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Fu L, Wang S, Liu L, Shibata Y, Okada M, Luu N, Shi YB. Simplifying Genotyping of Mutants from Genome Editing with a Parallel qPCR-Based iGenotype Index. Cells 2024; 13:247. [PMID: 38334640 PMCID: PMC10854663 DOI: 10.3390/cells13030247] [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: 12/14/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Targeted genome editing is a powerful tool in reverse genetic studies of gene function in many aspects of biological and pathological processes. The CRISPR/Cas system or engineered endonucleases such as ZFNs and TALENs are the most widely used genome editing tools that are introduced into cells or fertilized eggs to generate double-strand DNA breaks within the targeted region, triggering cellular DNA repair through either homologous recombination or non-homologous end joining (NHEJ). DNA repair through the NHEJ mechanism is usually error-prone, leading to point mutations or indels (insertions and deletions) within the targeted region. Some of the mutations in embryos are germline transmissible, thus providing an effective way to generate model organisms with targeted gene mutations. However, point mutations and short indels are difficult to be effectively genotyped, often requiring time-consuming and costly DNA sequencing to obtain reliable results. Here, we developed a parallel qPCR assay in combination with an iGenotype index to allow simple and reliable genotyping. The genotype-associated iGenotype indexes converged to three simple genotype-specific constant values (1, 0, -1) regardless of allele-specific primers used in the parallel qPCR assays or gene mutations at wide ranges of PCR template concentrations, thus resulting in clear genotype-specific cutoffs, established through statistical analysis, for genotype identification. While we established such a genotyping assay in the Xenopus tropicalis model, the approach should be applicable to genotyping of any organism or cells and can be potentially used for large-scale, automated genotyping.
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Affiliation(s)
- Liezhen Fu
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| | - Shouhong Wang
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Lusha Liu
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuki Shibata
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
- Department of Biology, Nippon Medical School, Tokyo 180-0023, Japan
| | - Morihiro Okada
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| | - Nga Luu
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (L.F.); (S.W.); (L.L.); (Y.S.); (M.O.); (N.L.)
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Zhang P, Abel L, Casanova JL, Yang R. Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE): An Experimental and Computational Approach for Analyzing CRISPR-Edited Cells. CRISPR J 2023; 6:462-472. [PMID: 37824834 PMCID: PMC10611965 DOI: 10.1089/crispr.2023.0021] [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: 04/03/2023] [Accepted: 09/10/2023] [Indexed: 10/14/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) creates double-stranded breaks, the repair of which generates indels around the target sites. These repairs can be mono-/multi-allelic, and the editing is often random and sometimes prolonged, resulting in considerable intercellular heterogeneity. The genotyping of CRISPR-Cas9-edited cells is challenging and the traditional genotyping methods are laborious. We introduce here a streamlined experimental and computational protocol for genotyping CRISPR-Cas9 genome-edited cells including cost-effective multiplexed sequencing and the software Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing (GMUSCLE). In this approach, CRISPR-Cas9-edited products are sequenced in great depth, then GMUSCLE quantitatively and qualitatively identifies the genotypes, which enable the selection and investigation of cell clones with genotypes of interest. We validate the protocol and software by performing CRISPR-Cas9-mediated disruption on interferon-α/β receptor alpha, multiplexed sequencing, and identifying the genotypes simultaneously for 20 cell clones. Besides the multiplexed sequencing ability of this protocol, GMUSCLE is also applicable for the sequencing data from bulk cell populations. GMUSCLE is publicly available at our HGIDSOFT server and GitHub.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France; Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France; Necker Hospital for Sick Children, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris, France; Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France; Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA; and Necker Hospital for Sick Children, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA; Necker Hospital for Sick Children, Paris, France
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3
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Fu L, Ma E, Okada M, Shibata Y, Shi YB. Competitive PCR with dual fluorescent primers enhances the specificity and reproducibility of genotyping animals generated from genome editing. Cell Biosci 2023; 13:83. [PMID: 37170319 PMCID: PMC10173569 DOI: 10.1186/s13578-023-01042-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
Targeted genome editing is a powerful tool for studying gene function in almost every aspect of biological and pathological processes. The most widely used genome editing approach is to introduce engineered endonucleases or CRISPR/Cas system into cells or fertilized eggs to generate double-strand DNA breaks within the targeted region, leading to DNA repair through homologous recombination or non-homologous end joining (NHEJ). DNA repair through NHEJ mechanism is an error-prone process that often results in point mutations or stretches of indels (insertions and deletions) within the targeted region. Such mutations in embryos are germline transmissible, thus providing an easy means to generate organisms with gene mutations. However, point mutations and short indels present difficulty for genotyping, often requiring labor intensive sequencing to obtain reliable results. Here, we developed a single-tube competitive PCR assay with dual fluorescent primers that allowed simple and reliable genotyping. While we used Xenopus tropicalis as a model organism, the approach should be applicable to genotyping of any organisms.
