1
|
Mielnicka M, Tabaro F, Sureka R, Acurzio B, Paoletti R, Scavizzi F, Raspa M, Crevenna AH, Lapouge K, Remans K, Boulard M. Trim66's paternal deficiency causes intrauterine overgrowth. Life Sci Alliance 2024; 7:e202302512. [PMID: 38719749 PMCID: PMC11077763 DOI: 10.26508/lsa.202302512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
The tripartite motif-containing protein 66 (TRIM66, also known as TIF1-delta) is a PHD-Bromo-containing protein primarily expressed in post-meiotic male germ cells known as spermatids. Biophysical assays showed that the TRIM66 PHD-Bromodomain binds to H3 N-terminus only when lysine 4 is unmethylated. We addressed TRIM66's role in reproduction by loss-of-function genetics in the mouse. Males homozygous for Trim66-null mutations produced functional spermatozoa. Round spermatids lacking TRIM66 up-regulated a network of genes involved in histone acetylation and H3K4 methylation. Profiling of H3K4me3 patterns in the sperm produced by the Trim66-null mutant showed minor alterations below statistical significance. Unexpectedly, Trim66-null males, but not females, sired pups overweight at birth, hence revealing that Trim66 mutations cause a paternal effect phenotype.
Collapse
Affiliation(s)
- Monika Mielnicka
- https://ror.org/01yr73893 Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Francesco Tabaro
- https://ror.org/01yr73893 Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Rahul Sureka
- https://ror.org/01yr73893 Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Basilia Acurzio
- https://ror.org/01yr73893 Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Monterotondo, Italy
| | | | - Ferdinando Scavizzi
- National Research Council (IBBC), CNR-Campus International Development (EMMA-INFRAFRONTIER-IMPC), Monterotondo, Italy
| | - Marcello Raspa
- National Research Council (IBBC), CNR-Campus International Development (EMMA-INFRAFRONTIER-IMPC), Monterotondo, Italy
| | - Alvaro H Crevenna
- https://ror.org/01yr73893 Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Karine Lapouge
- https://ror.org/01yr73893 European Molecular Biology Laboratory, Protein Expression and Purification Core Facility, Heidelberg, Germany
| | - Kim Remans
- https://ror.org/01yr73893 European Molecular Biology Laboratory, Protein Expression and Purification Core Facility, Heidelberg, Germany
| | - Matthieu Boulard
- https://ror.org/01yr73893 Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Monterotondo, Italy
| |
Collapse
|
2
|
Wu SHS, Kim S, Lee H, Lee JH, Park SY, Bakonyi R, Teriyapirom I, Hallay N, Pilat-Carotta S, Theussl HC, Kim J, Lee JH, Simons BD, Kim JK, Colozza G, Koo BK. Red2Flpe-SCON: a versatile, multicolor strategy for generating mosaic conditional knockout mice. Nat Commun 2024; 15:4963. [PMID: 38862535 PMCID: PMC11166929 DOI: 10.1038/s41467-024-49382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We develop the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We use the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which reveal that the stem cell gene, Sox2, is less essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.
Collapse
Affiliation(s)
- Szu-Hsien Sam Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Somi Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Heetak Lee
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Ji-Hyun Lee
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - So-Yeon Park
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Réka Bakonyi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Isaree Teriyapirom
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Natalia Hallay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Sandra Pilat-Carotta
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | | | - Jihoon Kim
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, South Korea
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Benjamin D Simons
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Jong Kyoung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Gabriele Colozza
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Bon-Kyoung Koo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea.
| |
Collapse
|
3
|
Miura H, Nakamura A, Kurosaki A, Kotani A, Motojima M, Tanaka K, Kakuta S, Ogiwara S, Ohmi Y, Komaba H, Schilit SLP, Morton CC, Gurumurthy CB, Ohtsuka M. Targeted insertion of conditional expression cassettes into the mouse genome using the modified i-PITT. BMC Genomics 2024; 25:568. [PMID: 38840068 PMCID: PMC11155135 DOI: 10.1186/s12864-024-10250-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 03/22/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Transgenic (Tg) mice are widely used in biomedical research, and they are typically generated by injecting transgenic DNA cassettes into pronuclei of one-cell stage zygotes. Such animals often show unreliable expression of the transgenic DNA, one of the major reasons for which is random insertion of the transgenes. We previously developed a method called "pronuclear injection-based targeted transgenesis" (PITT), in which DNA constructs are directed to insert at pre-designated genomic loci. PITT was achieved by pre-installing so called landing pad sequences (such as heterotypic LoxP sites or attP sites) to create seed mice and then injecting Cre recombinase or PhiC31 integrase mRNAs along with a compatible donor plasmid into zygotes derived from the seed mice. PITT and its subsequent version, improved PITT (i-PITT), overcome disadvantages of conventional Tg mice such as lack of consistent and reliable expression of the cassettes among different Tg mouse lines, and the PITT approach is superior in terms of cost and labor. One of the limitations of PITT, particularly using Cre-mRNA, is that the approach cannot be used for insertion of conditional expression cassettes using Cre-LoxP site-specific recombination. This is because the LoxP sites in the donor plasmids intended for achieving conditional expression of the transgene will interfere with the PITT recombination reaction with LoxP sites in the landing pad. RESULTS To enable the i-PITT method to insert a conditional expression cassette, we modified the approach by simultaneously using PhiC31o and FLPo mRNAs. We demonstrate the strategy by creating a model containing a conditional expression cassette at the Rosa26 locus with an efficiency of 13.7%. We also demonstrate that inclusion of FLPo mRNA excludes the insertion of vector backbones in the founder mice. CONCLUSIONS Simultaneous use of PhiC31 and FLP in i-PITT approach allows insertion of donor plasmids containing Cre-loxP-based conditional expression cassettes.
Collapse
Affiliation(s)
- Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Ayaka Nakamura
- Life Science Support Center, Tokai University, Kanagawa, Japan
| | - Aki Kurosaki
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Ai Kotani
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan
- Department of Innovative Medical Science, Tokai University School of Medicine, Kanagawa, Japan
- Division of Hematological Malignancy, Institute of Medical Sciences, Tokai University, Kanagawa, Japan
| | - Masaru Motojima
- Department of Clinical Pharmacology, Tokai University School of Medicine, Kanagawa, Japan
| | - Keiko Tanaka
- Departments of Basic Medicine, Tokai University School of Medicine, Kanagawa, Japan
- Division of Kidney, Diabetes and Endocrine Diseases, Okayama University Hospital, Okayama, Japan
| | - Shigeru Kakuta
- Laboratory of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Tokyo, Japan
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Sanae Ogiwara
- Life Science Support Center, Tokai University, Kanagawa, Japan
| | - Yuhsuke Ohmi
- Department of Clinical Engineering, Chubu University College of Life and Health Sciences, Kasugai, Aichi, Japan
| | - Hirotaka Komaba
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan
- Division of Nephrology, Endocrinology and Metabolism, Tokai University School of Medicine, Kanagawa, Japan
| | - Samantha L P Schilit
- Program in Genetics and Genomics and Certificate Program in Leder Human Biology and Translational Medicine, Biological and Biomedical Sciences Program, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Cynthia C Morton
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Institute Member, Broad Institute of Massachusetts Institute of Technology and Harvard University, Kendall Square, Cambridge, MA, USA
- Manchester Center for Hearing and Deafness, University of Manchester, Manchester, UK
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, Japan.
- The Institute of Medical Sciences, Tokai University, Kanagawa, Japan.
| |
Collapse
|
4
|
Dey D, Chakravarti R, Bhattacharjee O, Majumder S, Chaudhuri D, Ahmed KT, Roy D, Bhattacharya B, Arya M, Gautam A, Singh R, Gupta R, Ravichandiran V, Chattopadhyay D, Ghosh A, Giri K, Roy S, Ghosh D. 2.5A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9. J Biol Chem 2024:107439. [PMID: 38838774 DOI: 10.1016/j.jbc.2024.107439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
The therapeutic application of CRISPR-Cas9 is limited due to its off-target activity. To have a better understanding of this off-target effect, we have focused on its mismatch-prone PAM distal end. The off-target activity of SpCas9 depends directly on the nature of mismatches, which in turn results in deviation of the active site of SpCas9 due to structural instability in the RNA-DNA duplex strand. In order to test the hypothesis, we have designed an array of mismatched target sites at the PAM distal end and performed in vitro and cell line-based experiments, which showed a strong correlation for Cas9 activity. We found that target sites having multiple mismatches in the 18th to 15th position upstream of the PAM showed no to little activity. For further mechanistic validation, Molecular Dynamics simulations were performed, which revealed that certain mismatches showed elevated root mean square deviation (RMSD) values that can be attributed to conformational instability within the RNA-DNA duplex. Therefore, for successful prediction of the off-target effect of SpCas9, along with complementation-derived energy, the RNA-DNA duplex stability plays a crucial role.
Collapse
Affiliation(s)
- Dhritiman Dey
- National Institute of Pharmaceutical Education and Research-Kolkata
| | | | | | | | | | | | - Dipanjan Roy
- National Institute of Pharmaceutical Education and Research-Kolkata
| | | | - Mansi Arya
- National Institute of Pharmaceutical Education and Research-Kolkata
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany; International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology, Max-Planck-Ring,5, 72076 Tübingen, Germany
| | - Rajveer Singh
- National Institute of Pharmaceutical Education and Research-Kolkata
| | - Rahul Gupta
- Indian Institute of Chemical Biology-Kolkata
| | | | | | | | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Syamal Roy
- Indian Institute of Chemical Biology-Kolkata
| | - Dipanjan Ghosh
- National Institute of Pharmaceutical Education and Research-Kolkata.
| |
Collapse
|
5
|
Goodrich EJ, Deans MR. Emx2 lineage tracing reveals antecedent patterns of planar polarity in the mouse inner ear. Development 2024; 151:dev202425. [PMID: 38804528 DOI: 10.1242/dev.202425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
The planar polarized organization of hair cells in the vestibular maculae is unique because these sensory organs contain two groups of cells with oppositely oriented stereociliary bundles that meet at a line of polarity reversal (LPR). EMX2 is a transcription factor expressed by one hair cell group that reverses the orientation of their bundles, thereby forming the LPR. We generated Emx2-CreERt2 transgenic mice for genetic lineage tracing and demonstrate Emx2 expression before hair cell specification when the nascent utricle and saccule constitute a continuous prosensory domain. Precursors labeled by Emx2-CreERt2 at this stage give rise to hair cells located along one side of the LPR in the mature utricle or saccule, indicating that this boundary is first established in the prosensory domain. Consistent with this, Emx2-CreERt2 lineage tracing in Dreher mutants, where the utricle and saccule fail to segregate, labels a continuous field of cells along one side of a fused utriculo-saccular-cochlear organ. These observations reveal that LPR positioning is pre-determined in the developing prosensory domain, and that EMX2 expression defines lineages of hair cells with oppositely oriented stereociliary bundles.
