPR-edited plant without foreign DNA integration using Agrobacterium-mediated transformation (CPDAT method). This technique utilizes transient genetic transformation to introduce T-DNA coding gRNA and Cas9 into birch cells, and T-DNA will express to synthesize gRNA and Cas9 protein, which will form a complex to cleave the target DNA site. The genome may be mutated due to DNA repair, and these mutations will be preserved and accumulated not dependent on whether T-DNA is integrated into the genome or not. After transient transformation, birch plants were cut into explants to induce adventitious buds without antibiotic selection pressure. Each adventitious bud can be considered as an independent potentially CRISPR-edited line for mutation detection. CRISPR-edited birch plants without foreign DNA integration are further selected by screening CRISPR-edited lines without T-DNA integration. Among 65 randomly chosen independent lines, the mutation rate was 80.00% including 40.00% of lines with both alleles mutated. In addition, 5 lines out of 65 studied lines (7.69%) were CRISPR-edited birch plants without DNA integration. In conclusion, this innovative method presents a novel strategy for generating CRISPR-edited birch plants, thereby significantly enhancing the efficiency of generating common CRISPR-edited plants. These findings offer considerable potential to develop plant genome editing techniques further.
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Affiliation(s)
- Shilin Sun
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Xue Han
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Ruoxuan Jin
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Junbo Jiao
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Jingwen Wang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Siyuan Niu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Ziyao Yang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Di Wu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang 110866, China.
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Sachdev A, Gill K, Sckaff M, Birk AM, Aladesuyi Arogundade O, Brown KA, Chouhan RS, Issagholian-Lewin PO, Patel E, Watry HL, Bernardi MT, Keough KC, Tsai YC, Smith AST, Conklin BR, Clelland CD. Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision. Proc Natl Acad Sci U S A 2024; 121:e2307814121. [PMID: 38621131 DOI: 10.1073/pnas.2307814121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 03/01/2024] [Indexed: 04/17/2024] Open
Abstract
Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding single nucleotide polymorphism in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using digital droplet PCR (ddPCR), we determined that transcription from the mutant allele is upregulated at least 10-fold, and that sense transcription is independently regulated from each allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat poly-GP expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production, and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all dipeptide repeat proteins, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including antisense oligonucleotides (ASOs) and CRISPR gene editing.
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Affiliation(s)
| | - Kamaljot Gill
- Gladstone Institutes, San Francisco, CA 94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | - Maria Sckaff
- Gladstone Institutes, San Francisco, CA 94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
| | | | - Olubankole Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158
| | - Katherine A Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158
| | - Runvir S Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158
| | - Patrick Oliver Issagholian-Lewin
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158
| | - Esha Patel
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158
| | | | | | | | | | - Alec Simon Tulloch Smith
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
- The Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA 94158
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143
- Department of Pharmacology, University of California San Francisco, San Francisco, CA 94158
| | - Claire Dudley Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158
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Zhao X, He Y, Shao S, Ci Q, Chen L, Lu X, Liu Q, Chen J. CRISPR/Cas14 and G-Quadruplex DNAzyme-Driven Biosensor for Paper-Based Colorimetric Detection of African Swine Fever Virus. ACS Sens 2024. [PMID: 38635911 DOI: 10.1021/acssensors.4c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The highly contagious nature and 100% fatality rate contribute to the ongoing and expanding impact of the African swine fever virus (ASFV), causing significant economic losses worldwide. Herein, we developed a cascaded colorimetric detection using the combination of a CRISPR/Cas14a system, G-quadruplex DNAzyme, and microfluidic paper-based analytical device. This CRISPR/Cas14a-G4 biosensor could detect ASFV as low as 5 copies/μL and differentiate the wild-type and mutated ASFV DNA with 2-nt difference. Moreover, this approach was employed to detect ASFV in porcine plasma. A broad linear detection range was observed, and the limit of detection in spiked porcine plasma was calculated to be as low as 42-85 copies/μL. Our results indicate that the developed paper platform exhibits the advantages of high sensitivity, excellent specificity, and low cost, making it promising for clinical applications in the field of DNA disease detection and suitable for popularization in low-resourced areas.
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Affiliation(s)
- Xue Zhao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shengjie Shao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Qiaoqiao Ci
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lin Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
| | - Xiaonan Lu
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Qian Liu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Bioengineering, University of California, Riverside, California 92521, United States
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Greatbatch CJ, Lu Q, Hung S, Barnett AJ, Wing K, Liang H, Han X, Zhou T, Siggs OM, Mackey DA, Cook AL, Senabouth A, Liu GS, Craig JE, MacGregor S, Powell JE, Hewitt AW. High throughput functional profiling of genes at intraocular pressure loci reveals distinct networks for glaucoma. Hum Mol Genet 2024; 33:739-751. [PMID: 38272457 PMCID: PMC11031357 DOI: 10.1093/hmg/ddae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/18/2023] [Accepted: 04/06/2024] [Indexed: 01/27/2024] Open
Abstract
INTRODUCTION Primary open angle glaucoma (POAG) is a leading cause of blindness globally. Characterized by progressive retinal ganglion cell degeneration, the precise pathogenesis remains unknown. Genome-wide association studies (GWAS) have uncovered many genetic variants associated with elevated intraocular pressure (IOP), one of the key risk factors for POAG. We aimed to identify genetic and morphological variation that can be attributed to trabecular meshwork cell (TMC) dysfunction and raised IOP in POAG. METHODS 62 genes across 55 loci were knocked-out in a primary human TMC line. Each knockout group, including five non-targeting control groups, underwent single-cell RNA-sequencing (scRNA-seq) for differentially-expressed gene (DEG) analysis. Multiplexed fluorescence coupled with CellProfiler image analysis allowed for single-cell morphological profiling. RESULTS Many gene knockouts invoked DEGs relating to matrix metalloproteinases and interferon-induced proteins. We have prioritized genes at four loci of interest to identify gene knockouts that may contribute to the pathogenesis of POAG, including ANGPTL2, LMX1B, CAV1, and KREMEN1. Three genetic networks of gene knockouts with similar transcriptomic profiles were identified, suggesting a synergistic function in trabecular meshwork cell physiology. TEK knockout caused significant upregulation of nuclear granularity on morphological analysis, while knockout of TRIOBP, TMCO1 and PLEKHA7 increased granularity and intensity of actin and the cell-membrane. CONCLUSION High-throughput analysis of cellular structure and function through multiplex fluorescent single-cell analysis and scRNA-seq assays enabled the direct study of genetic perturbations at the single-cell resolution. This work provides a framework for investigating the role of genes in the pathogenesis of glaucoma and heterogenous diseases with a strong genetic basis.
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Affiliation(s)
- Connor J Greatbatch
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Qinyi Lu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Sandy Hung
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne St, East Melbourne 3002, Australia
| | - Alexander J Barnett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Helena Liang
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne St, East Melbourne 3002, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane 4006, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, 1 Flinders Dr, Bedford Park, South Australia 5042, Australia
| | - Owen M Siggs
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, Short Street, St George Hospital KOGARAH UNSW, Sydney 2217, Australia
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, 2 Verdun Street Nedlands WA 6009, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, 1 Flinders Dr, Bedford Park, South Australia 5042, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane 4006, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, 32 Gisborne St, East Melbourne 3002, Australia
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9
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Cho T, Hoeg L, Setiaputra D, Durocher D. NFATC2IP is a mediator of SUMO-dependent genome integrity. Genes Dev 2024; 38:233-252. [PMID: 38503515 DOI: 10.1101/gad.350914.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
The post-translational modification of proteins by SUMO is crucial for cellular viability and mammalian development in part due to the contribution of SUMOylation to genome duplication and repair. To investigate the mechanisms underpinning the essential function of SUMO, we undertook a genome-scale CRISPR/Cas9 screen probing the response to SUMOylation inhibition. This effort identified 130 genes whose disruption reduces or enhances the toxicity of TAK-981, a clinical-stage inhibitor of the SUMO E1-activating enzyme. Among the strongest hits, we validated and characterized NFATC2IP, an evolutionarily conserved protein related to the fungal Esc2 and Rad60 proteins that harbors tandem SUMO-like domains. Cells lacking NFATC2IP are viable but are hypersensitive to SUMO E1 inhibition, likely due to the accumulation of mitotic chromosome bridges and micronuclei. NFATC2IP primarily acts in interphase and associates with nascent DNA, suggesting a role in the postreplicative resolution of replication or recombination intermediates. Mechanistically, NFATC2IP interacts with the SMC5/6 complex and UBC9, the SUMO E2, via its first and second SUMO-like domains, respectively. AlphaFold-Multimer modeling suggests that NFATC2IP positions and activates the UBC9-NSMCE2 complex, the SUMO E3 ligase associated with SMC5/SMC6. We conclude that NFATC2IP is a key mediator of SUMO-dependent genomic integrity that collaborates with the SMC5/6 complex.
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Affiliation(s)
- Tiffany Cho
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada;
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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10
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Deleuze V, Soler E, Andrieu-Soler C. Protocol for efficient CRISPR-Cas9-mediated fluorescent tag knockin in hard-to-transfect erythroid cell lines. STAR Protoc 2024; 5:103016. [PMID: 38640065 DOI: 10.1016/j.xpro.2024.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024] Open
Abstract
Precise insertion of fluorescent tags by CRISPR-Cas9-mediated homologous recombination (HR) in mammalian genes is a powerful tool allowing to study gene function and protein gene products. Here, we present a protocol for efficient HR-mediated targeted insertion of fluorescent markers in the genome of hard-to-transfect erythroid cell lines MEL (mouse erythroleukemic) and MEDEP (mouse ES cell-derived erythroid progenitor line). We describe steps for plasmid construction, electroporation, amplification, and verification of genome editing. We then detail procedures for isolating positive clones and validating knockin clones. For complete details on the use and execution of this protocol, please refer to Deleuze et al.1.