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Affiliation(s)
- Liezhen Fu
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emily Ma
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Morihiro Okada
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuki Shibata
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Bo Shi
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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4
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Tepe ZG, Yazıcı YY, Tank U, Köse LI, Özer M, Aytekin C, Belkaya S. Inherited IRAK-4 Deficiency in Acute Human Herpesvirus-6 Encephalitis. J Clin Immunol 2023; 43:192-205. [PMID: 36205835 PMCID: PMC9540208 DOI: 10.1007/s10875-022-01369-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023]
Abstract
Human herpesvirus-6 (HHV-6) infection can rarely cause life-threatening conditions, such as encephalitis, in otherwise healthy children, with unclear pathogenesis. We studied a child who presented with acute HHV-6 encephalitis at the age of 10 months and who was homozygous for a novel missense mutation in IRAK4, encoding interleukin-1 receptor-associated kinase 4, identified by whole-exome sequencing. We tested the damaging impact of this mutation in silico by molecular dynamics simulations and in vitro by biochemical and functional experiments utilizing cell lines and patient's cells. We found that the mutation is severely hypomorphic, impairing both the expression and function of IRAK-4. Patient's leukocytes had barely detectable levels of IRAK-4 and diminished anti-viral immune responses to various stimuli inducing different Toll-like receptors and cytosolic nucleic acid sensors. Overall, these findings suggest that acute HHV-6 encephalitis can result from inborn errors of immunity to virus. This study represents the first report of isolated acute HHV-6 infection causing encephalitis in an inherited primary immunodeficiency, notably autosomal recessive (AR) partial IRAK-4 deficiency, and the first report of AR IRAK-4 deficiency presenting with a severe viral disease, notably HHV-6 encephalitis upon an acute infection, thereby expanding the clinical spectrum of IRAK-4 deficiency.
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Affiliation(s)
- Zeynep Güneş Tepe
- Department of Molecular Biology and Genetics, Faculty of Science, İhsan Doğramacı Bilkent University, Ankara, Turkey
| | - Yılmaz Yücehan Yazıcı
- Department of Molecular Biology and Genetics, Faculty of Science, İhsan Doğramacı Bilkent University, Ankara, Turkey
| | - Umut Tank
- Department of Molecular Biology and Genetics, Faculty of Science, İhsan Doğramacı Bilkent University, Ankara, Turkey
| | - Ladin Işık Köse
- Department of Molecular Biology and Genetics, Faculty of Science, İhsan Doğramacı Bilkent University, Ankara, Turkey
| | - Murat Özer
- Department of Pediatric Immunology, Dr. Sami Ulus Maternity and Children’s Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr. Sami Ulus Maternity and Children’s Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Serkan Belkaya
- Department of Molecular Biology and Genetics, Faculty of Science, İhsan Doğramacı Bilkent University, Ankara, Turkey
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5
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Liu M, Smith R, Liby T, Chiotti K, López CS, Korkola JE. INHBA is a mediator of aggressive tumor behavior in HER2+ basal breast cancer. Breast Cancer Res 2022; 24:18. [PMID: 35248133 PMCID: PMC8898494 DOI: 10.1186/s13058-022-01512-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 02/25/2022] [Indexed: 11/22/2022] Open
Abstract
Background Resistance to HER2-targeted therapeutics remains a significant clinical problem in HER2+ breast cancer patients with advanced disease. This may be particularly true for HER2+ patients with basal subtype disease, as recent evidence suggests they receive limited benefit from standard of care HER2-targeted therapies. Identification of drivers of resistance and aggressive disease that can be targeted clinically has the potential to impact patient outcomes. Methods We performed siRNA knockdown screens of genes differentially expressed between lapatinib-responsive and -resistant HER2+ breast cancer cells, which corresponded largely to luminal versus basal subtypes. We then validated hits in 2-d and 3-d cell culture systems. Results Knockdown of one of the genes, INHBA, significantly slowed growth and increased sensitivity to lapatinib in multiple basal HER2+ cell lines in both 2-d and 3-d cultures, but had no effect in luminal HER2+ cells. Loss of INHBA altered metabolism, eliciting a shift from glycolytic to oxidative phosphorylative metabolism, which was also associated with a decrease in tumor invasiveness. Analysis of breast cancer datasets showed that patients with HER2+ breast cancer and high levels of INHBA expression had worse outcomes than patients with low levels of INHBA expression. Conclusions Our data suggest that INHBA is associated with aggressiveness of the basal subtype of HER2+ tumors, resulting in poor response to HER2-targeted therapy and an invasive phenotype. We hypothesize that targeting this pathway could be an effective therapeutic strategy to reduce invasiveness of tumor cells and to improve therapeutic response. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01512-4.