Collapse
Affiliation(s)
- Ellison J Goodrich
- Department of Neurobiology, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT 84112, USA
| | - Michael R Deans
- Department of Neurobiology, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT 84112, USA
- Department of Otolaryngology - Head and Neck Surgery, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT 84132, USA
| |
Collapse
|
6
|
Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [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] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
Collapse
Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
| |
Collapse
|
7
|
Zhang Z, Zhang S, Wong HT, Li D, Feng B. Targeted Gene Insertion: The Cutting Edge of CRISPR Drug Development with Hemophilia as a Highlight. BioDrugs 2024; 38:369-385. [PMID: 38489061 PMCID: PMC11055778 DOI: 10.1007/s40259-024-00654-5] [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] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The remarkable advance in gene editing technology presents unparalleled opportunities for transforming medicine and finding cures for hereditary diseases. Human trials of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9)-based therapeutics have demonstrated promising results in disrupting or deleting target sequences to treat specific diseases. However, the potential of targeted gene insertion approaches, which offer distinct advantages over disruption/deletion methods, remains largely unexplored in human trials due to intricate technical obstacles and safety concerns. This paper reviews the recent advances in preclinical studies demonstrating in vivo targeted gene insertion for therapeutic benefits, targeting somatic solid tissues through systemic delivery. With a specific emphasis on hemophilia as a prominent disease model, we highlight advancements in insertion strategies, including considerations of DNA repair pathways, targeting site selection, and donor design. Furthermore, we discuss the complex challenges and recent breakthroughs that offer valuable insights for progressing towards clinical trials.
Collapse
Affiliation(s)
- Zhenjie Zhang
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Siqi Zhang
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
| | - Hoi Ting Wong
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo Feng
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| |
Collapse
|
8
|
Tokatly Latzer I, Roullet JB, Afshar-Saber W, Lee HHC, Bertoldi M, McGinty GE, DiBacco ML, Arning E, Tsuboyama M, Rotenberg A, Opladen T, Jeltsch K, García-Cazorla À, Juliá-Palacios N, Gibson KM, Sahin M, Pearl PL. Clinical and molecular outcomes from the 5-Year natural history study of SSADH Deficiency, a model metabolic neurodevelopmental disorder. J Neurodev Disord 2024; 16:21. [PMID: 38658850 PMCID: PMC11044349 DOI: 10.1186/s11689-024-09538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Succinic semialdehyde dehydrogenase deficiency (SSADHD) represents a model neurometabolic disease at the fulcrum of translational research within the Boston Children's Hospital Intellectual and Developmental Disabilities Research Centers (IDDRC), including the NIH-sponsored natural history study of clinical, neurophysiological, neuroimaging, and molecular markers, patient-derived induced pluripotent stem cells (iPSC) characterization, and development of a murine model for tightly regulated, cell-specific gene therapy. METHODS SSADHD subjects underwent clinical evaluations, neuropsychological assessments, biochemical quantification of γ-aminobutyrate (GABA) and related metabolites, electroencephalography (standard and high density), magnetoencephalography, transcranial magnetic stimulation, magnetic resonance imaging and spectroscopy, and genetic tests. This was parallel to laboratory molecular investigations of in vitro GABAergic neurons derived from induced human pluripotent stem cells (hiPSCs) of SSADHD subjects and biochemical analyses performed on a versatile murine model that uses an inducible and reversible rescue strategy allowing on-demand and cell-specific gene therapy. RESULTS The 62 SSADHD subjects [53% females, median (IQR) age of 9.6 (5.4-14.5) years] included in the study had a reported symptom onset at ∼ 6 months and were diagnosed at a median age of 4 years. Language developmental delays were more prominent than motor. Autism, epilepsy, movement disorders, sleep disturbances, and various psychiatric behaviors constituted the core of the disorder's clinical phenotype. Lower clinical severity scores, indicating worst severity, coincided with older age (R= -0.302, p = 0.03), as well as age-adjusted lower values of plasma γ-aminobutyrate (GABA) (R = 0.337, p = 0.02) and γ-hydroxybutyrate (GHB) (R = 0.360, p = 0.05). While epilepsy and psychiatric behaviors increase in severity with age, communication abilities and motor function tend to improve. iPSCs, which were differentiated into GABAergic neurons, represent the first in vitro neuronal model of SSADHD and express the neuronal marker microtubule-associated protein 2 (MAP2), as well as GABA. GABA-metabolism in induced GABAergic neurons could be reversed using CRISPR correction of the pathogenic variants or mRNA transfection and SSADHD iPSCs were associated with excessive glutamatergic activity and related synaptic excitation. CONCLUSIONS Findings from the SSADHD Natural History Study converge with iPSC and animal model work focused on a common disorder within our IDDRC, deepening our knowledge of the pathophysiology and longitudinal clinical course of a complex neurodevelopmental disorder. This further enables the identification of biomarkers and changes throughout development that will be essential for upcoming targeted trials of enzyme replacement and gene therapy.
Collapse
Affiliation(s)
- Itay Tokatly Latzer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- School of Medicine, Faculty of Medical and Health Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Jean-Baptiste Roullet
- Department of Pharmacotherapy, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Wardiya Afshar-Saber
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Henry H C Lee
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Gabrielle E McGinty
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Melissa L DiBacco
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Erland Arning
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Melissa Tsuboyama
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Alexander Rotenberg
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Thomas Opladen
- Division of Neuropediatrics & Metabolic Medicine, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Kathrin Jeltsch
- Division of Neuropediatrics & Metabolic Medicine, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Àngels García-Cazorla
- Neurometabolic Unit, Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Natalia Juliá-Palacios
- Neurometabolic Unit, Neurology Department, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - K Michael Gibson
- Department of Pharmacotherapy, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Phillip L Pearl
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA, 02115, USA.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Gao KM, Chiang K, Jiang Z, Korkmaz FT, Janardhan HP, Trivedi CM, Quinton LJ, Gingras S, Fitzgerald KA, Marshak-Rothstein A. Endothelial cell expression of a STING gain-of-function mutation initiates pulmonary lymphocytic infiltration. Cell Rep 2024; 43:114114. [PMID: 38625791 PMCID: PMC11108094 DOI: 10.1016/j.celrep.2024.114114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 03/13/2024] [Accepted: 03/29/2024] [Indexed: 04/18/2024] Open
Abstract
Patients afflicted with Stimulator of interferon gene (STING) gain-of-function mutations frequently present with debilitating interstitial lung disease (ILD) that is recapitulated in mice expressing the STINGV154M mutation (VM). Prior radiation chimera studies revealed an unexpected and critical role for non-hematopoietic cells in initiating ILD. To identify STING-expressing non-hematopoietic cell types required for the development of ILD, we use a conditional knockin (CKI) model and direct expression of the VM allele to hematopoietic cells, fibroblasts, epithelial cells, or endothelial cells. Only endothelial cell-targeted VM expression results in enhanced recruitment of immune cells to the lung associated with elevated chemokine expression and the formation of bronchus-associated lymphoid tissue, as seen in the parental VM strain. These findings reveal the importance of endothelial cells as instigators of STING-driven lung disease and suggest that therapeutic targeting of STING inhibitors to endothelial cells could potentially mitigate inflammation in the lungs of STING-associated vasculopathy with onset in infancy (SAVI) patients or patients afflicted with other ILD-related disorders.
Collapse
Affiliation(s)
- Kevin MingJie Gao
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Division of Rheumatology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kristy Chiang
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Division of Rheumatology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Zhaozhao Jiang
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Filiz T Korkmaz
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Harish P Janardhan
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Chinmay M Trivedi
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Lee J Quinton
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Sebastien Gingras
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| | - Ann Marshak-Rothstein
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| |
Collapse
|
11
|
Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
Collapse
Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| |
Collapse
|
12
|
Hernández-Morán BA, Taylor G, Lorente-Macías Á, Wood AJ. Degron tagging for rapid protein degradation in mice. Dis Model Mech 2024; 17:dmm050613. [PMID: 38666498 PMCID: PMC11073515 DOI: 10.1242/dmm.050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Degron tagging allows proteins of interest to be rapidly degraded, in a reversible and tuneable manner, in response to a chemical stimulus. This provides numerous opportunities for understanding disease mechanisms, modelling therapeutic interventions and constructing synthetic gene networks. In recent years, many laboratories have applied degron tagging successfully in cultured mammalian cells, spurred by rapid advances in the fields of genome editing and targeted protein degradation. In this At a Glance article, we focus on recent efforts to apply degron tagging in mouse models, discussing the distinct set of challenges and opportunities posed by the in vivo environment.
Collapse
Affiliation(s)
- Brianda A. Hernández-Morán
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Gillian Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| |
Collapse
|
13
|
Hermantara R, Richmond L, Taqi AF, Chilaka S, Jeantet V, Guerrini I, West K, West A. Improving CRISPR-Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration. J Biomed Sci 2024; 31:32. [PMID: 38532479 DOI: 10.1186/s12929-024-01020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR-Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency. METHOD Here we report the development of a multicolour fluorescence assay for studying CRISPR-Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR-Cas9 strategies. RESULT We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration. CONCLUSION Our results highlight the need for a more stringent assessment of CRISPR-Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
Collapse
Affiliation(s)
- Rio Hermantara
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
| | - Laura Richmond
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Aqeel Faisal Taqi
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sabari Chilaka
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Valentine Jeantet
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ileana Guerrini
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katherine West
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Adam West
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
14
|
Klocke B, Britzolaki A, Saurine J, Ott H, Krone K, Bahamonde K, Thelen C, Tzimas C, Sanoudou D, Kranias EG, Pitychoutis PM. A novel role for phospholamban in the thalamic reticular nucleus. Sci Rep 2024; 14:6376. [PMID: 38493225 PMCID: PMC10944534 DOI: 10.1038/s41598-024-56447-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
The thalamic reticular nucleus (TRN) is a brain region that influences vital neurobehavioral processes, including executive functioning and the generation of sleep rhythms. TRN dysfunction underlies hyperactivity, attention deficits, and sleep disturbances observed across various neurodevelopmental disorders. A specialized sarco-endoplasmic reticulum calcium (Ca2+) ATPase 2 (SERCA2)-dependent Ca2+ signaling network operates in the dendrites of TRN neurons to regulate their bursting activity. Phospholamban (PLN) is a prominent regulator of SERCA2 with an established role in myocardial Ca2+-cycling. Our findings suggest that the role of PLN extends beyond the cardiovascular system to impact brain function. Specifically, we found PLN to be expressed in TRN neurons of the adult mouse brain, and utilized global constitutive and innovative conditional genetic knockout mouse models in concert with electroencephalography (EEG)-based somnography and the 5-choice serial reaction time task (5-CSRTT) to investigate the role of PLN in sleep and executive functioning, two complex behaviors that map onto thalamic reticular circuits. The results of the present study indicate that perturbed PLN function in the TRN results in aberrant TRN-dependent phenotypes in mice (i.e., hyperactivity, impulsivity and sleep deficits) and support a novel role for PLN as a critical regulator of SERCA2 in the TRN neurocircuitry.