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Affiliation(s)
- Virginie Deleuze
- IGMM University Montpellier, CNRS, Montpellier, France; Laboratory of Excellence GR-Ex, Université' de Paris, Paris, France
| | - Eric Soler
- IGMM University Montpellier, CNRS, Montpellier, France; Laboratory of Excellence GR-Ex, Université' de Paris, Paris, France.
| | - Charlotte Andrieu-Soler
- IGMM University Montpellier, CNRS, Montpellier, France; Laboratory of Excellence GR-Ex, Université' de Paris, Paris, France.
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11
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Zhang Z, Zhang Y, Liu JL. eCRUIS captures RNA-protein interaction in vitro and in vivo. Exp Cell Res 2024; 438:114051. [PMID: 38631547 DOI: 10.1016/j.yexcr.2024.114051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/19/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
As an information bridge between DNA and protein, RNA regulates cellular processes and gene expression in various ways. From its synthesis to degradation, RNA is associated with a range of RNA-binding proteins. Therefore, it is necessary to develop innovative methods to study the interaction between RNA and proteins. Previously, we developed an RNA-centric method, called CRISPR-based RNA-United Interacting System (CRUIS), to capture RNA-protein interaction in cells. On this basis, here we develop an enhanced CRUIS (eCRUIS) by combining the power of dCas13d and the engineered promiscuous ligase TurboID. The current version allows us to rapidly label RNA-binding proteins on the target RNA within 30 minutes, potentially for in vivo use. By introducing bait-assay with exogenous RNA, we confirm that eCRUIS can effectively label RNA-binding proteins on bait RNA in a short time. eCRUIS provides a broader range of in vitro and in vivo applications for studying RNA-protein interactions.
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Affiliation(s)
- Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuanbing Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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12
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Nolan ND, Cui X, Robbings BM, Demirkol A, Pandey K, Wu WH, Hu HF, Jenny LA, Lin CS, Hass DT, Du J, Hurley JB, Tsang SH. CRISPR editing of anti-anemia drug target rescues independent preclinical models of retinitis pigmentosa. Cell Rep Med 2024; 5:101459. [PMID: 38518771 PMCID: PMC11031380 DOI: 10.1016/j.xcrm.2024.101459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/21/2023] [Accepted: 02/14/2024] [Indexed: 03/24/2024]
Abstract
Retinitis pigmentosa (RP) is one of the most common forms of hereditary neurodegeneration. It is caused by one or more of at least 3,100 mutations in over 80 genes that are primarily expressed in rod photoreceptors. In RP, the primary rod-death phase is followed by cone death, regardless of the underlying gene mutation that drove the initial rod degeneration. Dampening the oxidation of glycolytic end products in rod mitochondria enhances cone survival in divergent etiological disease models independent of the underlying rod-specific gene mutations. Therapeutic editing of the prolyl hydroxylase domain-containing protein gene (PHD2, also known as Egln1) in rod photoreceptors led to the sustained survival of both diseased rods and cones in both preclinical autosomal-recessive and dominant RP models. Adeno-associated virus-mediated CRISPR-based therapeutic reprogramming of the aerobic glycolysis node may serve as a gene-agnostic treatment for patients with various forms of RP.
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Affiliation(s)
- Nicholas D Nolan
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA
| | - Xuan Cui
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA
| | - Brian M Robbings
- Department of Biochemistry, The University of Washington, Seattle, WA 98195, USA; Diabetes Institute, The University of Washington, Seattle, WA 98195, USA
| | - Aykut Demirkol
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA; Vocational School of Health Services, Uskudar University, 34672 Istanbul, Turkey
| | - Kriti Pandey
- Department of Biochemistry, The University of Washington, Seattle, WA 98195, USA
| | - Wen-Hsuan Wu
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA
| | - Hannah F Hu
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA
| | - Laura A Jenny
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA
| | - Chyuan-Sheng Lin
- Herbert Irving Comprehensive Cancer Center, Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Departments of Ophthalmology, Pathology & Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniel T Hass
- Department of Biochemistry, The University of Washington, Seattle, WA 98195, USA
| | - Jianhai Du
- Department of Ophthalmology and Visual Sciences, West Virginia University, Morgantown, WV 26506, USA; Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26501, USA
| | - James B Hurley
- Department of Biochemistry, The University of Washington, Seattle, WA 98195, USA.
| | - Stephen H Tsang
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, NY 10032, USA; Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York-Presbyterian Hospital, New York, NY 10032, USA; Departments of Ophthalmology, Pathology & Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
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13
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Dorner L, Stratmann B, Bader L, Podobnik M, Irion U. Efficient genome editing using modified Cas9 proteins in zebrafish. Biol Open 2024; 13:bio060401. [PMID: 38545958 PMCID: PMC10997048 DOI: 10.1242/bio.060401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024] Open
Abstract
The zebrafish (Danio rerio) is an important model organism for basic as well as applied bio-medical research. One main advantage is its genetic tractability, which was greatly enhanced by the introduction of the CRISPR/Cas method a decade ago. The generation of loss-of-function alleles via the production of small insertions or deletions in the coding sequences of genes with CRISPR/Cas systems is now routinely achieved with high efficiency. The method is based on the error prone repair of precisely targeted DNA double strand breaks by non-homologous end joining (NHEJ) in the cell nucleus. However, editing the genome with base pair precision, by homology-directed repair (HDR), is by far less efficient and therefore often requires large-scale screening of potential carriers by labour intensive genotyping. Here we confirm that the Cas9 protein variant SpRY, with relaxed PAM requirement, can be used to target some sites in the zebrafish genome. In addition, we demonstrate that the incorporation of an artificial nuclear localisation signal (aNLS) into the Cas9 protein variants not only enhances the efficiency of gene knockout but also the frequency of HDR, thereby facilitating the efficient modification of single base pairs in the genome. Our protocols provide a guide for a cost-effective generation of versatile and potent Cas9 protein variants and efficient gene editing in zebrafish.
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Affiliation(s)
- Laura Dorner
- Max Planck Institute for Biology, RG Colour Pattern Evolution, Tuebingen, Max-Planck-Ring 5, 72076 Tuebingen, Germany
| | - Benedikt Stratmann
- Max Planck Institute for Biology, RG Colour Pattern Evolution, Tuebingen, Max-Planck-Ring 5, 72076 Tuebingen, Germany
| | - Laura Bader
- Max Planck Institute for Biology, RG Colour Pattern Evolution, Tuebingen, Max-Planck-Ring 5, 72076 Tuebingen, Germany
| | - Marco Podobnik
- Max Planck Institute for Biology, RG Colour Pattern Evolution, Tuebingen, Max-Planck-Ring 5, 72076 Tuebingen, Germany
| | - Uwe Irion
- Max Planck Institute for Biology, RG Colour Pattern Evolution, Tuebingen, Max-Planck-Ring 5, 72076 Tuebingen, Germany
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14
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Erhardt V, Snow CM, Hosur V. Protocol for large DNA transgenesis in mice using the Cas9+Bxb1 toolbox. STAR Protoc 2024; 5:103022. [PMID: 38625797 DOI: 10.1016/j.xpro.2024.103022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Precise integration of DNA constructs greater than 3 kb into mouse zygotes is difficult. Here, we present a protocol for large DNA transgenesis in mice using the Cas9+Bxb1 toolbox. We describe steps for choosing mouse strains with preplaced attachment sites. We then detail procedures for microinjecting mouse zygotes with the plasmid donor DNA construct to generate transgenic mice by recombination-mediated cassette exchange. This protocol has the potential for application in exploring the functional implications of large structural variations in cancer. For complete details on the use and execution of this protocol, please refer to Low et al.1 and Hosur et al.2.
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Affiliation(s)
- Valerie Erhardt
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Chrystal M Snow
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA.
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15
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Mariano CG, de Oliveira VC, Ambrósio CE. Gene editing in small and large animals for translational medicine: a review. Anim Reprod 2024; 21:e20230089. [PMID: 38628493 PMCID: PMC11019828 DOI: 10.1590/1984-3143-ar2023-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/16/2024] [Indexed: 04/19/2024] Open
Abstract
The CRISPR/Cas9 system is a simpler and more versatile method compared to other engineered nucleases such as Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs), and since its discovery, the efficiency of CRISPR-based genome editing has increased to the point that multiple and different types of edits can be made simultaneously. These advances in gene editing have revolutionized biotechnology by enabling precise genome editing with greater simplicity and efficacy than ever before. This tool has been successfully applied to a wide range of animal species, including cattle, pigs, dogs, and other small animals. Engineered nucleases cut the genome at specific target positions, triggering the cell's mechanisms to repair the damage and introduce a mutation to a specific genomic site. This review discusses novel genome-based CRISPR/Cas9 editing tools, methods developed to improve efficiency and specificity, the use of gene-editing on animal models and translational medicine, and the main challenges and limitations of CRISPR-based gene-editing approaches.
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Affiliation(s)
- Clésio Gomes Mariano
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo – USP, Pirassununga, SP, Brasil
| | - Vanessa Cristina de Oliveira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo – USP, Pirassununga, SP, Brasil
| | - Carlos Eduardo Ambrósio
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo – USP, Pirassununga, SP, Brasil
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16
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Ejaz RN, Taylor NMI, Steiner-Rebrova EM. Protocol for genomic recombineering in Yersinia ruckeri using CRISPR Cas12a coupled with the λ Red system. STAR Protoc 2024; 5:103014. [PMID: 38615317 PMCID: PMC11026829 DOI: 10.1016/j.xpro.2024.103014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/22/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Genomic manipulation of Yersinia ruckeri, a pathogen of salmonid fish species, is essential for understanding bacterial physiology and virulence. Here, we present a protocol for genomic recombineering in Y. ruckeri, a species reluctant to standard genomic engineering, using CRISPR Cas12a coupled with the λ Red system. We describe steps for identifying protospacer guides, preparing repair template plasmids, and electroporating Yersinia cells with Cpf1 and protospacer plasmids with homologous arms. We then detail procedures for genome editing and plasmid curing.
