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Shen K, Flood JJ, Zhang Z, Ha A, Shy B, Dueber J, Douglas S. Engineering an Escherichia coli strain for production of long single-stranded DNA. Nucleic Acids Res 2024; 52:4098-4107. [PMID: 38499480 PMCID: PMC11040142 DOI: 10.1093/nar/gkae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Long single-stranded DNA (ssDNA) is a versatile molecular reagent with applications including RNA-guided genome engineering and DNA nanotechnology, yet its production is typically resource-intensive. We introduce a novel method utilizing an engineered Escherichia coli 'helper' strain and phagemid system that simplifies long ssDNA generation to a straightforward transformation and purification procedure. Our method obviates the need for helper plasmids and their associated contamination by integrating M13mp18 genes directly into the E. coli chromosome. We achieved ssDNA lengths ranging from 504 to 20 724 nt with titers up to 250 μg/l following alkaline lysis purification. The efficacy of our system was confirmed through its application in primary T-cell genome modifications and DNA origami folding. The reliability, scalability and ease of our approach promise to unlock new experimental applications requiring large quantities of long ssDNA.
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Affiliation(s)
- Konlin Shen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158 USA
| | - Jake J Flood
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zhihuizi Zhang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158 USA
| | - Alvin Ha
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, 94158 USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, 94158 USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
| | - John E Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Shawn M Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158 USA
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Shy BR, Vykunta VS, Ha A, Talbot A, Roth TL, Nguyen DN, Pfeifer WG, Chen YY, Blaeschke F, Shifrut E, Vedova S, Mamedov MR, Chung JYJ, Li H, Yu R, Wu D, Wolf J, Martin TG, Castro CE, Ye L, Esensten JH, Eyquem J, Marson A. High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails. Nat Biotechnol 2023; 41:521-531. [PMID: 36008610 PMCID: PMC10065198 DOI: 10.1038/s41587-022-01418-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 07/02/2022] [Indexed: 01/12/2023]
Abstract
Enhancing CRISPR-mediated site-specific transgene insertion efficiency by homology-directed repair (HDR) using high concentrations of double-stranded DNA (dsDNA) with Cas9 target sequences (CTSs) can be toxic to primary cells. Here, we develop single-stranded DNA (ssDNA) HDR templates (HDRTs) incorporating CTSs with reduced toxicity that boost knock-in efficiency and yield by an average of around two- to threefold relative to dsDNA CTSs. Using small-molecule combinations that enhance HDR, we could further increase knock-in efficiencies by an additional roughly two- to threefold on average. Our method works across a variety of target loci, knock-in constructs and primary human cell types, reaching HDR efficiencies of >80-90%. We demonstrate application of this approach for both pathogenic gene variant modeling and gene-replacement strategies for IL2RA and CTLA4 mutations associated with Mendelian disorders. Finally, we develop a good manufacturing practice (GMP)-compatible process for nonviral chimeric antigen receptor-T cell manufacturing, with knock-in efficiencies (46-62%) and yields (>1.5 × 109 modified cells) exceeding those of conventional approaches.
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Affiliation(s)
- Brian R Shy
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
| | - Vivasvan S Vykunta
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alvin Ha
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexis Talbot
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
- INSERM U976, Saint Louis Research Institute, Paris City University, Paris, France
| | - Theodore L Roth
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Wolfgang G Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
- Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Yan Yi Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Franziska Blaeschke
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric Shifrut
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Shane Vedova
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Murad R Mamedov
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jing-Yi Jing Chung
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
| | - Hong Li
- Department of Research and Development, Reagent and Services Business Unit, Life Science Group, GenScript Biotech, Nanjing, China
| | - Ruby Yu
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David Wu
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey Wolf
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Thomas G Martin
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Lumeng Ye
- Department of Research and Development, Reagent and Services Business Unit, Life Science Group, GenScript Biotech, Nanjing, China
| | - Jonathan H Esensten
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
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Fukuda S, Narendran S, Varshney A, Nagasaka Y, Wang SB, Ambati K, Apicella I, Pereira F, Fowler BJ, Yasuma T, Hirahara S, Yasuma R, Huang P, Yerramothu P, Makin RD, Wang M, Baker KL, Marion KM, Huang X, Baghdasaryan E, Ambati M, Ambati VL, Banerjee D, Bonilha VL, Tolstonog GV, Held U, Ogura Y, Terasaki H, Oshika T, Bhattarai D, Kim KB, Feldman SH, Aguirre JI, Hinton DR, Kerur N, Sadda SR, Schumann GG, Gelfand BD, Ambati J. Alu complementary DNA is enriched in atrophic macular degeneration and triggers retinal pigmented epithelium toxicity via cytosolic innate immunity. SCIENCE ADVANCES 2021; 7:eabj3658. [PMID: 34586848 PMCID: PMC8480932 DOI: 10.1126/sciadv.abj3658] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/05/2021] [Indexed: 05/08/2023]
Abstract
Long interspersed nuclear element-1 (L1)–mediated reverse transcription (RT) of Alu RNA into cytoplasmic Alu complementary DNA (cDNA) has been implicated in retinal pigmented epithelium (RPE) degeneration. The mechanism of Alu cDNA–induced cytotoxicity and its relevance to human disease are unknown. Here we report that Alu cDNA is highly enriched in the RPE of human eyes with geographic atrophy, an untreatable form of age-related macular degeneration. We demonstrate that the DNA sensor cGAS engages Alu cDNA to induce cytosolic mitochondrial DNA escape, which amplifies cGAS activation, triggering RPE degeneration via the inflammasome. The L1-extinct rice rat was resistant to Alu RNA–induced Alu cDNA synthesis and RPE degeneration, which were enabled upon L1-RT overexpression. Nucleoside RT inhibitors (NRTIs), which inhibit both L1-RT and inflammasome activity, and NRTI derivatives (Kamuvudines) that inhibit inflammasome, but not RT, both block Alu cDNA toxicity, identifying inflammasome activation as the terminal effector of RPE degeneration.
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Affiliation(s)
- Shinichi Fukuda
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Siddharth Narendran
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Aravind Eye Hospital System, Madurai, India
| | - Akhil Varshney
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Yosuke Nagasaka
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shao-bin Wang
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kameshwari Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ivana Apicella
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Felipe Pereira
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Benjamin J. Fowler
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY, USA
| | - Tetsuhiro Yasuma
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Shuichiro Hirahara
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Reo Yasuma
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Peirong Huang
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Praveen Yerramothu
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ryan D. Makin
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Mo Wang
- Doheny Eye Institute, Los Angeles, CA, USA
| | | | | | | | - Elmira Baghdasaryan
- Doheny Eye Institute, Los Angeles, CA, USA
- Department of Ophthalmology, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, California, USA
| | - Meenakshi Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Center for Digital Image Evaluation, Charlottesville, VA, USA
| | - Vidya L. Ambati
- Center for Digital Image Evaluation, Charlottesville, VA, USA
| | - Daipayan Banerjee
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | - Genrich V. Tolstonog
- Department of Otolaryngology–Head and Neck Surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ulrike Held
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Yuichiro Ogura
- Department of Ophthalmology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuro Oshika
- Department of Ophthalmology, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Deepak Bhattarai
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Kyung Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Sanford H. Feldman
- Center for Comparative Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - J. Ignacio Aguirre
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - David R. Hinton
- Departments of Pathology and Ophthalmology, USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Nagaraj Kerur
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Srinivas R. Sadda
- Doheny Eye Institute, Los Angeles, CA, USA
- Department of Ophthalmology, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, California, USA
| | - Gerald G. Schumann
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Bradley D. Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
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