Collapse
Affiliation(s)
- Benjamin Klocke
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Aikaterini Britzolaki
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Joseph Saurine
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Hayden Ott
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Kylie Krone
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Kiara Bahamonde
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Connor Thelen
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA
| | - Christos Tzimas
- Molecular Biology Department, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Despina Sanoudou
- Molecular Biology Department, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
- 4th Department of Internal Medicine, Clinical Genomics and Pharmacogenomics Unit, Medical School, "Attikon" Hospital, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Evangelia G Kranias
- Molecular Biology Department, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Pothitos M Pitychoutis
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH, 45469-2320, USA.
| |
Collapse
|
15
|
Mesnard CS, Hays CL, Townsend LE, Barta CL, Gurumurthy CB, Thoreson WB. SYNAPTOTAGMIN-9 IN MOUSE RETINA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.27.546758. [PMID: 37425946 PMCID: PMC10327071 DOI: 10.1101/2023.06.27.546758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Synaptotagmin-9 (Syt9) is a Ca2+ sensor mediating fast synaptic release expressed in various parts of the brain. The presence and role of Syt9 in retina is unknown. We found evidence for Syt9 expression throughout the retina and created mice to conditionally eliminate Syt9 in a cre-dependent manner. We crossed Syt9fl/fl mice with Rho-iCre, HRGP-Cre, and CMV-cre mice to generate mice in which Syt9 was eliminated from rods (rodSyt9CKO), cones (coneSyt9CKO), or whole animals (CMVSyt9). CMVSyt9 mice showed an increase in scotopic electroretinogram (ERG) b-waves evoked by bright flashes with no change in a-waves. Cone-driven photopic ERG b-waves were not significantly different in CMVSyt9 knockout mice and selective elimination of Syt9 from cones had no effect on ERGs. However, selective elimination from rods decreased scotopic and photopic b-waves as well as oscillatory potentials. These changes occurred only with bright flashes where cone responses contribute. Synaptic release was measured in individual rods by recording anion currents activated by glutamate binding to presynaptic glutamate transporters. Loss of Syt9 from rods had no effect on spontaneous or depolarization-evoked release. Our data show that Syt9 is acts at multiple sites in the retina and suggest that it may play a role in regulating transmission of cone signals by rods.
Collapse
Affiliation(s)
- Chris S. Mesnard
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68106, USA
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Cassandra L. Hays
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68106, USA
- Department of Medical Education, Creighton University, Omaha, NE 68178
| | - Lou E. Townsend
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68106, USA
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Cody L. Barta
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | | | - Wallace B. Thoreson
- Truhlsen Eye Institute and Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, NE 68106, USA
- Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68106, USA
| |
Collapse
|
16
|
Chen X, Du J, Yun S, Xue C, Yao Y, Rao S. Recent advances in CRISPR-Cas9-based genome insertion technologies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102138. [PMID: 38379727 PMCID: PMC10878794 DOI: 10.1016/j.omtn.2024.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Programmable genome insertion (or knock-in) is vital for both fundamental and translational research. The continuously expanding number of CRISPR-based genome insertion strategies demonstrates the ongoing development in this field. Common methods for site-specific genome insertion rely on cellular double-strand breaks repair pathways, such as homology-directed repair, non-homologous end-joining, and microhomology-mediated end joining. Recent advancements have further expanded the toolbox of programmable genome insertion techniques, including prime editing, integrase coupled with programmable nuclease, and CRISPR-associated transposon. These tools possess their own capabilities and limitations, promoting tremendous efforts to enhance editing efficiency, broaden targeting scope and improve editing specificity. In this review, we first summarize recent advances in programmable genome insertion techniques. We then elaborate on the cons and pros of each technique to assist researchers in making informed choices when using these tools. Finally, we identify opportunities for future improvements and applications in basic research and therapeutics.
Collapse
Affiliation(s)
- Xinwen Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingjing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shaowei Yun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| |
Collapse
|
17
|
McCabe CV, Price PD, Codner GF, Allan AJ, Caulder A, Christou S, Loeffler J, Mackenzie M, Malzer E, Mianné J, Nowicki KJ, O’Neill EJ, Pike FJ, Hutchison M, Petit-Demoulière B, Stewart ME, Gates H, Wells S, Sanderson ND, Teboul L. Long-read sequencing for fast and robust identification of correct genome-edited alleles: PCR-based and Cas9 capture methods. PLoS Genet 2024; 20:e1011187. [PMID: 38457464 PMCID: PMC10954187 DOI: 10.1371/journal.pgen.1011187] [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: 08/11/2023] [Revised: 03/20/2024] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Recent developments in CRISPR/Cas9 genome-editing tools have facilitated the introduction of precise alleles, including genetic intervals spanning several kilobases, directly into the embryo. However, the introduction of donor templates, via homology directed repair, can be erroneous or incomplete and these techniques often produce mosaic founder animals. Thus, newly generated alleles must be verified at the sequence level across the targeted locus. Screening for the presence of the desired mutant allele using traditional sequencing methods can be challenging due to the size of the interval to be sequenced, together with the mosaic nature of founders. METHODOLOGY/PRINCIPAL FINDINGS In order to help disentangle the genetic complexity of these animals, we tested the application of Oxford Nanopore Technologies long-read sequencing at the targeted locus and found that the achievable depth of sequencing is sufficient to offset the sequencing error rate associated with the technology used to validate targeted regions of interest. We have assembled an analysis workflow that facilitates interrogating the entire length of a targeted segment in a single read, to confirm that the intended mutant sequence is present in both heterozygous animals and mosaic founders. We used this workflow to compare the output of PCR-based and Cas9 capture-based targeted sequencing for validation of edited alleles. CONCLUSION Targeted long-read sequencing supports in-depth characterisation of all experimental models that aim to produce knock-in or conditional alleles, including those that contain a mix of genome-edited alleles. PCR- or Cas9 capture-based modalities bring different advantages to the analysis.
Collapse
Affiliation(s)
| | - Peter D. Price
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Gemma F. Codner
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Elke Malzer
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | | | - Fran J. Pike
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Benoit Petit-Demoulière
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, Illkirch, France
| | | | - Hilary Gates
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| |
Collapse
|
18
|
Allyn BM, Hayer KE, Oyeniran C, Nganga V, Lee K, Mishra B, Sacan A, Oltz EM, Bassing CH. Locus folding mechanisms determine modes of antigen receptor gene assembly. J Exp Med 2024; 221:e20230985. [PMID: 38189780 PMCID: PMC10772921 DOI: 10.1084/jem.20230985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
Collapse
Affiliation(s)
- Brittney M. Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, USA
| | - Clement Oyeniran
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Vincent Nganga
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kyutae Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bikash Mishra
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ahmet Sacan
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Craig H. Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
19
|
Duddy G, Courtis K, Horwood J, Olsen J, Horsler H, Hodgson T, Varsani-Brown S, Abdullah A, Denti L, Lane H, Delaqua F, Janzen J, Strom M, Rosewell I, Crawley K, Davies B. Donor template delivery by recombinant adeno-associated virus for the production of knock-in mice. BMC Biol 2024; 22:26. [PMID: 38302906 PMCID: PMC10836013 DOI: 10.1186/s12915-024-01834-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The ability of recombinant adeno-associated virus to transduce preimplantation mouse embryos has led to the use of this delivery method for the production of genetically altered knock-in mice via CRISPR-Cas9. The potential exists for this method to simplify the production and extend the types of alleles that can be generated directly in the zygote, obviating the need for manipulations of the mouse genome via the embryonic stem cell route. RESULTS We present the production data from a total of 13 genetically altered knock-in mouse models generated using CRISPR-Cas9 electroporation of zygotes and delivery of donor repair templates via transduction with recombinant adeno-associated virus. We explore the efficiency of gene targeting at a total of 12 independent genetic loci and explore the effects of allele complexity and introduce strategies for efficient identification of founder animals. In addition, we investigate the reliability of germline transmission of the engineered allele from founder mice generated using this methodology. By comparing our production data against genetically altered knock-in mice generated via gene targeting in embryonic stem cells and their microinjection into blastocysts, we assess the animal cost of the two methods. CONCLUSIONS Our results confirm that recombinant adeno-associated virus transduction of zygotes provides a robust and effective delivery route for donor templates for the production of knock-in mice, across a range of insertion sizes (0.9-4.7 kb). We find that the animal cost of this method is considerably less than generating knock-in models via embryonic stem cells and thus constitutes a considerable 3Rs reduction.
Collapse
Affiliation(s)
- Graham Duddy
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | | | - Jessica Olsen
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Helen Horsler
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Tina Hodgson
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | | | - Laura Denti
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Hollie Lane
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Fabio Delaqua
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Julia Janzen
- Transnetyx Inc, 8110 Cordova Rd. Suite 119, Cordova, TN, 38016, USA
| | - Molly Strom
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Ian Rosewell
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | - Benjamin Davies
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
| |
Collapse
|
20
|
Lartey NL, van der Ent M, Alonzo R, Chen D, King PD. A temporally-restricted pattern of endothelial cell collagen 4 alpha 1 expression during embryonic development determined with a novel knockin Col4a1-P2A-eGFP mouse line. Genesis 2024; 62:e23539. [PMID: 37501352 PMCID: PMC10817998 DOI: 10.1002/dvg.23539] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
Classical collagen type IV comprising of a heterotrimer of two collagen IV alpha 1 chains and one collagen IV alpha 2 chain is the principal type of collagen synthesized by endothelial cells (EC) and is a major constituent of vascular basement membranes. In mouse and man, mutations in genes that encode collagen IV alpha 1 and alpha 2 result in vascular dysfunction. In addition, mutations in genes that encode the Ephrin receptor B4 (EPHB4) and the p120 Ras GTPase-activating protein (RASA1) that cause increased activation of the Ras mitogen-activated protein kinase (MAPK) signaling pathway in EC result in vascular dysfunction as a consequence of impaired export of collagen IV. To understand the pathogenesis of collagen IV-related vascular diseases and phenotypes it is necessary to identify at which times collagen IV is actively synthesized by EC. For this purpose, we used CRISPR/Cas9 targeting in mice to include immediately after the terminal Col4a1 codon a sequence that specifies a P2A peptide followed by enhanced green fluorescent protein (eGFP). Analysis of eGFP expression in Col4a1-P2A-eGFP mice revealed active embryonic EC synthesis of collagen IV alpha 1 through mid to late gestation followed by a sharp decline before birth. These results provide a contextual framework for understanding the basis for the varied vascular abnormalities resulting from perturbation of EC expression and export of functional collagen IV.
Collapse
Affiliation(s)
- Nathaniel L. Lartey
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
- These authors contributed equally
| | - Martijn van der Ent
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
- These authors contributed equally
| | - Roxann Alonzo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Di Chen
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Philip D. King
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| |
Collapse
|
21
|
Chanduri MVL, Kumar A, Weiss D, Emuna N, Barsukov I, Shi M, Tanaka K, Wang X, Datye A, Kanyo J, Collin F, Lam T, Schwarz UD, Bai S, Nottoli T, Goult BT, Humphrey JD, Schwartz MA. Mechanosensing through talin 1 contributes to tissue mechanical homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.03.556084. [PMID: 38328095 PMCID: PMC10849504 DOI: 10.1101/2023.09.03.556084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
It is widely believed that tissue mechanical properties, determined mainly by the extracellular matrix (ECM), are actively maintained. However, despite its broad importance to biology and medicine, tissue mechanical homeostasis is poorly understood. To explore this hypothesis, we developed mutations in the mechanosensitive protein talin1 that alter cellular sensing of ECM stiffness. Mutation of a novel mechanosensitive site between talin1 rod domain helix bundles 1 and 2 (R1 and R2) shifted cellular stiffness sensing curves, enabling cells to spread and exert tension on compliant substrates. Opening of the R1-R2 interface promotes binding of the ARP2/3 complex subunit ARPC5L, which mediates the altered stiffness sensing. Ascending aortas from mice bearing these mutations show increased compliance, less fibrillar collagen, and rupture at lower pressure. Together, these results demonstrate that cellular stiffness sensing regulates ECM mechanical properties. These data thus directly support the mechanical homeostasis hypothesis and identify a novel mechanosensitive interaction within talin that contributes to this mechanism.