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Affiliation(s)
- Rooshanie N Ejaz
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Eva M Steiner-Rebrova
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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17
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Haq I, Ngo JC, Roy N, Pan RL, Nawsheen N, Chiu R, Zhang Y, Fujita M, Soni RK, Wu X, Bennett DA, Menon V, Olah M, Sher F. An integrated toolkit for human microglia functional genomics. Stem Cell Res Ther 2024; 15:104. [PMID: 38600587 PMCID: PMC11005142 DOI: 10.1186/s13287-024-03700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Microglia, the brain's resident immune cells, play vital roles in brain development, and disorders like Alzheimer's disease (AD). Human iPSC-derived microglia (iMG) provide a promising model to study these processes. However, existing iMG generation protocols face challenges, such as prolonged differentiation time, lack of detailed characterization, and limited gene function investigation via CRISPR-Cas9. METHODS Our integrated toolkit for in-vitro microglia functional genomics optimizes iPSC differentiation into iMG through a streamlined two-step, 20-day process, producing iMG with a normal karyotype. We confirmed the iMG's authenticity and quality through single-cell RNA sequencing, chromatin accessibility profiles (ATAC-Seq), proteomics and functional tests. The toolkit also incorporates a drug-dependent CRISPR-ON/OFF system for temporally controlled gene expression. Further, we facilitate the use of multi-omic data by providing online searchable platform that compares new iMG profiles to human primary microglia: https://sherlab.shinyapps.io/IPSC-derived-Microglia/ . RESULTS Our method generates iMG that closely align with human primary microglia in terms of transcriptomic, proteomic, and chromatin accessibility profiles. Functionally, these iMG exhibit Ca2 + transients, cytokine driven migration, immune responses to inflammatory signals, and active phagocytosis of CNS related substrates including synaptosomes, amyloid beta and myelin. Significantly, the toolkit facilitates repeated iMG harvesting, essential for large-scale experiments like CRISPR-Cas9 screens. The standalone ATAC-Seq profiles of our iMG closely resemble primary microglia, positioning them as ideal tools to study AD-associated single nucleotide variants (SNV) especially in the genome regulatory regions. CONCLUSIONS Our advanced two-step protocol rapidly and efficiently produces authentic iMG. With features like the CRISPR-ON/OFF system and a comprehensive multi-omic data platform, our toolkit equips researchers for robust microglial functional genomic studies. By facilitating detailed SNV investigation and offering a sustainable cell harvest mechanism, the toolkit heralds significant progress in neurodegenerative disease drug research and therapeutic advancement.
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Affiliation(s)
- Imdadul Haq
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Jason C Ngo
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Nainika Roy
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Richard L Pan
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Nadiya Nawsheen
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rebecca Chiu
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Neuroimmunology Core, Center for Translational & Computational Neuroimmunology, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Ya Zhang
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Neuroimmunology Core, Center for Translational & Computational Neuroimmunology, Division of Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Masashi Fujita
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Rajesh K Soni
- Proteomics Core, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Xuebing Wu
- Department of Medicine, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Marta Olah
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Falak Sher
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and Aging Brain, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
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18
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Chen Z, Hu J, Dai J, Zhou C, Hua Y, Hua X, Zhao Y. Precise CRISPR/Cpf1 genome editing system in the Deinococcus radiodurans with superior DNA repair mechanisms. Microbiol Res 2024; 284:127713. [PMID: 38608339 DOI: 10.1016/j.micres.2024.127713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Deinococcus radiodurans, with its high homologous recombination (HR) efficiency of double-stranded DNA breaks (DSBs), is a model organism for studying genome stability maintenance and an attractive microbe for industrial applications. Here, we developed an efficient CRISPR/Cpf1 genome editing system in D. radiodurans by evaluating and optimizing double-plasmid strategies and four Cas effector proteins from various organisms, which can precisely introduce different types of template-dependent mutagenesis without off-target toxicity. Furthermore, the role of DNA repair genes in determining editing efficiency in D. radiodurans was evaluated by introducing the CRISPR/Cpf1 system into 13 mutant strains lacking various DNA damage response and repair factors. In addition to the crucial role of RecA-dependent HR required for CRISPR/Cpf1 editing, D. radiodurans showed higher editing efficiency when lacking DdrB, the single-stranded DNA annealing (SSA) protein involved in the RecA-independent DSB repair pathway. This suggests a possible competition between HR and SSA pathways in the CRISPR editing of D. radiodurans. Moreover, off-target effects were observed during the genome editing of the pprI knockout strain, a master DNA damage response gene in Deinococcus species, which suggested that precise regulation of DNA damage response is critical for a high-fidelity genome editing system.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Hu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Congli Zhou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China.
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19
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Lankford KP, Hulleman JD. Protocol for HiBiT tagging endogenous proteins using CRISPR-Cas9 gene editing. STAR Protoc 2024; 5:103000. [PMID: 38598333 PMCID: PMC11022101 DOI: 10.1016/j.xpro.2024.103000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/05/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024] Open
Abstract
We present a method of in vitro/in vivo protein detection by pairing CRISPR-Cas9 genome editing with the NanoBiT system. We describe steps for cell culturing, in vitro CRISPR-Cas9 ribonucleoprotein delivery, cell monitoring, efficiency assessments, and edit analysis through HiBiT assays. We then detail procedures to determine edit specificity through genomic DNA analysis, small interfering RNA reverse transfection, and HiBiT blotting. This protocol is simple to execute and multifunctional, and it enables high-throughput screens on endogenous proteins to be conducted with ease.
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Affiliation(s)
- Kaylee P Lankford
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - John D Hulleman
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, 2001 6(th) St. SE, Minneapolis, MN 55455, USA.
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20
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Wang Y, Zhai Y, Zhang M, Song C, Zhang Y, Zhang G. Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications. Cell Mol Biol Lett 2024; 29:48. [PMID: 38589794 PMCID: PMC11003099 DOI: 10.1186/s11658-024-00565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats and associated Cas protein (CRISPR-Cas), a powerful genome editing tool, has revolutionized gene function investigation and exhibits huge potential for clinical applications. CRISPR-Cas-mediated gene knockout has already become a routine method in research laboratories. However, in the last few years, accumulating evidences have demonstrated that genes knocked out by CRISPR-Cas may not be truly silenced. Functional residual proteins could be generated in such knockout organisms to compensate the putative loss of function, termed herein knockout escaping. In line with this, several CRISPR-Cas-mediated knockout screenings have discovered much less abnormal phenotypes than expected. How does knockout escaping happen and how often does it happen have not been systematically reviewed yet. Without knowing this, knockout results could easily be misinterpreted. In this review, we summarize these evidences and propose two main mechanisms allowing knockout escaping. To avoid the confusion caused by knockout escaping, several strategies are discussed as well as their advantages and disadvantages. On the other hand, knockout escaping also provides convenient tools for studying essential genes and treating monogenic disorders such as Duchenne muscular dystrophy, which are discussed in the end.
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Affiliation(s)
- Ying Wang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Yujing Zhai
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- School of Public Health, Qingdao University, Qingdao, China
| | - Mingzhe Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Chunlin Song
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuqing Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Gang Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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21
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Vos PD, Gandadireja AP, Rossetti G, Siira SJ, Mantegna JL, Filipovska A, Rackham O. Mutational rescue of the activity of high-fidelity Cas9 enzymes. Cell Rep Methods 2024:100756. [PMID: 38608689 DOI: 10.1016/j.crmeth.2024.100756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/02/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
Programmable DNA endonucleases derived from bacterial genetic defense systems, exemplified by CRISPR-Cas9, have made it significantly easier to perform genomic modifications in living cells. However, unprogrammed, off-target modifications can have serious consequences, as they often disrupt the function or regulation of non-targeted genes and compromise the safety of therapeutic gene editing applications. High-fidelity mutants of Cas9 have been established to enable more accurate gene editing, but these are typically less efficient. Here, we merge the strengths of high-fidelity Cas9 and hyperactive Cas9 variants to provide an enzyme, which we dub HyperDriveCas9, that yields the desirable properties of both parents. HyperDriveCas9 functions efficiently in mammalian cells and introduces insertion and deletion mutations into targeted genomic regions while maintaining a favorable off-target profile. HyperDriveCas9 is a precise and efficient tool for gene editing applications in science and medicine.
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Affiliation(s)
- Pascal D Vos
- Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia; Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Andrianto P Gandadireja
- Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia; Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
| | - Stefan J Siira
- Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
| | - Jessica L Mantegna
- Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia; Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Aleksandra Filipovska
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
| | - Oliver Rackham
- Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia; Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia.
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22
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He Y, Zhou X, Chang C, Chen G, Liu W, Li G, Fan X, Sun M, Miao C, Huang Q, Ma Y, Yuan F, Chang X. Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing. Mol Cell 2024; 84:1257-1270.e6. [PMID: 38377993 DOI: 10.1016/j.molcel.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/20/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for BEs capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG). Notably, after two rounds of testing fewer than 50 top-ranking variants, more than 50% exhibited over 1.5-fold enhancement in enzymatic activities. When eTDG was fused with nCas9, it induced programmable T-to-S (G/C) substitutions and corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel BEs but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data.
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Affiliation(s)
- Yan He
- Fudan University, 220 Handan Road, Shanghai 200433, China; School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xibin Zhou
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310014, China
| | - Chong Chang
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Ge Chen
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Weikuan Liu
- Fudan University, 220 Handan Road, Shanghai 200433, China; School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Geng Li
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xiaoqi Fan
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Mingsun Sun
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Chensi Miao
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Qianyue Huang
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Yunqing Ma
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Fajie Yuan
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310014, China.
| | - Xing Chang
- School of Medicine, Westlake University, Hangzhou, Zhejiang 310014, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310014, China; Research Center for Industries of the Future (RCIF), Westlake University, Hangzhou, Zhejiang 310014, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310014, China; Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.