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Affiliation(s)
- Moqing Liu
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Rebecca Smith
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Tiera Liby
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Kami Chiotti
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Claudia S López
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.,Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR, USA
| | - James E Korkola
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
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Sharma SK, Gupta OP, Pathaw N, Sharma D, Maibam A, Sharma P, Sanasam J, Karkute SG, Kumar S, Bhattacharjee B. CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security. Front Nutr 2022; 8:751512. [PMID: 34977113 PMCID: PMC8716883 DOI: 10.3389/fnut.2021.751512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/31/2021] [Indexed: 12/14/2022] Open
Abstract
Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.
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Affiliation(s)
| | - Om Prakash Gupta
- Division of Quality & Basic Science, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neeta Pathaw
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Albert Maibam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Parul Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jyotsana Sanasam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - Suhas Gorakh Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| | - Sandeep Kumar
- Department of Plant Pathology, Odisha University of Agriculture & Technology, Bhubaneswar, India
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7
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Rubinstein CD, McLean DT, Lehman BP, Meudt JJ, Schomberg DT, Krentz KJ, Reichert JL, Meyer MB, Adams M, Konsitzke CM, Shanmuganayagam D. Assessment of Mosaicism and Detection of Cryptic Alleles in CRISPR/Cas9-Engineered Neurofibromatosis Type 1 and TP53 Mutant Porcine Models Reveals Overlooked Challenges in Precision Modeling of Human Diseases. Front Genet 2021; 12:721045. [PMID: 34630515 PMCID: PMC8495252 DOI: 10.3389/fgene.2021.721045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Genome editing in pigs has been made efficient, practical, and economically viable by the CRISPR/Cas9 platform, representing a promising new era in translational modeling of human disease for research and preclinical development of therapies and devices. Porcine embryo microinjection provides a universally available, efficient option over somatic-cell nuclear transfer, but requires that critical considerations be made in genotypic validation of the models that routinely go unaddressed. Accurate validation of genotypes is especially important when modeling genetic disorders, such as neurofibromatosis type 1 (NF1) that exhibits complex genotype–phenotypic relationships. NF1, an autosomal dominant disorder, is particularly hard to model as it manifests very differently across patients, and even within families, with over 3,000 disease-associated mutations of the neurofibromin 1 (NF1) gene identified. The precise nature of the mutations plays a role in the complex phenotypic presentation of the disorder that includes benign and malignant peripheral and central nervous system tumors, a variety of motor deficits and debilitating cognitive impairments and musculoskeletal, cardiovascular, and gastrointestinal disorders. NF1 can also often involve mutations in passenger genes such as TP53. In this manuscript, we describe the creation of three novel porcine models of NF1 and a model additionally harboring a mutation in TP53 by embryo microinjection of CRISPR/Cas9. We present the challenges encountered in validation of genotypes and the methodological strategies developed to counter the hurdles. We present simple options for quantifying level of mosaicism: a quantitative method (targeted amplicon sequencing) for small edits such as SNPs and indels and a semiquantitative method (competitive PCR) for large edits. Characterization of mosaicism allowed for strategic selection of founder pigs for rapid, economical expansion of genetically defined lines. We also present commonly observed unexpected DNA repair products (i.e., structural variants or cryptic alleles) that are refractory to PCR amplification and thus evade detection. We present the use of copy number variance assays to overcome hurdles in detecting cryptic alleles. The report provides a framework for genotypic validation of porcine models created by embryo microinjection and the expansion of lines in an efficient manner.