Collapse
|
22
|
Pilarte KA, Reichert EC, Green YS, Halberg LMT, McFarland SA, Mimche PN, Golkowski M, Kamdem SD, Maguire KM, Summers SA, Maschek JA, Reelitz JW, Cox JE, Evason KJ, Koh MY. HAF Prevents Hepatocyte Apoptosis and Hepatocellular Carcinoma through Transcriptional Regulation of the NF-κB pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574894. [PMID: 38260413 PMCID: PMC10802431 DOI: 10.1101/2024.01.09.574894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Hepatocellular carcinoma (HCC) incidence is increasing worldwide due to the obesity epidemic, which drives metabolic dysfunction-associated steatohepatitis (MASH) that can lead to HCC. However, the molecular pathways that lead to MASH-HCC are poorly understood. We have previously reported that male mice with global haploinsufficiency of hypoxia-associated factor, HAF ( SART1 +/ - ) spontaneously develop MASH/HCC. However, the cell type(s) responsible for HCC associated with HAF loss are unclear. Results SART1 -floxed mice were crossed with mice expressing Cre-recombinase within hepatocytes (Alb-Cre; hepS -/- ) or macrophages (LysM-Cre, macS -/- ). Only hepS -/- mice (both male and female) developed HCC suggesting that HAF protects against HCC primarily within hepatocytes. HAF-deficient macrophages showed decreased P-p65 and P-p50 and in many major components of the NF-κB pathway, which was recapitulated using HAF siRNA in vitro . HAF depletion increased apoptosis both in vitro and in vivo , suggesting that HAF mediates a tumor suppressor role by suppressing hepatocyte apoptosis. We show that HAF regulates NF-κB activity by controlling transcription of TRADD and RIPK1 . Mice fed a high-fat diet (HFD) showed marked suppression of HAF, P-p65 and TRADD within their livers after 26 weeks, but manifest profound upregulation of HAF, P-65 and TRADD within their livers after 40 weeks of HFD, implicating deregulation of the HAF-NF-κB axis in the progression to MASH. In humans, HAF was significantly decreased in livers with simple steatosis but significantly increased in HCC compared to normal liver. Conclusions HAF is novel transcriptional regulator of the NF-κB pathway that protects against hepatocyte apoptosis and is a key determinant of cell fate during progression to MASH and MASH-HCC.
Collapse
|
23
|
Jeong M, Choi JH, Jang H, Sohn DH, Wang Q, Lee J, Yao L, Lee EJ, Fan J, Pratelli M, Wang EH, Snyder CN, Wang XY, Shin S, Gittis AH, Sung TC, Spitzer NC, Lim BK. Viral vector-mediated transgene delivery with novel recombinase systems for targeting neuronal populations defined by multiple features. Neuron 2024; 112:56-72.e4. [PMID: 37909037 PMCID: PMC10916502 DOI: 10.1016/j.neuron.2023.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 05/21/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023]
Abstract
A comprehensive understanding of neuronal diversity and connectivity is essential for understanding the anatomical and cellular mechanisms that underlie functional contributions. With the advent of single-cell analysis, growing information regarding molecular profiles leads to the identification of more heterogeneous cell types. Therefore, the need for additional orthogonal recombinase systems is increasingly apparent, as heterogeneous tissues can be further partitioned into increasing numbers of specific cell types defined by multiple features. Critically, new recombinase systems should work together with pre-existing systems without cross-reactivity in vivo. Here, we introduce novel site-specific recombinase systems based on ΦC31 bacteriophage recombinase for labeling multiple cell types simultaneously and a novel viral strategy for versatile and robust intersectional expression of any transgene. Together, our system will help researchers specifically target different cell types with multiple features in the same animal.
Collapse
Affiliation(s)
- Minju Jeong
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyeonseok Jang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Qingdi Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joann Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Li Yao
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eun Ji Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiachen Fan
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marta Pratelli
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric H Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christen N Snyder
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiao-Yun Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sora Shin
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA, USA; Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - Aryn H Gittis
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tsung-Chang Sung
- Transgenic Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicholas C Spitzer
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Kook Lim
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
24
|
Papaioannou VE, Behringer RR. Mouse Gene-Targeting Strategies for Maximum Ease and Versatility. Cold Spring Harb Protoc 2024; 2024:107957. [PMID: 37932102 DOI: 10.1101/pdb.over107957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Well-planned strategies are an essential prerequisite for any mutational analysis involving gene targeting. Consideration of the advantages or disadvantages of different methods will aid in the production of a final product that is both technically feasible and versatile. Strategies for gene-targeting experiments in the mouse are discussed, including the rationale behind some of the common elements of gene-targeting vectors, such as homologous DNA and the use of different site-specific recombinases. We detail positive and negative selection as well as screening strategies for homologous recombination events in embryonic stem (ES) cells. For the planning stages of making different types of alleles, we first consider general strategies and then provide details specific to either homologous recombination in ES cells or making alleles by gene editing with CRISPR-Cas in preimplantation embryos. The types of alleles considered are null or knockout alleles, reporter gene knock-in alleles, point mutations, and conditional null alleles.
Collapse
Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| |
Collapse
|
25
|
Gim GM, Jang G. Outlook on genome editing application to cattle. J Vet Sci 2024; 25:e10. [PMID: 38311323 PMCID: PMC10839183 DOI: 10.4142/jvs.23133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/04/2023] [Accepted: 08/20/2023] [Indexed: 02/07/2024] Open
Abstract
In livestock industry, there is growing interest in methods to increase the production efficiency of livestock to address food shortages, given the increasing global population. With the advancements in gene engineering technology, it is a valuable tool and has been intensively utilized in research specifically focused on human disease. In historically, this technology has been used with livestock to create human disease models or to produce recombinant proteins from their byproducts. However, in recent years, utilizing gene editing technology, cattle with identified genes related to productivity can be edited, thereby enhancing productivity in response to climate change or specific disease instead of producing recombinant proteins. Furthermore, with the advancement in the efficiency of gene editing, it has become possible to edit multiple genes simultaneously. This cattle breed improvement has been achieved by discovering the genes through the comprehensive analysis of the entire genome of cattle. The cattle industry has been able to address gene bottlenecks that were previously impossible through conventional breeding systems. This review concludes that gene editing is necessary to expand the cattle industry, improving productivity in the future. Additionally, the enhancement of cattle through gene editing is expected to contribute to addressing environmental challenges associated with the cattle industry. Further research and development in gene editing, coupled with genomic analysis technologies, will significantly contribute to solving issues that conventional breeding systems have not been able to address.
Collapse
Affiliation(s)
| | - Goo Jang
- LARTBio Inco, Seoul 06221, Korea
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul 08826, Korea
- Comparative medicine Disease Research Center, Seoul National University, Seoul 08826, Korea
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia.
| |
Collapse
|
26
|
Sorourian S, Behzad Behbahani A, Forouzanfar M, Jafarinia M, Safari F. Time and Cost-Effective Genome Editing Protocol for Simultaneous Caspase 8 Associated Protein 2 Gene Knock in/out in Chinese Hamster Ovary Cells Using CRISPR-Cas9 System. IRANIAN JOURNAL OF BIOTECHNOLOGY 2024; 22:e3714. [PMID: 38827341 PMCID: PMC11139449 DOI: 10.30498/ijb.2024.398567.3714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/27/2023] [Indexed: 06/04/2024]
Abstract
Background CHO cells are preferred for producing biopharmaceuticals, and genome editing technologies offer opportunities to enhance recombinant protein production. Targeting apoptosis-related genes, such as Caspases 8-Associated Protein 2 (CASP8AP2), improves CHO cell viability and productivity. Integrating robust strategies with the CRISPR-Cas9 system enables its application in CHO cell engineering. Objectives This study was performed to develop a cost-effective protocol using the CRISPR-Cas9 system combined with the HITI strategy for simultaneous CASP8AP2 gene deletion/insertion in CHO cells and to assess its impact on cell viability and protein expression. Materials and Methods We developed an efficient protocol for CHO cell engineering by combining CRISPR/Cas9 with the HITI strategy. Two distinct sgRNA sequences were designed to target the 3' UTR region of the CASP8AP2 gene using CHOPCHOP software. The gRNAs were cloned into PX459 and PX460-1 vectors and transfected into CHO cells using the cost-effective PEI reagent. A manual selection system was employed to streamline the process of single-cell cloning. MTT assays assessed gene silencing and cell viability at 24, 48, and 72 hours. Flow cytometry evaluated protein expression in CASP8AP2-silenced CHO cells. Results The study confirmed the robustness of combining CRISPR-Cas9 with the HITI strategy, achieving a high 60% efficiency in generating knockout clones. PEI transfection successfully delivered the constructs to nearly 65% of the clones, with the majority being homozygous. The protocol proved feasible for resource-limited labs, requiring only an inverted fluorescent microscope. CASP8AP2 knockout (CHO-KO) cells exhibited significantly extended cell viability compared to CHO-K1 cells when treated with NaBu, with IC50 values of 7.28 mM and 14.25 mM at 48 hours, respectively (P-value 24 hours ≤ 0.0001, 48 hours ≤ 0.0001, P-value 72 hours = 0.0007). CHO CASP8AP2-silenced cells showed a 1.3-fold increase in JRed expression compared to native cells. Conclusions CRISPR-Cas9 and HITI strategy was used to efficiently engineer CHO cells for simultaneous CASP8AP2 gene deletion/insertion, which improved cell viability and protein expression.
Collapse
Affiliation(s)
- Soofia Sorourian
- Department of Biology, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Abbas Behzad Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Forouzanfar
- Department of Biology, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Mojtaba Jafarinia
- Department of Biology, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
27
|
Li X, Ren M, Gu Y, Zhu T, Zhang Y, Li J, Li C, Wang G, Song L, Bi Z, Liu Z. In situ regeneration of inner hair cells in the damaged cochlea by temporally regulated co-expression of Atoh1 and Tbx2. Development 2023; 150:dev201888. [PMID: 38078650 DOI: 10.1242/dev.201888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Cochlear inner hair cells (IHCs) are primary sound receptors, and are therefore a target for developing treatments for hearing impairment. IHC regeneration in vivo has been widely attempted, although not yet in the IHC-damaged cochlea. Moreover, the extent to which new IHCs resemble wild-type IHCs remains unclear, as is the ability of new IHCs to improve hearing. Here, we have developed an in vivo mouse model wherein wild-type IHCs were pre-damaged and nonsensory supporting cells were transformed into IHCs by ectopically expressing Atoh1 transiently and Tbx2 permanently. Notably, the new IHCs expressed the functional marker vGlut3 and presented similar transcriptomic and electrophysiological properties to wild-type IHCs. Furthermore, the formation efficiency and maturity of new IHCs were higher than those previously reported, although marked hearing improvement was not achieved, at least partly due to defective mechanoelectrical transduction (MET) in new IHCs. Thus, we have successfully regenerated new IHCs resembling wild-type IHCs in many respects in the damaged cochlea. Our findings suggest that the defective MET is a critical barrier that prevents the restoration of hearing capacity and should thus facilitate future IHC regeneration studies.