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23
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Jalil S, Keskinen T, Juutila J, Sartori Maldonado R, Euro L, Suomalainen A, Lapatto R, Kuuluvainen E, Hietakangas V, Otonkoski T, Hyvönen ME, Wartiovaara K. Genetic and functional correction of argininosuccinate lyase deficiency using CRISPR adenine base editors. Am J Hum Genet 2024; 111:714-728. [PMID: 38579669 PMCID: PMC11023919 DOI: 10.1016/j.ajhg.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024] Open
Abstract
Argininosuccinate lyase deficiency (ASLD) is a recessive metabolic disorder caused by variants in ASL. In an essential step in urea synthesis, ASL breaks down argininosuccinate (ASA), a pathognomonic ASLD biomarker. The severe disease forms lead to hyperammonemia, neurological injury, and even early death. The current treatments are unsatisfactory, involving a strict low-protein diet, arginine supplementation, nitrogen scavenging, and in some cases, liver transplantation. An unmet need exists for improved, efficient therapies. Here, we show the potential of a lipid nanoparticle-mediated CRISPR approach using adenine base editors (ABEs) for ASLD treatment. To model ASLD, we first generated human-induced pluripotent stem cells (hiPSCs) from biopsies of individuals homozygous for the Finnish founder variant (c.1153C>T [p.Arg385Cys]) and edited this variant using the ABE. We then differentiated the hiPSCs into hepatocyte-like cells that showed a 1,000-fold decrease in ASA levels compared to those of isogenic non-edited cells. Lastly, we tested three different FDA-approved lipid nanoparticle formulations to deliver the ABE-encoding RNA and the sgRNA targeting the ASL variant. This approach efficiently edited the ASL variant in fibroblasts with no apparent cell toxicity and minimal off-target effects. Further, the treatment resulted in a significant decrease in ASA, to levels of healthy donors, indicating restoration of the urea cycle. Our work describes a highly efficient approach to editing the disease-causing ASL variant and restoring the function of the urea cycle. This method relies on RNA delivered by lipid nanoparticles, which is compatible with clinical applications, improves its safety profile, and allows for scalable production.
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Affiliation(s)
- Sami Jalil
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Keskinen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juhana Juutila
- Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Rocio Sartori Maldonado
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Liliya Euro
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Suomalainen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Risto Lapatto
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Emilia Kuuluvainen
- Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences University of Helsinki, Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mervi E Hyvönen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; New Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kirmo Wartiovaara
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Clinical Genetics, Helsinki University Hospital, Helsinki, Finland.
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24
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Verma A, Sharma T, Awasthi A. CRISPR and Gene Editing: A Game-Changer in Drug Development. Curr Pharm Des 2024; 30:CPD-EPUB-139561. [PMID: 38584552 DOI: 10.2174/0113816128298080240328053845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/12/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
Abstract
CRISPR and gene editing technologies have emerged as transformative tools in medicine, offering unprecedented precision in targeting genetic disorders and revolutionizing drug development. This review explores the multifaceted impact of CRISPR across various medical domains, from hereditary diseases to infectious diseases and cancer. The potential of CRISPR in personalized medicine, therapeutic innovation, and pandemic prevention is highlighted, along with its role in reshaping traditional drug development processes. However, alongside its promise, ethical considerations loom large, particularly regarding germline editing and equitable access to treatments. The commercialization of CRISPR poses further challenges, raising questions about affordability and healthcare equity. Collaboration among scientists, policymakers, and the public is emphasized to navigate the ethical and societal implications of CRISPR responsibly. As the field advances, it is essential to ensure that the benefits of CRISPR are realized while addressing potential risks and maintaining a commitment to the well-being of future generations.
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Affiliation(s)
- Abhishek Verma
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab 142001, India
| | - Tarun Sharma
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab 142001, India
| | - Ankit Awasthi
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab 142001, India
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25
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Zirin J, Jusiak B, Lopes R, Ewen-Campen B, Bosch JA, Risbeck A, Forman C, Villalta C, Hu Y, Perrimon N. Expanding the Drosophila toolkit for dual control of gene expression. eLife 2024; 12:RP94073. [PMID: 38569007 PMCID: PMC10990484 DOI: 10.7554/elife.94073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The ability to independently control gene expression in two different tissues in the same animal is emerging as a major need, especially in the context of inter-organ communication studies. This type of study is made possible by technologies combining the GAL4/UAS and a second binary expression system such as the LexA system or QF system. Here, we describe a resource of reagents that facilitate combined use of the GAL4/UAS and a second binary system in various Drosophila tissues. Focusing on genes with well-characterized GAL4 expression patterns, we generated a set of more than 40 LexA-GAD and QF2 insertions by CRISPR knock-in and verified their tissue specificity in larvae. We also built constructs that encode QF2 and LexA-GAD transcription factors in a single vector. Following successful integration of this construct into the fly genome, FLP/FRT recombination is used to isolate fly lines that express only QF2 or LexA-GAD. Finally, using new compatible shRNA vectors, we evaluated both LexA and QF systems for in vivo gene knockdown and are generating a library of such RNAi fly lines as a community resource. Together, these LexA and QF system vectors and fly lines will provide a new set of tools for researchers who need to activate or repress two different genes in an orthogonal manner in the same animal.
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Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Barbara Jusiak
- Department of Physiology and Biophysics, University of California, IrvineIrvineUnited States
| | - Raphael Lopes
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Justin A Bosch
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Corey Forman
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | | | - Yanhui Hu
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolBostonUnited States
- Howard Hughes Medical InstituteBostonUnited States
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26
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Mishra AK, Ye T, Banday S, Thakare RP, Su CTT, Pham NNH, Ali A, Kulshreshtha A, Chowdhury SR, Simone TM, Hu K, Zhu LJ, Eisenhaber B, Deibler SK, Simin K, Thompson PR, Kelliher MA, Eisenhaber F, Malonia SK, Green MR. Targeting the GPI transamidase subunit GPAA1 abrogates the CD24 immune checkpoint in ovarian cancer. Cell Rep 2024; 43:114041. [PMID: 38573857 DOI: 10.1016/j.celrep.2024.114041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
CD24 is frequently overexpressed in ovarian cancer and promotes immune evasion by interacting with its receptor Siglec10, present on tumor-associated macrophages, providing a "don't eat me" signal that prevents targeting and phagocytosis by macrophages. Factors promoting CD24 expression could represent novel immunotherapeutic targets for ovarian cancer. Here, using a genome-wide CRISPR knockout screen, we identify GPAA1 (glycosylphosphatidylinositol anchor attachment 1), a factor that catalyzes the attachment of a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins, as a positive regulator of CD24 cell surface expression. Genetic ablation of GPAA1 abolishes CD24 cell surface expression, enhances macrophage-mediated phagocytosis, and inhibits ovarian tumor growth in mice. GPAA1 shares structural similarities with aminopeptidases. Consequently, we show that bestatin, a clinically advanced aminopeptidase inhibitor, binds to GPAA1 and blocks GPI attachment, resulting in reduced CD24 cell surface expression, increased macrophage-mediated phagocytosis, and suppressed growth of ovarian tumors. Our study highlights the potential of targeting GPAA1 as an immunotherapeutic approach for CD24+ ovarian cancers.
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Affiliation(s)
- Alok K Mishra
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Tianyi Ye
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Shahid Banday
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ritesh P Thakare
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Chinh Tran-To Su
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A(∗)STAR), 30 Biopolis Street, Matrix, #07-01, Singapore 138671, Singapore
| | - Ngoc N H Pham
- Faculty of Biology and Biotechnology, University of Science, Vietnam National University, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Amjad Ali
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ankur Kulshreshtha
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Shreya Roy Chowdhury
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tessa M Simone
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Kai Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine and Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A(∗)STAR), 30 Biopolis Street, Matrix, #07-01, Singapore 138671, Singapore; Lausitz Advanced Scientific Applications (LASA) gGmbH, Straße der Einheit 2-24, 02943 Weißwasser, Germany
| | - Sara K Deibler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karl Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A(∗)STAR), 30 Biopolis Street, Matrix, #07-01, Singapore 138671, Singapore; Lausitz Advanced Scientific Applications (LASA) gGmbH, Straße der Einheit 2-24, 02943 Weißwasser, Germany; School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Sunil K Malonia
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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27
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Zhang H, Chen B, Wang Z, Peng K, Liu Y, Wang Z. Resensitizing tigecycline- and colistin-resistant Escherichia coli using an engineered conjugative CRISPR/Cas9 system. Microbiol Spectr 2024; 12:e0388423. [PMID: 38385691 DOI: 10.1128/spectrum.03884-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Tigecycline and colistin were referred to as the "last resort" antibiotics in defending against carbapenem-resistant, Gram-negative bacterial infections, and are currently widely used in clinical treatment. However, the emergence and prevalence of plasmid-mediated tet(X4) and mcr-1 genes pose a serious threat to the therapeutic application of tigecycline and colistin, respectively. In this research, a tigecycline- and colistin-resistant bacteria resensitization system was developed based on efficient and specific DNA damage caused by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Associated Protein 9 (Cas9) nucleases. A conjugation method was used to deliver the resensitization system, which harbors two single-guide RNAs targeting tet(X4) and mcr-1 genes and constitutively expressed Cas9. The conjugation efficiency was nearly 100% after conjugation condition optimization in vitro, and the resensitivity efficiency for clinical isolates was over 90%. In addition, when performing resensitization in vivo, the resistance marker was replaced with a glutamate-based, chromosomal, plasmid-balanced lethal system to prevent the introduction of additional resistance genes in clinical settings, making this strategy a therapeutic approach to combat the in vivo spread of antibiotic resistance genes (ARGs) among bacterial pathogens. As a proof of concept, this resensitive system can significantly decrease the counts of tigecycline- and colistin-resistant bacteria to 1% in vivo. Our study demonstrates the efficacy and adaptability of CRISPR-Cas systems as powerful and programmable antimicrobials in resensitizing tet(X4)- and mcr-1-mediated, tigecycline- and colistin-resistant strains, and opens up new pathways for the development of CRISPR-based tools for selective bacterial pathogen elimination and precise microbiome composition change. IMPORTANCE The emergence of plasmid-encoded tet(X4) and mcr-1 isolated from human and animal sources has affected the treatment of tigecycline and colistin, and has posed a significant threat to public health. Tigecycline and colistin are considered as the "last line of defense" for the treatment of multidrug-resistant (MDR) Gram-negative bacterial infections, so there is an urgent need to find a method that can resensitize tet(X4)-mediated tigecycline-resistant and mcr-1-mediated colistin-resistant bacteria. In this study, we developed a glutamate-based, chromosomal, plasmid-balanced lethal conjugative CRISPR/Cas9 system, which can simultaneously resensitize tet(X4)-mediated tigecycline-resistant and mcr-1-mediated colistin-resistant Escherichia coli. The counts of tigecycline- and colistin-resistant bacteria decreased to 1% in vivo after the resensitization system was administered. This study opens up new pathways for the development of CRISPR-based tools for selective bacterial pathogen elimination and precise microbiome composition change.