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Affiliation(s)
| | - Dalton T McLean
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Dominic T Schomberg
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kathy J Krentz
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jamie L Reichert
- Swine Research and Teaching Center, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Marie Adams
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Charles M Konsitzke
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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8
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Kumari R, Roy U, Desai S, Nilavar NM, Van Nieuwenhuijze A, Paranjape A, Radha G, Bawa P, Srivastava M, Nambiar M, Balaji KN, Liston A, Choudhary B, Raghavan SC. MicroRNA miR-29c regulates RAG1 expression and modulates V(D)J recombination during B cell development. Cell Rep 2021; 36:109390. [PMID: 34260911 DOI: 10.1016/j.celrep.2021.109390] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 03/07/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Recombination activating genes (RAGs), consisting of RAG1 and RAG2, are stringently regulated lymphoid-specific genes, which initiate V(D)J recombination in developing lymphocytes. We report the regulation of RAG1 through a microRNA (miRNA), miR-29c, in a B cell stage-specific manner in mice and humans. Various lines of experimentation, including CRISPR-Cas9 genome editing, demonstrate the target specificity and direct interaction of miR-29c to RAG1. Modulation of miR-29c levels leads to change in V(D)J recombination efficiency in pre-B cells. The miR-29c expression is inversely proportional to RAG1 in a B cell developmental stage-specific manner, and miR-29c null mice exhibit a reduction in mature B cells. A negative correlation of miR-29c and RAG1 levels is also observed in leukemia patients, suggesting the potential use of miR-29c as a biomarker and a therapeutic target. Thus, our results reveal the role of miRNA in the regulation of RAG1 and its relevance in cancer.
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Affiliation(s)
- Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Namrata M Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | | | - Amita Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Gudapureddy Radha
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pushpinder Bawa
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Mrinal Srivastava
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR), Hyderabad 500046, India
| | - Mridula Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | | | - Adrian Liston
- Immunology Programme, Babraham Institute, Cambridge, United Kingdom
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India.
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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9
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Yang R, Mele F, Worley L, Langlais D, Rosain J, Benhsaien I, Elarabi H, Croft CA, Doisne JM, Zhang P, Weisshaar M, Jarrossay D, Latorre D, Shen Y, Han J, Ogishi M, Gruber C, Markle J, Al Ali F, Rahman M, Khan T, Seeleuthner Y, Kerner G, Husquin LT, Maclsaac JL, Jeljeli M, Errami A, Ailal F, Kobor MS, Oleaga-Quintas C, Roynard M, Bourgey M, El Baghdadi J, Boisson-Dupuis S, Puel A, Batteux F, Rozenberg F, Marr N, Pan-Hammarström Q, Bogunovic D, Quintana-Murci L, Carroll T, Ma CS, Abel L, Bousfiha A, Di Santo JP, Glimcher LH, Gros P, Tangye SG, Sallusto F, Bustamante J, Casanova JL. Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria. Cell 2020; 183:1826-1847.e31. [PMID: 33296702 PMCID: PMC7770098 DOI: 10.1016/j.cell.2020.10.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022]
Abstract
Inborn errors of human interferon gamma (IFN-γ) immunity underlie mycobacterial disease. We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. The patient has extremely low counts of circulating Mycobacterium-reactive natural killer (NK), invariant NKT (iNKT), mucosal-associated invariant T (MAIT), and Vδ2+ γδ T lymphocytes, and of Mycobacterium-non reactive classic TH1 lymphocytes, with the residual populations of these cells also producing abnormally small amounts of IFN-γ. Other lymphocyte subsets develop normally but produce low levels of IFN-γ, with the exception of CD8+ αβ T and non-classic CD4+ αβ TH1∗ lymphocytes, which produce IFN-γ normally in response to mycobacterial antigens. Human T-bet deficiency thus underlies mycobacterial disease by preventing the development of innate (NK) and innate-like adaptive lymphocytes (iNKT, MAIT, and Vδ2+ γδ T cells) and IFN-γ production by them, with mycobacterium-specific, IFN-γ-producing, purely adaptive CD8+ αβ T, and CD4+ αβ TH1∗ cells unable to compensate for this deficit.