Collapse
Affiliation(s)
- Xiang Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Minhui Ren
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunpeng Gu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Zhu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu Zhang
- Department of Otolaryngology-Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Jie Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangqin Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Song
- Department of Otolaryngology-Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Zhenghong Bi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiyong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| |
Collapse
|
28
|
Schaefer MA, Roy P, Chava S, Meyerson A, Duncan AL, Chee L, Hewitt KJ. Physiological and regenerative functions of sterile-α motif protein-14 in hematopoiesis. Exp Hematol 2023; 128:38-47. [PMID: 37722652 PMCID: PMC10947990 DOI: 10.1016/j.exphem.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
Sterile α-motif domain-14 (Samd14) protein expression increases the regenerative capacity of the erythroid system. Samd14 is transcriptionally upregulated and promotes cell signaling via the receptor tyrosine kinase Kit in a critical window of acute erythroid regeneration. We generated a hematopoietic-specific conditional Samd14 knockout mouse model (Samd14-CKO) to study the role of Samd14 in hematopoiesis. The Samd14-CKO mouse was viable and exhibited no steady-state hematopoietic phenotype. Samd14-CKO mice were hypersensitive to 5-fluorouracil, resulting in more severe anemia during recovery and impaired erythroid progenitor colony formation. Ex vivo, Samd14-CKO hematopoietic progenitors were defective in their ability to form mast cells. Samd14-CKO mast cells exhibited altered Kit/stem cell factor (SCF), IL-3/IL-3R signaling, and less granularity than Samd14-FL/FL cells. Our findings indicate that Samd14 promotes both erythroid and mast cell functions. The Samd14-CKO mouse phenotype exhibits striking similarities to the KitW/W-v mice, which carry Kit mutations resulting in reduced tyrosine kinase-dependent signaling, causing mast cell and erythroid abnormalities. The Samd14-CKO mouse model is a new tool for studying hematologic pathologies involving Kit signaling.
Collapse
Affiliation(s)
- Meg A Schaefer
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Pooja Roy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Srinivas Chava
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Ainsley Meyerson
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Andrew L Duncan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Linda Chee
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Kyle J Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE.
| |
Collapse
|
29
|
Pan Y, Li S, He S, Wang G, Li C, Liu Z, Xiang M. Fgf8 P2A-3×GFP/+: A New Genetic Mouse Model for Specifically Labeling and Sorting Cochlear Inner Hair Cells. Neurosci Bull 2023; 39:1762-1774. [PMID: 37233921 PMCID: PMC10661496 DOI: 10.1007/s12264-023-01069-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/08/2023] [Indexed: 05/27/2023] Open
Abstract
The cochlear auditory epithelium contains two types of sound receptors, inner hair cells (IHCs) and outer hair cells (OHCs). Mouse models for labelling juvenile and adult IHCs or OHCs exist; however, labelling for embryonic and perinatal IHCs or OHCs are lacking. Here, we generated a new knock-in Fgf8P2A-3×GFP/+ (Fgf8GFP/+) strain, in which the expression of a series of three GFP fragments is controlled by endogenous Fgf8 cis-regulatory elements. After confirming that GFP expression accurately reflects the expression of Fgf8, we successfully obtained both embryonic and neonatal IHCs with high purity, highlighting the power of Fgf8GFP/+. Furthermore, our fate-mapping analysis revealed, unexpectedly, that IHCs are also derived from inner ear progenitors expressing Insm1, which is currently regarded as an OHC marker. Thus, besides serving as a highly favorable tool for sorting early IHCs, Fgf8GFP/+ will facilitate the isolation of pure early OHCs by excluding IHCs from the entire hair cell pool.
Collapse
Affiliation(s)
- Yi Pan
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shuting Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunji He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Guangqin Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhiyong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Mingliang Xiang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
30
|
Liu L, Wei J, Chen C, Liang Q, Wang B, Wu W, Li G, Zheng X. Electroporation-based Easi-CRISPR yields biallelic insertions of EGFP-HiBiT cassette in immortalized chicken oviduct epithelial cells. Poult Sci 2023; 102:103112. [PMID: 37806084 PMCID: PMC10568294 DOI: 10.1016/j.psj.2023.103112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Laying hens are an excellent experimental oviduct model for studying reproduction biology. Because chicken oviduct epithelial cells (cOECs) have a crucial role in synthesizing and secreting ovalbumin, laying hens have been regarded an ideal bioreactor for producing pharmaceuticals in egg white through transgene or gene editing of the ovalbumin (OVA) gene. However, related studies in cOECs are largely limited because of the lack of immortalized model cells. In addition, the editing efficiency of conventional CRISPR-HDR knock-in in chicken cells is suboptimal (ranging from 1 to 10%) and remains elevated. Here, primary cOECs were isolated from young laying hens, then infected with a retrovirus vector of human telomerase reverse transcriptase (hTERT), and immortalized cOECs were established. Subsequently, an electroporation-based Easi-CRISPR (Efficient additions with ssDNA inserts-CRISPR) method was adopted to integrate an EGFP-HiBiT cassette into the chicken OVA locus (immediately upstream of the stop codon). The immortalized cOECs reflected the self-renewal capability and phenotype of oviduct epithelial cells. This is because these cells not only maintained stable proliferation and normal karyotype and had no potential for malignant transformation, but also expressed oviduct markers and an epithelial marker and had a morphology similar to that of primary cOECs. EGFP expression was detected in the edited cells through microscopy, flow cytometry, and HiBiT/Western blotting. The EGFP-HiBiT knock-in efficiency reached 27.9% after a single round of electroporation, which was determined through genotyping and DNA sequencing. Two single cell clones contained biallelic insertions of EGFP-HiBiT donor cassettes. In conclusion, our established immortalized cOECs could act as an in vitro cell model for gene editing in chicken, and this electroporation-based Easi-CRISPR strategy will contribute to the generation of avian bioreactors and other gene-edited (GE) birds.
Collapse
Affiliation(s)
- Lingkang Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China
| | - Jinyu Wei
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Buffalo Research Institute, Chinese Academy of Agricultural Sciences and Guangxi Zhuang Nationality Autonomous Region, Nanning 530004, China
| | - Chen Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Qianxue Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Boyong Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wende Wu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China
| | - Gonghe Li
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China
| | - Xibang Zheng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China.
| |
Collapse
|
31
|
Navarro S, Vögtle T, Groß N, Preu J, Englert M, Nieswandt B, Bösl MR, Stegner D. Mutations of the dimerization site of glycoprotein (GP) VI result in abolished expression. Thromb Res 2023; 232:89-92. [PMID: 37951045 DOI: 10.1016/j.thromres.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Affiliation(s)
- Stefano Navarro
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany; University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Timo Vögtle
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany; University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Nina Groß
- University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Julia Preu
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany; University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Maximilian Englert
- University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Bernhard Nieswandt
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany; University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Michael R Bösl
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany; University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany.
| | - David Stegner
- Julius-Maximilians-Universität Würzburg, Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany; University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany.
| |
Collapse
|
32
|
Klocke B, Britzolaki A, Saurine J, Ott H, Krone K, Bahamonde K, Thelen C, Tzimas C, Sanoudou D, Kranias EG, Pitychoutis PM. A Novel Role for Phospholamban in the Thalamic Reticular Nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568306. [PMID: 38045420 PMCID: PMC10690257 DOI: 10.1101/2023.11.22.568306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The thalamic reticular nucleus (TRN) is a critical brain region that greatly influences vital neurobehavioral processes, including executive functioning and the generation of sleep rhythms. Recently, TRN dysfunction was suggested to underlie hyperactivity, attention deficits, and sleep disturbances observed across various devastating neurodevelopmental disorders, including autism, schizophrenia and attention-deficit/hyperactivity disorder (ADHD). Notably, a highly specialized sarco- endoplasmic reticulum calcium (Ca 2+ ) ATPase 2 (SERCA2)-dependent Ca 2+ signaling network operates in the dendrites of TRN neurons to regulate their high-frequency bursting activity. Phospholamban (PLN) is a prominent regulator of the SERCA2 with an established role in maintaining Ca 2+ homeostasis in the heart; although the interaction of PLN with SERCA2 has been largely regarded as cardiac-specific, our findings challenge this view and suggest that the role of PLN extends beyond the cardiovascular system to impact brain function. Specifically, we found PLN to be expressed in the TRN neurons of the adult mouse brain and utilized global constitutive and innovative conditional genetic mouse models, in combination with 5-choice serial reaction time task (5-CSRTT) and electroencephalography (EEG)-based somnography to assess the role of PLN in regulating executive functioning and sleep, two complex behaviors that map onto thalamic reticular circuits. Overall, the results of the present study show that perturbed PLN function in the TRN results in aberrant thalamic reticular behavioral phenotypes in mice (i.e., hyperactivity, impulsivity and sleep deficits) and support a novel role for PLN as a critical regulator of the SERCA2 in the thalamic reticular neurocircuitry.
Collapse
|
33
|
Jose B, Punetha M, Tripathi MK, Khanna S, Yadav V, Singh AK, Kumar B, Singh K, Chouhan VS, Sarkar M. CRISPR/Cas mediated disruption of BMPR-1B gene and introduction of FecB mutation into the Caprine embryos using Easi-CRISPR strategy. Theriogenology 2023; 211:125-133. [PMID: 37619525 DOI: 10.1016/j.theriogenology.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Bone Morphogenetic Proteins play a significant role in ovarian physiology and contribute to the reproductive fitness of mammals. The BMPR-1B/FecB mutation, a loss of function mutation increases litter size by 1-2 with each number of mutated alleles in sheep. Considering demand-supply gap of the meat industry, and low replacement rate of indigenous caprine species, the conservative BMPR-1B locus can be explored, and FecB mutated goats can be produced. The experiment one produced CRISPR/Cas mediated KO transferable caprine embryos, and experiment two generated caprine embryos with desired FecB mutation using Easi-CRISPR strategy. In the KO experiment, Cas9 and BMPR-1B guide RNA (100:100ng/ul) were electroporated into single stage caprine zygotes at 750V, 10 ms and 1pulse using Neon transfection system. In the second experiment, phosphorothioate (PS) modified single-stranded oligodeoxynucleotide (ssODN) was used as an HDR template along with CRISPR components (100:100ng/ul, ssODN 100ng/ul). The precise time and method of electroporation, RNP format of CRISPR components and PS modified asymmetric ssODN were the factors that affected the production of mosaicism free BMPR-1B edited caprine embryos. The editing efficiency of KO and KI experiments was 68.52 and 63.16% respectively, and successful production of goats with higher mean ovulation rate can be realized with addition of embryo transfer technology to these experiments.