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Affiliation(s)
- Haijie Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Bo Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zeyu Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Kai Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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Zheng Z, Xu L, Dou H, Zhou Y, Feng X, He X, Tian Z, Song L, Gao Y, Mo G, Hu J, Zhao H, Wei H, Church GM, Yang L. Testing multiplexed anti-ASFV CRISPR-Cas9 in reducing African swine fever virus. Microbiol Spectr 2024:e0216423. [PMID: 38563791 DOI: 10.1128/spectrum.02164-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/20/2024] [Indexed: 04/04/2024] Open
Abstract
African swine fever (ASF) is a highly fatal viral disease that poses a significant threat to domestic pigs and wild boars globally. In our study, we aimed to explore the potential of a multiplexed CRISPR-Cas system in suppressing ASFV replication and infection. By engineering CRISPR-Cas systems to target nine specific loci within the ASFV genome, we observed a substantial reduction in viral replication in vitro. This reduction was achieved through the concerted action of both Type II and Type III RNA polymerase-guided gRNA expression. To further evaluate its anti-viral function in vivo, we developed a pig strain expressing the multiplexable CRISPR-Cas-gRNA via germline genome editing. These transgenic pigs exhibited normal health with continuous expression of the CRISPR-Cas-gRNA system, and a subset displayed latent viral replication and delayed infection. However, the CRISPR-Cas9-engineered pigs did not exhibit a survival advantage upon exposure to ASFV. To our knowledge, this study represents the first instance of a living organism engineered via germline editing to assess resistance to ASFV infection using a CRISPR-Cas system. Our findings contribute valuable insights to guide the future design of enhanced viral immunity strategies. IMPORTANCE ASFV is currently a devastating disease with no effective vaccine or treatment available. Our study introduces a multiplexed CRISPR-Cas system targeting nine specific loci in the ASFV genome. This innovative approach successfully inhibits ASFV replication in vitro, and we have successfully engineered pig strains to express this anti-ASFV CRISPR-Cas system constitutively. Despite not observing survival advantages in these transgenic pigs upon ASFV challenges, we did note a delay in infection in some cases. To the best of our knowledge, this study constitutes the first example of a germline-edited animal with an anti-virus CRISPR-Cas system. These findings contribute to the advancement of future anti-viral strategies and the optimization of viral immunity technologies.
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Affiliation(s)
- Zezhong Zheng
- South China Agricultural University, Guangzhou, China
| | - Lei Xu
- Qihan Biotechnology, Hangzhou, China
| | | | | | - Xu Feng
- Qihan Biotechnology, Hangzhou, China
| | | | - Zhen Tian
- Qihan Biotechnology, Hangzhou, China
| | | | | | | | - Jiapan Hu
- Qihan Biotechnology, Hangzhou, China
| | - Hongye Zhao
- Yunan Agriculture University, Kunming, China
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Djajawi TM, Wichmann J, Vervoort SJ, Kearney CJ. Tumor immune evasion: insights from CRISPR screens and future directions. FEBS J 2024; 291:1386-1399. [PMID: 37971319 DOI: 10.1111/febs.17003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Despite the clinical success of cancer immunotherapies including immune checkpoint blockade and adoptive cellular therapies across a variety of cancer types, many patients do not respond or ultimately relapse; however, the molecular underpinnings of this are not fully understood. Thus, a system-level understating of the routes to tumor immune evasion is required to inform the design of the next generation of immunotherapy approaches. CRISPR screening approaches have proved extremely powerful in identifying genes that promote tumor immune evasion or sensitize tumor cells to destruction by the immune system. These large-scale efforts have brought to light decades worth of fundamental immunology and have uncovered the key immune-evasion pathways subverted in cancers in an acquired manner in patients receiving immune-modulatory therapies. The comprehensive discovery of the main pathways involved in immune evasion has spurred the development and application of novel immune therapies to target this process. Although successful, conventional CRISPR screening approaches are hampered by a number of limitations, which obfuscate a complete understanding of the precise molecular regulation of immune evasion in cancer. Here, we provide a perspective on screening approaches to interrogate tumor-lymphocyte interactions and their limitations, and discuss further development of technologies to improve such approaches and discovery capability.
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Affiliation(s)
- Tirta Mario Djajawi
- Olivia Newton-John Cancer Research Institute, Heidelberg, Vic., Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Vic., Australia
| | - Johannes Wichmann
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Stephin J Vervoort
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Conor J Kearney
- Olivia Newton-John Cancer Research Institute, Heidelberg, Vic., Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Vic., Australia
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Lanza DG, Mao J, Lorenzo I, Liao L, Seavitt JR, Ljungberg MC, Simpson EM, DeMayo FJ, Heaney JD. An oocyte-specific Cas9-expressing mouse for germline CRISPR/Cas9-mediated genome editing. Genesis 2024; 62:e23589. [PMID: 38523431 PMCID: PMC10987075 DOI: 10.1002/dvg.23589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Cas9 transgenes can be employed for genome editing in mouse zygotes. However, using transgenic instead of exogenous Cas9 to produce gene-edited animals creates unique issues including ill-defined transgene integration sites, the potential for prolonged Cas9 expression in transgenic embryos, and increased genotyping burden. To overcome these issues, we generated mice harboring an oocyte-specific, Gdf9 promoter driven, Cas9 transgene (Gdf9-Cas9) targeted as a single copy into the Hprt1 locus. The X-linked Hprt1 locus was selected because it is a defined integration site that does not influence transgene expression, and breeding of transgenic males generates obligate transgenic females to serve as embryo donors. Using microinjections and electroporation to introduce sgRNAs into zygotes derived from transgenic dams, we demonstrate that Gdf9-Cas9 mediates genome editing as efficiently as exogenous Cas9 at several loci. We show that genome editing efficiency is independent of transgene inheritance, verifying that maternally derived Cas9 facilitates genome editing. We also show that paternal inheritance of Gdf9-Cas9 does not mediate genome editing, confirming that Gdf9-Cas9 is not expressed in embryos. Finally, we demonstrate that off-target mutagenesis is equally rare when using transgenic or exogenous Cas9. Together, these results show that the Gdf9-Cas9 transgene is a viable alternative to exogenous Cas9.
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Affiliation(s)
- Denise G. Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
| | - Jianqiang Mao
- Department of Molecular & Cellular Biology, Baylor College of Medicine Houston, TX, USA 77030
| | - Isabel Lorenzo
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
| | - Lan Liao
- Department of Molecular & Cellular Biology, Baylor College of Medicine Houston, TX, USA 77030
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
- Present address: The Jackson Laboratory 600 Main St., Bar Harbor, Maine, ME, USA 04609
| | - M. Cecilia Ljungberg
- Department of Pediatrics – Neurology, Baylor College of Medicine Houston, TX, USA 77030
- Duncan Neurological Research Institute, Texas Children’s Hospital Houston, TX, USA 77030
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital Department of Medical Genetics, The University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Francesco J. DeMayo
- Reproductive and Developmental Biology Laboratory National Institute of Environmental Health Sciences Research Triangle Park, NC, USA 27709
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, TX, USA 77030
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31
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Manjunath LE, Singh A, Devi Kumar S, Vasu K, Kar D, Sellamuthu K, Eswarappa SM. Transcript-specific induction of stop codon readthrough using a CRISPR-dCas13 system. EMBO Rep 2024; 25:2118-2143. [PMID: 38499809 PMCID: PMC11015002 DOI: 10.1038/s44319-024-00115-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using a CRISPR-dCas13 system. Using specific guide RNAs, we target dCas13 to the region downstream of canonical stop codons of mammalian AGO1 and VEGFA mRNAs, known to exhibit natural SCR. Readthrough assays reveal enhanced SCR of these mRNAs (both exogenous and endogenous) caused by the dCas13-gRNA complexes. This effect is associated with ribosomal pausing, which has been reported for several SCR events. Our data show that CRISPR-dCas13 can also induce SCR across premature termination codons (PTCs) in the mRNAs of green fluorescent protein and TP53. We demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA and hereditary spherocytosis-causing PTC in SPTA1 mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Karthi Sellamuthu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- University of Texas Medical Branch, Galveston, TX, USA
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
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Grünhofer P, Heimerich I, Pohl S, Oertel M, Meng H, Zi L, Lucignano K, Bokhari SNH, Guo Y, Li R, Lin J, Fladung M, Kreszies T, Stöcker T, Schoof H, Schreiber L. Suberin deficiency and its effect on the transport physiology of young poplar roots. New Phytol 2024; 242:137-153. [PMID: 38366280 DOI: 10.1111/nph.19588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The precise functions of suberized apoplastic barriers in root water and nutrient transport physiology have not fully been elucidated. While lots of research has been performed with mutants of Arabidopsis, little to no data are available for mutants of agricultural crop or tree species. By employing a combined set of physiological, histochemical, analytical, and transport physiological methods as well as RNA-sequencing, this study investigated the implications of remarkable CRISPR/Cas9-induced suberization defects in young roots of the economically important gray poplar. While barely affecting overall plant development, contrary to literature-based expectations significant root suberin reductions of up to 80-95% in four independent mutants were shown to not evidently affect the root hydraulic conductivity during non-stress conditions. In addition, subliminal iron deficiency symptoms and increased translocation of a photosynthesis inhibitor as well as NaCl highlight the involvement of suberin in nutrient transport physiology. The multifaceted nature of the root hydraulic conductivity does not allow drawing simplified conclusions such as that the suberin amount must always be correlated with the water transport properties of roots. However, the decreased masking of plasma membrane surface area could facilitate the uptake but also leakage of beneficial and harmful solutes.