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Affiliation(s)
- Rui Yang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA.
| | - Federico Mele
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Lisa Worley
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - David Langlais
- Department of Human Genetics, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada; McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Ibithal Benhsaien
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Houda Elarabi
- Pediatrics Department, Hassan II Hospital, 80030 Dakhla, Morocco
| | - Carys A Croft
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France; University of Paris, 75006 Paris, France
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Peng Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Marc Weisshaar
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - David Jarrossay
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Daniela Latorre
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yichao Shen
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Jing Han
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Masato Ogishi
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Janet Markle
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Fatima Al Ali
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | | | - Taushif Khan
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Lucas T Husquin
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France
| | - Julia L Maclsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Mohamed Jeljeli
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Abderrahmane Errami
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Manon Roynard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Mathieu Bourgey
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics, Montreal, QC H3A 0G1, Canada
| | | | - Stéphanie Boisson-Dupuis
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Fréderic Batteux
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Flore Rozenberg
- University of Paris, 75006 Paris, France; Virology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, PO 34110, Qatar
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, 75005 Paris, France
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe Gros
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Federica Sallusto
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland; Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jacinta Bustamante
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Study Center for Primary Immunodeficiencies, Necker Children Hospital, AP-HP, 75015 Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
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10
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Cheng X, Mwaura BW, Chang Stauffer SR, Bezanilla M. A Fully Functional ROP Fluorescent Fusion Protein Reveals Roles for This GTPase in Subcellular and Tissue-Level Patterning. THE PLANT CELL 2020; 32:3436-3451. [PMID: 32917738 PMCID: PMC7610296 DOI: 10.1105/tpc.20.00440] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/25/2020] [Accepted: 09/07/2020] [Indexed: 05/18/2023]
Abstract
Rho of Plants (ROPs) are GTPases that regulate polarity and patterned wall deposition in plants. As these small, globular proteins have many interactors, it has been difficult to ensure that methods to visualize ROP in live cells do not affect ROP function. Here, motivated by work in fission yeast (Schizosaccharomyces pombe), we generated a fluorescent moss (Physcomitrium [Physcomitrella] patens) ROP4 fusion protein by inserting mNeonGreen after Gly-134. Plants harboring tagged ROP4 and no other ROP genes were phenotypically normal. Plants lacking all four ROP genes comprised an unpatterned clump of spherical cells that were unable to form gametophores, demonstrating that ROP is essentially for spatial patterning at the cellular and tissue levels. The functional ROP fusion protein formed a steep gradient at the apical plasma membranes of growing tip cells. ROP also predicted the site of branch formation in the apical cell at the onset of mitosis, which occurs one to two cell cycles before a branch cell emerges. While fluorescence recovery after photobleaching studies demonstrated that ROP dynamics do not depend on the cytoskeleton, acute depolymerization of the cytoskeleton removed ROP from the membrane only in recently divided cells, pointing to a feedback mechanism between the cell cycle, cytoskeleton, and ROP.
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Affiliation(s)
- Xiaohang Cheng
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Bethany W Mwaura
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | | | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
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11
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Rensing SA, Goffinet B, Meyberg R, Wu SZ, Bezanilla M. The Moss Physcomitrium ( Physcomitrella) patens: A Model Organism for Non-Seed Plants. THE PLANT CELL 2020; 32:1361-1376. [PMID: 32152187 PMCID: PMC7203925 DOI: 10.1105/tpc.19.00828] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/17/2020] [Accepted: 03/05/2020] [Indexed: 05/06/2023]
Abstract
Since the discovery two decades ago that transgenes are efficiently integrated into the genome of Physcomitrella patens by homologous recombination, this moss has been a premier model system to study evolutionary developmental biology questions, stem cell reprogramming, and the biology of nonvascular plants. P patens was the first non-seed plant to have its genome sequenced. With this level of genomic information, together with increasing molecular genetic tools, a large number of reverse genetic studies have propelled the use of this model system. A number of technological advances have recently opened the door to forward genetics as well as extremely efficient and precise genome editing in P patens Additionally, careful phylogenetic studies with increased resolution have suggested that P patens emerged from within Physcomitrium Thus, rather than Physcomitrella patens, the species should be named Physcomitrium patens Here we review these advances and describe the areas where P patens has had the most impact on plant biology.