Collapse
Affiliation(s)
- Bosco Jose
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Meeti Punetha
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India.
| | - Manoj Kumar Tripathi
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Shivani Khanna
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Vijay Yadav
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Amit Kumar Singh
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Brijesh Kumar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Kiranjeet Singh
- Division of Surgery, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Vikrant Singh Chouhan
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Mihir Sarkar
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| |
Collapse
|
34
|
Mirabella PN, Fenselau H. Advanced neurobiological tools to interrogate metabolism. Nat Rev Endocrinol 2023; 19:639-654. [PMID: 37674015 DOI: 10.1038/s41574-023-00885-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2023] [Indexed: 09/08/2023]
Abstract
Engineered neurobiological tools for the manipulation of cellular activity, such as chemogenetics and optogenetics, have become a cornerstone of modern neuroscience research. These tools are invaluable for the interrogation of the central control of metabolism as they provide a direct means to establish a causal relationship between brain activity and biological processes at the cellular, tissue and organismal levels. The utility of these methods has grown substantially due to advances in cellular-targeting strategies, alongside improvements in the resolution and potency of such tools. Furthermore, the potential to recapitulate endogenous cellular signalling has been enriched by insights into the molecular signatures and activity dynamics of discrete brain cell types. However, each modulatory tool has a specific set of advantages and limitations; therefore, tool selection and suitability are of paramount importance to optimally interrogate the cellular and circuit-based underpinnings of metabolic outcomes within the organism. Here, we describe the key principles and uses of engineered neurobiological tools. We also highlight inspiring applications and outline critical considerations to be made when using these tools within the field of metabolism research. We contend that the appropriate application of these biotechnological advances will enable the delineation of the central circuitry regulating systemic metabolism with unprecedented potential.
Collapse
Affiliation(s)
- Paul Nicholas Mirabella
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Cologne, Germany
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Cologne, Germany
| | - Henning Fenselau
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Cologne, Germany.
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Cologne, Germany.
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
| |
Collapse
|
35
|
Han W, Liang H, Bao J. Efficient Large DNA Fragment Knock-in by Long dsDNA with 3'-Overhangs Mediated CRISPR Knock-in (LOCK) in Mammalian Cells. Bio Protoc 2023; 13:e4853. [PMID: 37900108 PMCID: PMC10603260 DOI: 10.21769/bioprotoc.4853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 10/31/2023] Open
Abstract
An efficient and precise genome-editing approach is in high demand in any molecular biology or cell biology laboratory worldwide. However, despite a recent rapid progress in the toolbox tailored for precise genome-editing, including the base editors and prime editors, there is still a need for a cost-effective knock-in (KI) approach amenable for long donor DNA cargos with high efficiency. By harnessing the high-efficient double-strand break (DSB) repair pathway of microhomology-mediated end joining, we previously showed that a specially designed 3'-overhang double-strand DNA (odsDNA) donor harboring 50-nt homology arm (HA) allows high-efficient exogenous DNA KI when combined with CRISPR-Cas9 technology. The lengths of the 3'-overhangs of odsDNA donors could be manipulated by the five consecutive phosphorothioate (PT) modifications. In this protocol, we detail the stepwise procedures to conduct the LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in) method for gene-sized (~1-3 kb) KI in mammalian cells.
Collapse
Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Research Center for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| |
Collapse
|
36
|
Villar-Pazos S, Thomas L, Yang Y, Chen K, Lyles JB, Deitch BJ, Ochaba J, Ling K, Powers B, Gingras S, Kordasiewicz HB, Grubisha MJ, Huang YH, Thomas G. Neural deficits in a mouse model of PACS1 syndrome are corrected with PACS1- or HDAC6-targeting therapy. Nat Commun 2023; 14:6547. [PMID: 37848409 PMCID: PMC10582149 DOI: 10.1038/s41467-023-42176-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/29/2023] [Indexed: 10/19/2023] Open
Abstract
PACS1 syndrome is a neurodevelopmental disorder (NDD) caused by a recurrent de novo missense mutation in PACS1 (p.Arg203Trp (PACS1R203W)). The mechanism by which PACS1R203W causes PACS1 syndrome is unknown, and no curative treatment is available. Here, we use patient cells and PACS1 syndrome mice to show that PACS1 (or PACS-1) is an HDAC6 effector and that the R203W substitution increases the PACS1/HDAC6 interaction, aberrantly potentiating deacetylase activity. Consequently, PACS1R203W reduces acetylation of α-tubulin and cortactin, causing the Golgi ribbon in hippocampal neurons and patient-derived neural progenitor cells (NPCs) to fragment and overpopulate dendrites, increasing their arborization. The dendrites, however, are beset with varicosities, diminished spine density, and fewer functional synapses, characteristic of NDDs. Treatment of PACS1 syndrome mice or patient NPCs with PACS1- or HDAC6-targeting antisense oligonucleotides, or HDAC6 inhibitors, restores neuronal structure and synaptic transmission in prefrontal cortex, suggesting that targeting PACS1R203W/HDAC6 may be an effective therapy for PACS1 syndrome.
Collapse
Affiliation(s)
- Sabrina Villar-Pazos
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Laurel Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Yunhan Yang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Kun Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jenea B Lyles
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Bradley J Deitch
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | | | - Karen Ling
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | | | - Sebastien Gingras
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Melanie J Grubisha
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yanhua H Huang
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Translational Neuroscience Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA.
| |
Collapse
|
37
|
Niemi NM, Serrano LR, Muehlbauer LK, Balnis CE, Wei L, Smith AJ, Kozul KL, Forny M, Connor OM, Rashan EH, Shishkova E, Schueler KL, Keller MP, Attie AD, Friedman JR, Pagan JK, Coon JJ, Pagliarini DJ. PPTC7 maintains mitochondrial protein content by suppressing receptor-mediated mitophagy. Nat Commun 2023; 14:6431. [PMID: 37833277 PMCID: PMC10575892 DOI: 10.1038/s41467-023-42069-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
PPTC7 is a resident mitochondrial phosphatase essential for maintaining proper mitochondrial content and function. Newborn mice lacking Pptc7 exhibit aberrant mitochondrial protein phosphorylation, suffer from a range of metabolic defects, and fail to survive beyond one day after birth. Using an inducible knockout model, we reveal that loss of Pptc7 in adult mice causes marked reduction in mitochondrial mass and metabolic capacity with elevated hepatic triglyceride accumulation. Pptc7 knockout animals exhibit increased expression of the mitophagy receptors BNIP3 and NIX, and Pptc7-/- mouse embryonic fibroblasts (MEFs) display a major increase in mitophagy that is reversed upon deletion of these receptors. Our phosphoproteomics analyses reveal a common set of elevated phosphosites between perinatal tissues, adult liver, and MEFs, including multiple sites on BNIP3 and NIX, and our molecular studies demonstrate that PPTC7 can directly interact with and dephosphorylate these proteins. These data suggest that Pptc7 deletion causes mitochondrial dysfunction via dysregulation of several metabolic pathways and that PPTC7 may directly regulate mitophagy receptor function or stability. Overall, our work reveals a significant role for PPTC7 in the mitophagic response and furthers the growing notion that management of mitochondrial protein phosphorylation is essential for ensuring proper organelle content and function.
Collapse
Affiliation(s)
- Natalie M Niemi
- Morgridge Institute for Research, Madison, WI, 53715, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Lia R Serrano
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Laura K Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Catherine E Balnis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lianjie Wei
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Andrew J Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Keri-Lyn Kozul
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Merima Forny
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Olivia M Connor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Edrees H Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jonathan R Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Julia K Pagan
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4102, Australia
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, 53715, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| |
Collapse
|
38
|
Strawn IK, Steiner PJ, Newton MS, Baumer ZT, Whitehead TA. A method for generating user-defined circular single-stranded DNA from plasmid DNA using Golden Gate intramolecular ligation. Biotechnol Bioeng 2023; 120:3057-3066. [PMID: 37366288 PMCID: PMC10527171 DOI: 10.1002/bit.28471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023]
Abstract
Construction of user-defined long circular single stranded DNA (cssDNA) and linear single stranded DNA (lssDNA) is important for various biotechnological applications. Many current methods for synthesis of these ssDNA molecules do not scale to multikilobase constructs. Here we present a robust methodology for generating user-defined cssDNA employing Golden Gate assembly, a nickase, and exonuclease degradation. Our technique is demonstrated for three plasmids with insert sizes ranging from 2.1 to 3.4 kb, requires no specialized equipment, and can be accomplished in 5 h with a yield of 33%-43% of the theoretical. To produce lssDNA, we evaluated different CRISPR-Cas9 cleavage conditions and reported a 52 ± 8% cleavage efficiency of cssDNA. Thus, our current method does not compete with existing protocols for lssDNA generation. Nevertheless, our protocol can make long, user-defined cssDNA readily available to biotechnology researchers.
Collapse
Affiliation(s)
- Isabell K. Strawn
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Paul J. Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Matilda S. Newton
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
- Current address: Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Zachary T. Baumer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80305, USA
| |
Collapse
|
39
|
Maher J, Stagg N, Cain G, Andaya R, Katavolos P, Gallardo-Chang F, Pham A, Ye X, Januario T, Alcantar T, Caothien R, Roose-Girma M, Zhang D, Li R, Chen S, Yauch RL. Smarca2 genetic ablation is phenotypically benign in a safety assessment of tamoxifen-inducible conditional knockout rats. Toxicol Appl Pharmacol 2023; 475:116627. [PMID: 37453479 DOI: 10.1016/j.taap.2023.116627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
SMARCA2 and SMARCA4 are the ATPases of the SWI/SNF chromatin remodeling complex, which play a significant role in regulating transcriptional activity and DNA repair in cells. SMARCA2 has become an appealing synthetic-lethal, therapeutic target in oncology, as mutational loss of SMARCA4 in many cancers leads to a functional dependency on residual SMARCA2 activity. Thus, for therapeutic development, an important step is understanding any potential safety target-associated liabilities of SMARCA2 inhibition. To best mimic a SMARCA2 therapeutic, a tamoxifen-inducible (TAMi) conditional knockout (cKO) rat was developed using CRISPR technology to understand the safety profile of Smarca2 genetic ablation in a model system that avoids potential juvenile and developmental phenotypes. As the rat is the prototypical rodent species utilized in toxicology studies, a comprehensive toxicological and pathological assessment was conducted in both heterozygote and homozygous knockout rats at timepoints up to 28 days, alongside relevant corresponding controls. To our knowledge, this represents the first TAMi cKO rat model utilized for safety assessment evaluations. No significant target-associated phenotypes were observed when Smarca2 was ablated in mature (11- to 15-week-old) rats; however subsequent induction of SMARCA4 was evident that could indicate potential compensatory activity. Similar to mouse models, rat CreERT2-transgene and TAMi toxicities were characterized to avoid confounding study interpretation. In summary, a lack of significant safety findings in Smarca2 cKO rats highlights the potential for therapeutics targeting selective SMARCA2 ATPase activity; such therapies are predicted to be tolerated in patients without eliciting significant on-target toxicities.