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Affiliation(s)
- Paul Grünhofer
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Ines Heimerich
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Svenja Pohl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Marlene Oertel
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Hongjun Meng
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Lin Zi
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Kevin Lucignano
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Syed Nadeem Hussain Bokhari
- Department Plant Biophysics and Biochemistry, Institute of Plant Molecular Biology, Czech Academy of Sciences, Biology Centre, Branišovská 31/1160, CZ-37005, České Budějovice, Czech Republic
| | - Yayu Guo
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinxing Lin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, Sieker Landstraße 2, 22927, Grosshansdorf, Germany
| | - Tino Kreszies
- Department of Crop Sciences, Plant Nutrition and Crop Physiology, University of Göttingen, Carl-Sprengel-Weg 1, 37075, Göttingen, Germany
| | - Tyll Stöcker
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
| | - Heiko Schoof
- Department of Crop Bioinformatics, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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Hu J, Luo M, Zhou X, Wang Z, Yan L, Hong D, Yang G, Zhang X. RING-type E3 ligase BnaJUL1 ubiquitinates and degrades BnaTBCC1 to regulate drought tolerance in Brassica napus L. Plant Cell Environ 2024; 47:1023-1040. [PMID: 37984059 DOI: 10.1111/pce.14770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/26/2023] [Accepted: 09/27/2023] [Indexed: 11/22/2023]
Abstract
Drought stress poses a persistent threat to field crops and significantly limits global agricultural productivity. Plants employ ubiquitin-dependent degradation as a crucial post-translational regulatory mechanism to swiftly adapt to changing environmental conditions. JUL1 is a RING-type E3 ligase related to drought stress in Arabidopsis. In this study, we explored the function of BnaJUL1 (a homologous gene of JUL1 in Brassica napus) and discovered a novel gene BnaTBCC1 participating in drought tolerance. First, we utilised BnaJUL1-cri materials through the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 system. Second, we confirmed that BnaJUL1 regulated drought tolerance through the drought tolerance assay and transcriptome analysis. Then, we identified a series of proteins interacting with BnaJUL1 through yeast library screening, including BnaTBCC1 (a tubulin binding cofactor C domain-containing protein); whose homologous gene TBCC1 knockdown mutants (tbcc1-1) exhibited ABA-sensitive germination in Arabidopsis, we then confirmed the involvement of BnaTBCC1 in drought tolerance in both Arabidopsis and Brassica. Finally, we established that BnaJUL1 could ubiquitinate and degrade BnaTBCC1 to regulate drought tolerance. Consequently, our study unveils BnaJUL1 as a novel regulator that ubiquitinates and degrades BnaTBCC1 to modulate drought tolerance and provided desirable germplasm for further breeding of drought tolerance in rapeseed.
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Affiliation(s)
- Jin Hu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Mudan Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xianming Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhaoyang Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Li Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohui Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
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Moriya A, Otsuka K, Naoi R, Terahata M, Takeda K, Kondo S, Adachi-Yamada T. Creation of Knock-In Alleles of Insulin Receptor Tagged by Fluorescent Proteins mCherry or EYFP in Fruit Fly Drosophila melanogaster. Zoolog Sci 2024; 41:230-243. [PMID: 38587918 DOI: 10.2108/zs230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/19/2023] [Indexed: 04/10/2024]
Abstract
The insulin/insulin-like growth factor-like signaling (IIS) pathway is highly conserved across metazoans and regulates numerous physiological functions, including development, metabolism, fecundity, and lifespan. The insulin receptor (InR), a crucial membrane receptor in the IIS pathway, is known to be ubiquitously expressed in various tissues, albeit at generally low levels, and its subcellular localization remains incompletely characterized. In this study, we employed CRISPR-mediated mutagenesis in the fruit fly Drosophila to create knock-in alleles of InR tagged with fluorescent proteins (InR::mCherry or InR::EYFP). By inserting the coding sequence of the fluorescent proteins mCherry or EYFP near the end of the coding sequence of the endogenous InR gene, we could trace the natural InR protein through their fluorescence. As an example, we investigated epithelial cells of the male accessory gland (AG), an internal reproductive organ, and identified two distinct patterns of InR::mCherry localization. In young AG, InR::mCherry accumulated on the basal plasma membrane between cells, whereas in mature AG, it exhibited intracellular localization as multiple puncta, indicating endocytic recycling of InR during cell growth. In the AG senescence accelerated by the mutation of Diuretic hormone 31 (Dh31), the presence of InR::mCherry puncta was more pronounced compared to the wild type. These findings raise expectations for the utility of the newly created InR::mCherry/EYFP alleles for studying the precise expression levels and subcellular localization of InR. Furthermore, this fluorescently tagged allele approach can be extended to investigate other membrane receptors with low abundance, facilitating the direct examination of their true expression and localization.
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Affiliation(s)
- Ayano Moriya
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Kei Otsuka
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Riku Naoi
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Mayu Terahata
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Koji Takeda
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Shu Kondo
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takashi Adachi-Yamada
- Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan,
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
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35
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Yong J, Wu M, Carroll BJ, Xu ZP, Zhang R. Enhancing plant biotechnology by nanoparticle delivery of nucleic acids. Trends Genet 2024; 40:352-363. [PMID: 38320883 DOI: 10.1016/j.tig.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Plant biotechnology plays a crucial role in developing modern agriculture and plant science research. However, the delivery of exogenous genetic material into plants has been a long-standing obstacle. Nanoparticle-based delivery systems are being established to address this limitation and are proving to be a feasible, versatile, and efficient approach to facilitate the internalization of functional RNA and DNA by plants. The nanoparticle-based delivery systems can also be designed for subcellular delivery and controlled release of the biomolecular cargo. In this review, we provide a concise overview of the recent advances in nanocarriers for the delivery of biomolecules into plants, with a specific focus on applications to enhance RNA interference, foreign gene transfer, and genome editing in plants.
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Affiliation(s)
- Jiaxi Yong
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Miaomiao Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhi Ping Xu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Institute of Biomedical Health Technology and Engineering and Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, P. R. China 518107
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Indooroopilly, Queensland 4068, Australia.
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Sarkar P, Santiago Vazquez J, Zhou M, Levy A, Mou Z, Orbović V. Multiplexed gene editing in citrus by using a multi-intron containing Cas9 gene. Transgenic Res 2024; 33:59-66. [PMID: 38564120 DOI: 10.1007/s11248-024-00380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Several expression systems have been developed in clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) framework allowing for gene editing of disease-associated genes across diverse citrus varieties. In this study, we present a new approach employing a multi-intron containing Cas9 gene plus multiple gRNAs separated with tRNA sequences to target the phytoene desaturase gene in both 'Carrizo' citrange and 'Duncan' grapefruit. Notably, using this unified vector significantly boosted editing efficiency in both citrus varieties, showcasing mutations in all three designated targets. The implementation of this multiplex gene editing system with a multi-intron-containing Cas9 plus a gRNA-tRNA array demonstrates a promising avenue for efficient citrus genome editing, equipping us with potent tools in the ongoing battle against several diseases such as canker and huanglongbing.
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Affiliation(s)
- Poulami Sarkar
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Jorge Santiago Vazquez
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Mingxi Zhou
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32602, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
| | - Amit Levy
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
- Department of Cell Sciences and Microbiology, University of Florida, Gainesville, FL, 32611, USA
| | - Zhonglin Mou
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32602, USA
| | - Vladimir Orbović
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA.
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Srivastava R, Davison CW, Krull AG, Entriken SM, Zumbrock A, Cortes Hidalgo MD, Adair KJ, Escherich AM, Lara JN, Neverman EC, Hodnefield M, McElligtot E, Sandquist EJ, Ogilvie C, Lafontant P, Essner JJ. An Undergraduate Course in CRISPR/Cas9-Mediated Gene Editing in Zebrafish. Zebrafish 2024; 21:162-170. [PMID: 38621214 DOI: 10.1089/zeb.2023.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
We have developed a one-credit semester-long research experience for undergraduate students that involves the use of CRISPR/Cas9 to edit genes in zebrafish. The course is available to students at all stages of their undergraduate training and can be taken up to four times. Students select a gene of interest to edit as the basis of their semester-long project. To select a gene, exploration of developmental processes and human disease is encouraged. As part of the course, students use basic bioinformatic tools, design guide RNAs, inject zebrafish embryos, and analyze both the molecular consequences of gene editing and phenotypic outcomes. Over the 10 years we have offered the course, enrollment has grown from less than 10 students to more than 60 students per semester. Each year, we choose a different gene editing strategy to explore based on recent publications of gene editing methodologies. These have included making CRISPants, targeted integrations, and large gene deletions. In this study, we present how we structure the course and our assessment of the course over the past 3 years.
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Affiliation(s)
- Renu Srivastava
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Connor W Davison
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Abigail G Krull
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Seth M Entriken
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Amanda Zumbrock
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | | | - Kiernan J Adair
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Anna M Escherich
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Jonathan N Lara
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Emma C Neverman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Megan Hodnefield
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Elyse McElligtot
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | | | - Craig Ogilvie
- The Graduate School, Montana State University, Bozeman, Montana, USA
| | | | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
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Mitsiades CS. Proteasome Inhibitors in Multiple Myeloma: Biological Insights on Mechanisms of Action or Resistance Informed by Functional Genomics. Hematol Oncol Clin North Am 2024; 38:321-336. [PMID: 38278626 DOI: 10.1016/j.hoc.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
During the last 20 years, proteasome inhibitors have been a cornerstone for the therapeutic management of multiple myeloma (MM). This review highlights how MM research has evolved over time in terms of our understanding of the mechanistic basis for the pronounced clinical activity of proteasome inhibitors in MM, compared with the limited clinical applications of this drug class outside the setting of plasma cell dyscrasias.