Collapse
Affiliation(s)
- Jonathan Maher
- Genentech, Inc., South San Francisco, CA 94080, USA; Pliant Therapeutics, Inc., South San Francisco, CA 94080, USA
| | - Nicola Stagg
- Genentech, Inc., South San Francisco, CA 94080, USA; Turning Point Therapeutics, Inc., San Diego, CA 92121, USA
| | - Gary Cain
- Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Paula Katavolos
- Genentech, Inc., South San Francisco, CA 94080, USA; Bristol Myers Squibb, New Brunswick, NJ 08901, USA; 23&Me, Inc., South San Francisco, CA 94080, USA
| | | | - Anna Pham
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Xiaofen Ye
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Tom Januario
- Genentech, Inc., South San Francisco, CA 94080, USA
| | | | | | | | - Donglu Zhang
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Ruina Li
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Shu Chen
- Genentech, Inc., South San Francisco, CA 94080, USA
| | | |
Collapse
|
40
|
Denorme F, Armstrong ND, Stoller ML, Portier I, Tugolukova EA, Tanner RM, Montenont E, Bhatlekar S, Cody M, Rustad JL, Ajanel A, Tolley ND, Murray DC, Boyle JL, Nieman MT, McKenzie SE, Yost CC, Lange LA, Cushman M, Irvin MR, Bray PF, Campbell RA. The predominant PAR4 variant in individuals of African ancestry worsens murine and human stroke outcomes. J Clin Invest 2023; 133:e169608. [PMID: 37471144 PMCID: PMC10503801 DOI: 10.1172/jci169608] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023] Open
Abstract
Protease-activated receptor 4 (PAR4) (gene F2RL3) harbors a functional dimorphism, rs773902 A/G (encoding Thr120/Ala120, respectively) and is associated with greater platelet aggregation. The A allele frequency is more common in Black individuals, and Black individuals have a higher incidence of ischemic stroke than White individuals. However, it is not known whether the A allele is responsible for worse stroke outcomes. To directly test the in vivo effect of this variant on stroke, we generated mice in which F2rl3 was replaced by F2RL3, thereby expressing human PAR4 (hPAR4) with either Thr120 or Ala120. Compared with hPAR4 Ala120 mice, hPAR4 Thr120 mice had worse stroke outcomes, mediated in part by enhanced platelet activation and platelet-neutrophil interactions. Analyses of 7,620 Black subjects with 487 incident ischemic strokes demonstrated the AA genotype was a risk for incident ischemic stroke and worse functional outcomes. In humanized mice, ticagrelor with or without aspirin improved stroke outcomes in hPAR4 Ala120 mice, but not in hPAR4 Thr120 mice. P selectin blockade improved stroke outcomes and reduced platelet-neutrophil interactions in hPAR4 Thr120 mice. Our results may explain some of the racial disparity in stroke and support the need for studies of nonstandard antiplatelet therapies for patients expressing PAR4 Thr120.
Collapse
Affiliation(s)
- Frederik Denorme
- Program in Molecular Medicine and
- Department of Neurology, Division of Vascular Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | | | | | - Rikki M. Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | | | | | | | | | | | | | - Julie L. Boyle
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Marvin T. Nieman
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Steven E. McKenzie
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Christian Con Yost
- Program in Molecular Medicine and
- Department of Pediatrics, Division of Neonatology, University of Utah, Salt Lake City, Utah, USA
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mary Cushman
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, Vermont, USA
| | - Marguerite R. Irvin
- Department of Neurology, Division of Vascular Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Paul F. Bray
- Program in Molecular Medicine and
- Department of Internal Medicine, Division of Hematology and Hematologic Malignancies, and
| | - Robert A. Campbell
- Program in Molecular Medicine and
- Department of Internal Medicine, Division of Hematology and Hematologic Malignancies, and
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| |
Collapse
|
41
|
Wiegreffe C, Ehricke S, Schmid L, Andratschke J, Britsch S. Using i-GONAD for Cell-Type-Specific and Systematic Analysis of Developmental Transcription Factors In Vivo. BIOLOGY 2023; 12:1236. [PMID: 37759634 PMCID: PMC10526018 DOI: 10.3390/biology12091236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Transcription factors (TFs) regulate gene expression via direct DNA binding together with cofactors and in chromatin remodeling complexes. Their function is thus regulated in a spatiotemporal and cell-type-specific manner. To analyze the functions of TFs in a cell-type-specific context, genome-wide DNA binding, as well as the identification of interacting proteins, is required. We used i-GONAD (improved genome editing via oviductal nucleic acids delivery) in mice to genetically modify TFs by adding fluorescent reporter and affinity tags that can be exploited for the imaging and enrichment of target cells as well as chromatin immunoprecipitation and pull-down assays. As proof-of-principle, we showed the functional genetic modification of the closely related developmental TFs, Bcl11a and Bcl11b, in defined cell types of newborn mice. i-GONAD is a highly efficient procedure for modifying TF-encoding genes via the integration of small insertions, such as reporter and affinity tags. The novel Bcl11a and Bcl11b mouse lines, described in this study, will be used to improve our understanding of the Bcl11 family's function in neurodevelopment and associated disease.
Collapse
Affiliation(s)
- Christoph Wiegreffe
- Medical Faculty, Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | | | | | | | | |
Collapse
|
42
|
Du W, Ergin V, Loeb C, Huang M, Silver S, Armstrong AM, Huang Z, Gurumurthy CB, Staecker H, Liu X, Chen ZY. Rescue of auditory function by a single administration of AAV-TMPRSS3 gene therapy in aged mice of human recessive deafness DFNB8. Mol Ther 2023; 31:2796-2810. [PMID: 37244253 PMCID: PMC10491991 DOI: 10.1016/j.ymthe.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 05/29/2023] Open
Abstract
Patients with mutations in the TMPRSS3 gene suffer from recessive deafness DFNB8/DFNB10. For these patients, cochlear implantation is the only treatment option. Poor cochlear implantation outcomes are seen in some patients. To develop biological treatment for TMPRSS3 patients, we generated a knockin mouse model with a frequent human DFNB8 TMPRSS3 mutation. The Tmprss3A306T/A306T homozygous mice display delayed onset progressive hearing loss similar to human DFNB8 patients. Using AAV2 as a vector to carry a human TMPRSS3 gene, AAV2-hTMPRSS3 injection in the adult knockin mouse inner ear results in TMPRSS3 expression in the hair cells and the spiral ganglion neurons. A single AAV2-hTMPRSS3 injection in Tmprss3A306T/A306T mice of an average age of 18.5 months leads to sustained rescue of the auditory function to a level similar to wild-type mice. AAV2-hTMPRSS3 delivery rescues the hair cells and the spiral ganglions neurons. This study demonstrates successful gene therapy in an aged mouse model of human genetic deafness. It lays the foundation to develop AAV2-hTMPRSS3 gene therapy to treat DFNB8 patients, as a standalone therapy or in combination with cochlear implantation.
Collapse
Affiliation(s)
- Wan Du
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Volkan Ergin
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Corena Loeb
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Mingqian Huang
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Stewart Silver
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Ariel Miura Armstrong
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Zaohua Huang
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | - Hinrich Staecker
- Kansas University Center for Hearing and Balance Disorders, Kansas City, KS 66160, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Zheng-Yi Chen
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Eaton-Peabody Laboratories, Massachusetts Eye and Ear, Boston, MA 02114, USA.
| |
Collapse
|
43
|
Thoreson WB, Chhunchha B. EAAT5 glutamate transporter rapidly binds glutamate with micromolar affinity in mouse rods. J Gen Physiol 2023; 155:e202313349. [PMID: 37477643 PMCID: PMC10359920 DOI: 10.1085/jgp.202313349] [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: 01/24/2023] [Revised: 04/17/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Light responses of rod photoreceptor cells in the retina are encoded by changes in synaptic glutamate release that is in turn shaped by reuptake involving EAAT5 plasma membrane glutamate transporters. Heterologously expressed EAAT5 activates too slowly upon glutamate binding to support significant uptake. We tested EAAT5 activation in mouse rods in vivo by stimulating glutamate transporter anion currents (IA(glu)) with UV flash photolysis of MNI-glutamate, varying flash intensity to vary glutamate levels. Responses to uncaging rose rapidly with time constants of 2-3 ms, similar to IA(glu) events arising from spontaneous release. Spontaneous release events and IA(glu) evoked by weak flashes also declined with similar time constants of 40-50 ms. Stronger flashes evoked responses that decayed more slowly. Time constants were twofold faster at 35°C, suggesting that they reflect transporter kinetics, not diffusion. Selective EAAT1 and EAAT2 inhibitors had no significant effect, suggesting IA(glu) in rods arises solely from EAAT5. We calibrated glutamate levels attained during flash photolysis by expressing a fluorescent glutamate sensor iGluSnFr in cultured epithelial cells. We compared fluorescence at different glutamate concentrations to fluorescence evoked by photolytic uncaging of MNI-glutamate. The relationship between flash intensity and glutamate yielded EC50 values for EAAT5 amplitude, decay time, and rise time of ∼10 μM. Micromolar affinity and rapid activation of EAAT5 in rods show it can rapidly bind synaptic glutamate. However, we also found that EAAT5 currents are saturated by the synchronous release of only a few vesicles, suggesting limited capacity and a role for glial uptake at higher release rates.
Collapse
Affiliation(s)
- Wallace B. Thoreson
- Department of Ophthalmology and Visual Sciences, Truhlsen Eye Institute, Omaha, NE, USA
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bhavana Chhunchha
- Department of Ophthalmology and Visual Sciences, Truhlsen Eye Institute, Omaha, NE, USA
| |
Collapse
|
44
|
Maes B, Fayazpour F, Catrysse L, Lornet G, Van De Velde E, De Wolf C, De Prijck S, Van Moorleghem J, Vanheerswynghels M, Deswarte K, Descamps B, Vanhove C, Van der Schueren B, Vangoitsenhoven R, Hammad H, Janssens S, Lambrecht BN. STE20 kinase TAOK3 regulates type 2 immunity and metabolism in obesity. J Exp Med 2023; 220:e20210788. [PMID: 37347461 PMCID: PMC10287548 DOI: 10.1084/jem.20210788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/23/2023] Open
Abstract
Healthy adipose tissue (AT) contains ST2+ Tregs, ILC2s, and alternatively activated macrophages that are lost in mice or humans on high caloric diet. Understanding how this form of type 2 immunity is regulated could improve treatment of obesity. The STE20 kinase Thousand And One amino acid Kinase-3 (TAOK3) has been linked to obesity in mice and humans, but its precise function is unknown. We found that ST2+ Tregs are upregulated in visceral epididymal white AT (eWAT) of Taok3-/- mice, dependent on IL-33 and the kinase activity of TAOK3. Upon high fat diet feeding, metabolic dysfunction was attenuated in Taok3-/- mice. ST2+ Tregs disappeared from eWAT in obese wild-type mice, but this was not the case in Taok3-/- mice. Mechanistically, AT Taok3-/- Tregs were intrinsically more responsive to IL-33, through higher expression of ST2, and expressed more PPARγ and type 2 cytokines. Thus, TAOK3 inhibits adipose tissue Tregs and regulates immunometabolism under excessive caloric intake.
Collapse
Affiliation(s)
- Bastiaan Maes
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory for Endoplasmic Reticulum Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Farzaneh Fayazpour
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory for Endoplasmic Reticulum Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Leen Catrysse
- Cellular and Molecular (Patho)Physiology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Guillaume Lornet
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Evelien Van De Velde
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory for Endoplasmic Reticulum Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Caroline De Wolf
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sofie De Prijck
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Justine Van Moorleghem
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Manon Vanheerswynghels
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kim Deswarte
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Benedicte Descamps
- Department of Electronics and Information Systems, IBiTech-MEDISIP-Infinity Lab, Ghent University, Ghent, Belgium
| | - Christian Vanhove
- Department of Electronics and Information Systems, IBiTech-MEDISIP-Infinity Lab, Ghent University, Ghent, Belgium
| | - Bart Van der Schueren
- Department of Chronic Diseases and Metabolism, Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
- Department of Endocrinology, University Hospitals Leuven, Leuven, Belgium
| | - Roman Vangoitsenhoven
- Department of Chronic Diseases and Metabolism, Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
- Department of Endocrinology, University Hospitals Leuven, Leuven, Belgium
| | - Hamida Hammad
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sophie Janssens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory for Endoplasmic Reticulum Stress and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Bart N. Lambrecht
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Pulmonary Medicine, Erasmus University Medical Center Rotterdam, Rotterdam Netherlands
| |
Collapse
|
45
|
Mahmoudian RA, Farshchian M, Golyan FF, Mahmoudian P, Alasti A, Moghimi V, Maftooh M, Khazaei M, Hassanian SM, Ferns GA, Mahaki H, Shahidsales S, Avan A. Preclinical tumor mouse models for studying esophageal cancer. Crit Rev Oncol Hematol 2023; 189:104068. [PMID: 37468084 DOI: 10.1016/j.critrevonc.2023.104068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Preclinical models are extensively employed in cancer research because they can be manipulated in terms of their environment, genome, molecular biology, organ systems, and physical activity to mimic human behavior and conditions. The progress made in in vivo cancer research has resulted in significant advancements, enabling the creation of spontaneous, metastatic, and humanized mouse models. Most recently, the remarkable and extensive developments in genetic engineering, particularly the utilization of CRISPR/Cas9, transposable elements, epigenome modifications, and liquid biopsies, have further facilitated the design and development of numerous mouse models for studying cancer. In this review, we have elucidated the production and usage of current mouse models, such as xenografts, chemical-induced models, and genetically engineered mouse models (GEMMs), for studying esophageal cancer. Additionally, we have briefly discussed various gene-editing tools that could potentially be employed in the future to create mouse models specifically for esophageal cancer research.
Collapse
Affiliation(s)
- Reihaneh Alsadat Mahmoudian
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Moein Farshchian
- Division of Oncology, Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Fatemeh Fardi Golyan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvaneh Mahmoudian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Alasti
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Moghimi
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Department of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Hanie Mahaki
- Vascular & Endovascular Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
| |
Collapse
|
46
|
Davies FCJ, Marshall GF, Pegram E, Gadd D, Abbott CM. Endogenous epitope tagging of eEF1A2 in mice reveals early embryonic expression of eEF1A2 and subcellular compartmentalisation of neuronal eEF1A1 and eEF1A2. Mol Cell Neurosci 2023; 126:103879. [PMID: 37429391 DOI: 10.1016/j.mcn.2023.103879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
All vertebrate species express two independently-encoded forms of translation elongation factor eEF1A. In humans and mice eEF1A1 and eEF1A2 are 92 % identical at the amino acid level, but the well conserved developmental switch between the two variants in specific tissues suggests the existence of important functional differences. Heterozygous mutations in eEF1A2 result in neurodevelopmental disorders in humans; the mechanism of pathogenicity is unclear, but one hypothesis is that there is a dominant negative effect on eEF1A1 during development. The high degree of similarity between the eEF1A proteins has complicated expression analysis in the past; here we describe a gene edited mouse line in which we have introduced a V5 tag in the gene encoding eEF1A2. Expression analysis using anti-V5 and anti-eEF1A1 antibodies demonstrates that, in contrast to the prevailing view that eEF1A2 is only expressed postnatally, it is expressed from as early as E11.5 in the developing neural tube. Two colour immunofluorescence also reveals coordinated switching between eEF1A1 and eEF1A2 in different regions of postnatal brain. Completely reciprocal expression of the two variants is seen in post-weaning mouse brain with eEF1A1 expressed in oligodendrocytes and astrocytes and eEF1A2 in neuronal soma. Although eEF1A1 is absent from neuronal cell bodies after development, it is widely expressed in axons. This expression does not appear to coincide with myelin sheaths originating from oligodendrocytes but rather results from localised translation within the axon, suggesting that both variants are transcribed in neurons but show completely distinct subcellular localisation at the protein level. These findings will form an underlying framework for understanding how missense mutations in eEF1A2 result in neurodevelopmental disorders.
Collapse
Affiliation(s)
- Faith C J Davies
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Grant F Marshall
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Eleanor Pegram
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom
| | - Danni Gadd
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom
| | - Catherine M Abbott
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom.
| |
Collapse
|
47
|
Berry SB, Espich S, Thuong NTT, Chang X, Dorajoo R, Khor CC, Heng CK, Yuan JM, Fox D, Anaya-Sanchez A, Tenney L, Chang CJ, Kotov DI, Vance RE, Dunstan SJ, Darwin KH, Stanley SA. Disruption of Aldehyde Dehydrogenase 2 protects against bacterial infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554661. [PMID: 37662190 PMCID: PMC10473740 DOI: 10.1101/2023.08.24.554661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ALDH2*2 (rs671) allele is one of the most common genetic mutations in humans, yet the positive evolutionary selective pressure to maintain this mutation is unknown, despite its association with adverse health outcomes. ALDH2 is responsible for the detoxification of metabolically produced aldehydes, including lipid-peroxidation end products derived from inflammation. Here, we demonstrate that host-derived aldehydes 4-hydroxynonenal (4HNE), malondialdehyde (MDA), and formaldehyde (FA), all of which are metabolized by ALDH2, are directly toxic to the bacterial pathogens Mycobacterium tuberculosis and Francisella tularensis at physiological levels. We find that Aldh2 expression in macrophages is decreased upon immune stimulation, and that bone marrow-derived macrophages from Aldh2 -/- mice contain elevated aldehydes relative to wild-type mice. Macrophages deficient for Aldh2 exhibited enhanced control of Francisella infection. Finally , mice lacking Aldh2 demonstrated increased resistance to pulmonary infection by M. tuberculosis , including in a hypersusceptible model of tuberculosis, and were also resistant to Francisella infection. We hypothesize that the absence of ALDH2 contributes to the host's ability to control infection by pathogens such as M. tuberculosis and F. tularensis , and that host-derived aldehydes act as antimicrobial factors during intracellular bacterial infections. One sentence summary Aldehydes produced by host cells contribute to the control of bacterial infections.
Collapse
|
48
|
Davis DJ, McNew JF, Maresca-Fichter H, Chen K, Telugu BP, Bryda EC. Efficient DNA knock-in using AAV-mediated delivery with 2-cell embryo CRISPR-Cas9 electroporation. Front Genome Ed 2023; 5:1256451. [PMID: 37694158 PMCID: PMC10485772 DOI: 10.3389/fgeed.2023.1256451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
Recent advances in CRISPR-Cas genome editing technology have been instrumental in improving the efficiency to produce genetically modified animal models. In this study we have combined four very promising approaches to come up with a highly effective pipeline to produce knock-in mouse and rat models. The four combined methods include: AAV-mediated DNA delivery, single-stranded DNA donor templates, 2-cell embryo modification, and CRISPR-Cas ribonucleoprotein (RNP) electroporation. Using this new combined approach, we were able to produce successfully targeted knock-in rat models containing either Cre or Flp recombinase sequences with knock-in efficiencies over 90%. Furthermore, we were able to produce a knock-in mouse model containing a Cre recombinase targeted insertion with over 50% knock-in efficiency directly comparing efficiencies to other commonly used approaches. Our modified AAV-mediated DNA delivery with 2-cell embryo CRISPR-Cas9 RNP electroporation technique has proven to be highly effective for generating both knock-in mouse and knock-in rat models.
Collapse
Affiliation(s)
- Daniel J. Davis
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, United States
| | - James F. McNew
- Comparative Medicine Program, University of Missouri, Columbia, MO, United States
| | - Hailey Maresca-Fichter
- School of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Kaiwen Chen
- School of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Bhanu P. Telugu
- Department of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Elizabeth C. Bryda
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, United States
- Rat Resource and Research Center, Columbia, MO, United States
| |
Collapse
|
49
|
Adlat S, Vázquez Salgado AM, Lee M, Yin D, Wangensteen KJ. Emerging and potential use of CRISPR in human liver disease. Hepatology 2023:01515467-990000000-00538. [PMID: 37607734 PMCID: PMC10881897 DOI: 10.1097/hep.0000000000000578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
CRISPR is a gene editing tool adapted from naturally occurring defense systems from bacteria. It is a technology that is revolutionizing the interrogation of gene functions in driving liver disease, especially through genetic screens and by facilitating animal knockout and knockin models. It is being used in models of liver disease to identify which genes are critical for liver pathology, especially in genetic liver disease, hepatitis, and in cancer initiation and progression. It holds tremendous promise in treating human diseases directly by editing DNA. It could disable gene function in the case of expression of a maladaptive protein, such as blocking transthyretin as a therapy for amyloidosis, or to correct gene defects, such as restoring the normal functions of liver enzymes fumarylacetoacetate hydrolase or alpha-1 antitrypsin. It is also being studied for treatment of hepatitis B infection. CRISPR is an exciting, evolving technology that is facilitating gene characterization and discovery in liver disease and holds the potential to treat liver diseases safely and permanently.
Collapse
Affiliation(s)
- Salah Adlat
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | |
Collapse
|
50
|
Su L, Gong X, Zhou J, Li H. An efficient and recyclable electroeluter: from homemade to modular design for potential mass production. LAB ON A CHIP 2023; 23:3874-3881. [PMID: 37539696 DOI: 10.1039/d3lc00428g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Electrophoresis is one of the most powerful techniques to separate nucleic acids or protein molecules. The recovery of purified components from the gel is key to downstream analysis or function study. Here, we provide a cost-effective electroeluter in both homemade and module-assembled versions. The recovery yield can reach as high as >90% for single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and protein in practical testing, which outperforms a commercial kit as well as a purchased electroeluter. It fully addresses the existing concerns in this field. First of all, for almost all kits, there remains ambiguity in recovering ssDNA to satisfy specific demands, which is generally ignored. Secondly, the recovery of dsDNA from agarose gel with consumables is vulnerable to a lot of factors and involves chemicals/materials that are not friendly to the environment and operating personnel. Thirdly, recovery from polyacrylamide matrices is very difficult, and the most exploited diffusion method through crush-and-soak suffers from low yield even after a long-time diffusion. Lastly, there is a universal problem in scaling up, especially for commercial electroeluters. The present electroelution method addresses the above issues, and it is believed that it will facilitate associated research and find widespread application.
Collapse
Affiliation(s)
- Linhan Su
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| | - Xueting Gong
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| | - Ju Zhou
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| | - Hailong Li
- College of Chemistry, Jilin University, 130012 Changchun, People's Republic of China.
| |
Collapse
|