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Affiliation(s)
- Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA.
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39
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Wang L, Wang J, Feng D, Wang B, Jahan-Mihan Y, Wang Y, Bi Y, Lim D, Ji B. A simple and effective genotyping workflow for rapid detection of CRISPR genome editing. Am J Physiol Gastrointest Liver Physiol 2024; 326:G473-G481. [PMID: 38410866 DOI: 10.1152/ajpgi.00013.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024]
Abstract
Genetically engineered mouse models play a pivotal role in the modeling of diseases, exploration of gene functions, and the development of novel therapies. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated genome editing technology has revolutionized the process of developing such models by enabling precise genome modifications of the multiple interested genes simultaneously. Following genome editing, an efficient genotyping methodology is crucial for subsequent characterization. However, current genotyping methods are laborious, time-consuming, and costly. Here, using targeting the mouse trypsinogen genes as an example, we introduced common applications of CRISPR-Cas9 editing and a streamlined cost-effective genotyping workflow for CRISPR-edited mouse models, in which Sanger sequencing is required only at the initial steps. In the F0 mice, we focused on identifying the presence of positive editing by PCR followed by Sanger sequencing without the need to know the exact sequences, simplifying the initial screening. In the F1 mice, Sanger sequencing and algorithms decoding were used to identify the precise editing. Once the edited sequence was established, a simple and effective genotyping strategy was established to distinguish homozygous and heterozygous status by PCR from tail DNA. The genotyping workflow applies to deletions as small as one nucleotide, multiple-gene knockout, and knockin studies. This simplified, efficient, and cost-effective genotyping shall be instructive to new investigators who are unfamiliar with characterizing CRISPR-Cas9-edited mouse strains.NEW & NOTEWORTHY This study presents a streamlined, cost-effective genotyping workflow for clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) edited mouse models, focusing on trypsinogen genes. It simplifies initial F0 mouse screening using PCR and Sanger sequencing without needing exact sequences. For F1 mice, precise editing is identified through Sanger sequencing and algorithm decoding. The workflow includes a novel PCR strategy for distinguishing homozygous and heterozygous statuses in subsequent generations, effective for small deletions, multiple-gene knockouts, and knockins.
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Affiliation(s)
- Lingxiang Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jiale Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Dongfeng Feng
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Bin Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yasmin Jahan-Mihan
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ying Wang
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States
| | - DoYoung Lim
- The Transgenic and Knockout Core, Mayo Clinic, Rochester, Minnesota, United States
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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41
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Yeh HY, Cox NA, Hinton A, Berrang ME. Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats ( CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers. J Food Prot 2024; 87:100250. [PMID: 38382707 DOI: 10.1016/j.jfp.2024.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C. jejuni is critical as they may confer bacterial resistance to bacteriophage treatment. Therefore, in this study, we explored the distribution of the CRISPR arrays from 178 C. jejuni isolated from chicken livers between January and July 2018. Genomic DNA of C. jejuni isolates was extracted, and CRISPR type 1 sequences were amplified by PCR. Amplicons were purified and sequenced by the Sanger dideoxy sequencing method. Direct repeats (DRs) and spacers of CRISPR sequences were identified using the CRISPRFinder program. Further, spacer sequences were submitted to the CRISPRTarget to identify potential homology to bacteriophage types. Even though CRISPR-Cas is reportedly not an active system in Campylobacter, a total of 155 (87%) C. jejuni isolates were found to harbor CRISPR sequences; one type of DR was identified in all 155 isolates. The CRISPR loci lengths ranged from 97 to 431 nucleotides. The numbers of spacers ranged from one to six. A total of 371 spacer sequences were identified in the 155 isolates that could be grouped into 51 distinctive individual sequences. Further comparison of these 51 spacer sequences with those in databases showed that most spacer sequences were homologous to Campylobacter bacteriophage DA10. The results of our study provide important information relative to the development of an effective bacteriophage treatment to mitigate Campylobacter during poultry production.
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Affiliation(s)
- Hung-Yueh Yeh
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA.
| | - Nelson A Cox
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Arthur Hinton
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Mark E Berrang
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
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42
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Hesping E, Boddey JA. Whole-genome CRISPR screens to understand Apicomplexan-host interactions. Mol Microbiol 2024; 121:717-726. [PMID: 38225194 DOI: 10.1111/mmi.15221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/17/2024]
Abstract
Apicomplexan parasites are aetiological agents of numerous diseases in humans and livestock. Functional genomics studies in these parasites enable the identification of biological mechanisms and protein functions that can be targeted for therapeutic intervention. Recent improvements in forward genetics and whole-genome screens utilising CRISPR/Cas technology have revolutionised the functional analysis of genes during Apicomplexan infection of host cells. Here, we highlight key discoveries from CRISPR/Cas9 screens in Apicomplexa or their infected host cells and discuss remaining challenges to maximise this technology that may help answer fundamental questions about parasite-host interactions.
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Affiliation(s)
- Eva Hesping
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Justin A Boddey
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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43
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Sedeek K, Mohammed N, Zhou Y, Zuccolo A, Sanikommu K, Kantharajappa S, Al-Bader N, Tashkandi M, Wing RA, Mahfouz MM. Multitrait engineering of Hassawi red rice for sustainable cultivation. Plant Sci 2024; 341:112018. [PMID: 38325660 DOI: 10.1016/j.plantsci.2024.112018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the red Hassawi rice, a native landrace of Saudi Arabia, tolerates local drought and high-salinity conditions and produces grain with diverse health-promoting phytochemicals. However, Hassawi has a long growth cycle, high cultivation costs, low productivity, and susceptibility to lodging. Here, to improve these undesirable traits via genome editing, we established efficient regeneration and Agrobacterium-mediated transformation protocols for Hassawi. In addition, we generated the first high-quality reference genome and targeted the key flowering repressor gene, Hd4, thus shortening the plant's lifecycle and height. Using CRISPR/Cas9 multiplexing, we simultaneously disrupted negative regulators of flowering time (Hd2, Hd4, and Hd5), grain size (GS3), grain number (GN1a), and plant height (Sd1). The resulting homozygous mutant lines flowered extremely early (∼56 days) and had shorter stems (approximately 107 cm), longer grains (by 5.1%), and more grains per plant (by 50.2%), thereby enhancing overall productivity. Furthermore, the awns of grains were 86.4% shorter compared to unedited plants. Moreover, the modified rice grain displayed improved nutritional attributes. As a result, the modified Hassawi rice combines several desirable traits that can incentivize large-scale cultivation and reduce malnutrition.
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Affiliation(s)
- Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nahed Mohammed
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Krishnaveni Sanikommu
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sunitha Kantharajappa
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manal Tashkandi
- Department of Biological Science, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA; International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031 Laguna, Philippines
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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44
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Romano A, Mortellaro A. The New Frontiers of Gene Therapy and Gene Editing in Inflammatory Diseases. Hum Gene Ther 2024; 35:219-231. [PMID: 38323580 DOI: 10.1089/hum.2023.210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
Inflammatory diseases are conditions characterized by abnormal and often excessive immune responses, leading to tissue and organ inflammation. The complexity of these disorders arises from the intricate interplay of genetic factors and immune responses, which challenges conventional therapeutic approaches. However, the field of genetic manipulation has sparked unprecedented optimism in addressing these complex disorders. This review aims to comprehensively explore the application of gene therapy and gene editing in the context of inflammatory diseases, offering solutions that range from correcting genetic defects to precise immune modulation. These therapies have exhibited remarkable potential in ameliorating symptoms, improving quality of life, and even achieving disease remission. As we delve into recent breakthroughs and therapeutic applications, we illustrate how these advancements offer novel and transformative solutions for conditions that have traditionally eluded conventional treatments. By examining successful case studies and preclinical research, we emphasize the favorable results and substantial transformative impacts that gene-based interventions have demonstrated in patients and animal models of inflammatory diseases such as chronic granulomatous disease, cryopyrin-associated syndromes, and adenosine deaminase 2 deficiency, as well as those of multifactorial origins such as arthropathies (osteoarthritis, rheumatoid arthritis) and inflammatory bowel disease. In conclusion, gene therapy and gene editing offer transformative opportunities to address the underlying causes of inflammatory diseases, ushering in a new era of precision medicine and providing hope for personalized, targeted treatments.
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Affiliation(s)
- Alessandro Romano
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandra Mortellaro
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
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Wang X, Li Y, A S, Lyu J, Wang X, He Z, Lara-Sáez I, Li M, Wang W. Cyclization-enhanced poly(β-amino ester)s vectors for efficient CRISPR gene editing therapy. J Control Release 2024; 368:444-452. [PMID: 38401849 DOI: 10.1016/j.jconrel.2024.02.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
Among non-viral gene delivery vectors, poly(β-amino ester)s (PAEs) are one of the most versatile candidates because of their wide monomer availability, high polymer flexibility, and superior gene transfection performance both in vitro and in vivo. Over two decades, PAEs have evolved from linear to highly branched structures, significantly enhancing gene delivery efficacy. Building on the proven efficient sets of monomers in highly branched PAEs (HPAEs), this work introduced a new class of cyclic PAEs (CPAEs) constructed via an A2 + B4 + C2 cyclization synthesis strategy and identified their markedly improved gene transfection capabilities in gene delivery applications. Two sets of cyclic PAEs (CPAEs) with rings of different sizes and topologies were obtained. Their chemical structures were confirmed via two-dimensional nuclear magnetic resonance and the photoluminescence phenomena, and their DNA delivery behaviours were investigated and compared with the HPAE counterparts. In vitro assessments demonstrated that the CPAEs with a macrocyclic architecture (MCPAEs), significantly enhanced DNA intracellular uptake and facilitated efficient gene expression while maintaining perfect biocompatibility. The top-performance MCPAEs have been further employed to deliver a plasmid coding dual single guide RNA-guided CRISPR-Cas9 machinery to delete COL7A1 exon 80 containing the c.6527dupC mutation. In recessive dystrophic epidermolysis bullosa (RDEB) patient-derived epidermal keratinocytes, MCPAEs facilitated the CRISPR plasmid delivery and achieved efficient targeted gene editing in multiple colonies.
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Affiliation(s)
- Xianqing Wang
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Yinghao Li
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Sigen A
- School of Medicine, Anhui University of Science and Technology, Huainan 232001, China
| | - Jing Lyu
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland.
| | - Xi Wang
- Institute of Precision Medicine (AUST-IPM), Anhui University of Science and Technology, Huainan 232001, China
| | - Zhonglei He
- Institute of Precision Medicine (AUST-IPM), Anhui University of Science and Technology, Huainan 232001, China
| | - Irene Lara-Sáez
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ming Li
- Department of Dermatology, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, China
| | - Wenxin Wang
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland.
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46
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Calbry J, Goudounet G, Charlot F, Guyon-Debast A, Perroud PF, Nogué F. The SpRY Cas9 variant release the PAM sequence constraint for genome editing in the model plant Physcomitrium patens. Transgenic Res 2024; 33:67-74. [PMID: 38573428 PMCID: PMC11021247 DOI: 10.1007/s11248-024-00381-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Genome editing via CRISPR/Cas has enabled targeted genetic modifications in various species, including plants. The requirement for specific protospacer-adjacent motifs (PAMs) near the target gene, as seen with Cas nucleases like SpCas9, limits its application. PAMless SpCas9 variants, designed with a relaxed PAM requirement, have widened targeting options. However, these so-call PAMless SpCas9 still show variation of editing efficiency depending on the PAM and their efficiency lags behind the native SpCas9. Here we assess the potential of a PAMless SpCas9 variant for genome editing in the model plant Physcomitrium patens. For this purpose, we developed a SpRYCas9i variant, where expression was optimized, and tested its editing efficiency using the APT as a reporter gene. We show that the near PAMless SpRYCas9i effectively recognizes specific PAMs in P. patens that are not or poorly recognized by the native SpCas9. Pattern of mutations found using the SpRYCas9i are similar to the ones found with the SpCas9 and we could not detect off-target activity for the sgRNAs tested in this study. These findings contribute to advancing versatile genome editing techniques in plants.
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Affiliation(s)
- Julie Calbry
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Guillaume Goudounet
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Florence Charlot
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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Meltzer WA, Gupta A, Lin PN, Brown RA, Benyamien-Roufaeil DS, Khatri R, Mahurkar AA, Song Y, Taylor RJ, Zalzman M. Reprogramming Chromosome Ends by Functional Histone Acetylation. Int J Mol Sci 2024; 25:3898. [PMID: 38612707 PMCID: PMC11011970 DOI: 10.3390/ijms25073898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Cancers harness embryonic programs to evade aging and promote survival. Normally, sequences at chromosome ends called telomeres shorten with cell division, serving as a countdown clock to limit cell replication. Therefore, a crucial aspect of cancerous transformation is avoiding replicative aging by activation of telomere repair programs. Mouse embryonic stem cells (mESCs) activate a transient expression of the gene Zscan4, which correlates with chromatin de-condensation and telomere extension. Head and neck squamous cell carcinoma (HNSCC) cancers reactivate ZSCAN4, which in turn regulates the phenotype of cancer stem cells (CSCs). Our study reveals a new role for human ZSCAN4 in facilitating functional histone H3 acetylation at telomere chromatin. Next-generation sequencing indicates ZSCAN4 enrichment at telomere chromatin. These changes correlate with ZSCAN4-induced histone H3 acetylation and telomere elongation, while CRISPR/Cas9 knockout of ZSCAN4 leads to reduced H3 acetylation and telomere shortening. Our study elucidates the intricate involvement of ZSCAN4 and its significant contribution to telomere chromatin remodeling. These findings suggest that ZSCAN4 induction serves as a novel link between 'stemness' and telomere maintenance. Targeting ZSCAN4 may offer new therapeutic approaches to effectively limit or enhance the replicative lifespan of stem cells and cancer cells.
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Affiliation(s)
- W Alex Meltzer
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Aditi Gupta
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Phyo Nay Lin
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert A Brown
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Daniel S Benyamien-Roufaeil
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Raju Khatri
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Anup A Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rodney J Taylor
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Marlene and Stewart Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michal Zalzman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Marlene and Stewart Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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48
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Wang S, Gong X, Xiao F, Yang Y. Recent advances in host-focused molecular tools for investigating host-gut microbiome interactions. Front Microbiol 2024; 15:1335036. [PMID: 38605718 PMCID: PMC11007152 DOI: 10.3389/fmicb.2024.1335036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities in the human gut play a significant role in regulating host gene expression, influencing a variety of biological processes. To understand the molecular mechanisms underlying host-microbe interactions, tools that can dissect signaling networks are required. In this review, we discuss recent advances in molecular tools used to study this interplay, with a focus on those that explore how the microbiome regulates host gene expression. These tools include CRISPR-based whole-body genetic tools for deciphering host-specific genes involved in the interaction process, Cre-loxP based tissue/cell-specific gene editing approaches, and in vitro models of host-derived organoids. Overall, the application of these molecular tools is revolutionizing our understanding of how host-microbiome interactions contribute to health and disease, paving the way for improved therapies and interventions that target microbial influences on the host.
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Affiliation(s)
- Siyao Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Xu Gong
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Yun Yang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
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49
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Jia H, Omar AA, Xu J, Dalmendray J, Wang Y, Feng Y, Wang W, Hu Z, Grosser JW, Wang N. Generation of transgene-free canker-resistant Citrus sinensis cv. Hamlin in the T0 generation through Cas12a/CBE co-editing. Front Plant Sci 2024; 15:1385768. [PMID: 38595767 PMCID: PMC11002166 DOI: 10.3389/fpls.2024.1385768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Citrus canker disease affects citrus production. This disease is caused by Xanthomonas citri subsp. citri (Xcc). Previous studies confirmed that during Xcc infection, PthA4, a transcriptional activator like effector (TALE), is translocated from the pathogen to host plant cells. PthA4 binds to the effector binding elements (EBEs) in the promoter region of canker susceptibility gene LOB1 (EBEPthA4-LOBP) to activate its expression and subsequently cause canker symptoms. Previously, the Cas12a/CBE co-editing method was employed to disrupt EBEPthA4-LOBP of pummelo, which is highly homozygous. However, most commercial citrus cultivars are heterozygous hybrids and more difficult to generate homozygous/biallelic mutants. Here, we employed Cas12a/CBE co-editing method to edit EBEPthA4-LOBP of Hamlin (Citrus sinensis), a commercial heterozygous hybrid citrus cultivar grown worldwide. Binary vector GFP-p1380N-ttLbCas12a:LOBP1-mPBE:ALS2:ALS1 was constructed and shown to be functional via Xcc-facilitated agroinfiltration in Hamlin leaves. This construct allows the selection of transgene-free regenerants via GFP, edits ALS to generate chlorsulfuron-resistant regenerants as a selection marker for genome editing resulting from transient expression of the T-DNA via nCas9-mPBE:ALS2:ALS1, and edits gene(s) of interest (i.e., EBEPthA4-LOBP in this study) through ttLbCas12a, thus creating transgene-free citrus. Totally, 77 plantlets were produced. Among them, 8 plantlets were transgenic plants (#HamGFP1 - #HamGFP8), 4 plantlets were transgene-free (#HamNoGFP1 - #HamNoGFP4), and the rest were wild type. Among 4 transgene-free plantlets, three lines (#HamNoGFP1, #HamNoGFP2 and #HamNoGFP3) contained biallelic mutations in EBEpthA4, and one line (#HamNoGFP4) had homozygous mutations in EBEpthA4. We achieved 5.2% transgene-free homozygous/biallelic mutation efficiency for EBEPthA4-LOBP in C. sinensis cv. Hamlin, compared to 1.9% mutation efficiency for pummelo in a previous study. Importantly, the four transgene-free plantlets and 3 transgenic plantlets that survived were resistant against citrus canker. Taken together, Cas12a/CBE co-editing method has been successfully used to generate transgene-free canker-resistant C. sinensis cv. Hamlin in the T0 generation via biallelic/homozygous editing of EBEpthA4 of the canker susceptibility gene LOB1.
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Affiliation(s)
- Hongge Jia
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Ahmad A. Omar
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Javier Dalmendray
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Yuanchun Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Yu Feng
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Wenting Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Zhuyuan Hu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Jude W. Grosser
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
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50
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Workman RE, Stoltzfus MJ, Keith NC, Euler CW, Bondy-Denomy J, Modell JW. Anti- CRISPR proteins trigger a burst of CRISPR-Cas9 expression that enhances phage defense. Cell Rep 2024; 43:113849. [PMID: 38427560 DOI: 10.1016/j.celrep.2024.113849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/04/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
CRISPR-Cas immune systems provide bacteria with adaptive immunity against bacteriophages, but they are often transcriptionally repressed to mitigate auto-immunity. In some cases, CRISPR-Cas expression increases in response to a phage infection, but the mechanisms of induction are largely unknown, and it is unclear whether induction occurs strongly and quickly enough to benefit the bacterial host. In S. pyogenes, Cas9 is both an immune effector and auto-repressor of CRISPR-Cas expression. Here, we show that phage-encoded anti-CRISPR proteins relieve Cas9 auto-repression and trigger a rapid increase in CRISPR-Cas levels during a single phage infective cycle. As a result, fewer cells succumb to lysis, leading to a striking survival benefit after multiple rounds of infection. CRISPR-Cas induction also reduces lysogeny, thereby limiting a route for horizontal gene transfer. Altogether, we show that Cas9 is not only a CRISPR-Cas effector and repressor but also a phage sensor that can mount an anti-anti-CRISPR transcriptional response.
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Affiliation(s)
- Rachael E Workman
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marie J Stoltzfus
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas C Keith
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chad W Euler
- Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA, USA
| | - Joshua W Modell
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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