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Affiliation(s)
- Stefan A Rensing
- Faculty of Biology, Plant Cell Biology, Philipps University of Marburg, 35037 Marburg an der Lahn, Hesse, Germany
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | - Rabea Meyberg
- Faculty of Biology, Plant Cell Biology, Philipps University of Marburg, 35037 Marburg an der Lahn, Hesse, Germany
| | - Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
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12
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Lin B, Sun J, Fraser IDC. Single-tube genotyping for small insertion/deletion mutations: simultaneous identification of wild type, mutant and heterozygous alleles. Biol Methods Protoc 2020; 5:bpaa007. [PMID: 33782652 DOI: 10.1093/biomethods/bpaa007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/17/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
Current methods of genotyping small insertion/deletion (indel) mutations are costly, laborious, and can be unreliable. To address this, we have developed a method for small indel genotyping in a single polymerase chain reaction, with wild-type, heterozygous and mutant alleles distinguishable by band pattern in routine agarose gel electrophoresis. We demonstrate this method with multiple genes to distinguish 10 bp, 4 bp and even 1 bp deletions from the wild type. Through systematic testing of numerous primer designs, we also propose guidelines for genotyping small indel mutations. Our method provides a convenient approach to genotyping small indels derived from clustered regularly interspaced short palindromic repeats-mediated gene editing, N-ethyl-N-nitrosourea induced mutagenesis or diagnosis of naturally occurring polymorphisms/mutations.
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Affiliation(s)
- Bin Lin
- Signaling Systems Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jing Sun
- Signaling Systems Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Liu P, Liang B, Liu M, Lebbink JH, Li S, Qian M, Lavrijsen M, Peppelenbosch MP, Chen X, Smits R. Oncogenic Mutations in Armadillo Repeats 5 and 6 of β-Catenin Reduce Binding to APC, Increasing Signaling and Transcription of Target Genes. Gastroenterology 2020; 158:1029-1043.e10. [PMID: 31857074 PMCID: PMC7179799 DOI: 10.1053/j.gastro.2019.11.302] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS The β-catenin signaling pathway is one of the most commonly deregulated pathways in cancer cells. Amino acid substitutions within armadillo repeats 5 and 6 (K335, W383, and N387) of β-catenin are found in several tumor types, including liver tumors. We investigated the mechanisms by which these substitutions increase signaling and the effects on liver carcinogenesis in mice. METHODS Plasmids encoding tagged full-length β-catenin (CTNNB1) or β-catenin with the K335I or N387K substitutions, along with MET, were injected into tails of FVB/N mice. Tumor growth was monitored, and livers were collected and analyzed by histology, immunohistochemistry, and quantitative reverse-transcription polymerase chain reaction. Tagged full-length and mutant forms of β-catenin were expressed in HEK293, HCT116, and SNU449 cells, which were analyzed by immunoblots and immunoprecipitation. A panel of β-catenin variants and cell lines with knock-in mutations were analyzed for differences in N-terminal phosphorylation, half-life, and association with other proteins in the signaling pathway. RESULTS Mice injected with plasmids encoding K335I or N387K β-catenin and MET developed larger, more advanced tumors than mice injected with plasmids encoding WT β-catenin and MET. K335I and N387K β-catenin bound APC with lower affinity than WT β-catenin but still interacted with scaffold protein AXIN1 and in the nucleus with TCF7L2. This interaction resulted in increased transcription of genes regulated by β-catenin. Studies of protein structures supported the observed changes in relative binding affinities. CONCLUSION Expression of β-catenin with mutations in armadillo repeats 5 and 6, along with MET, promotes formation of liver tumors in mice. In contrast to N-terminal mutations in β-catenin that directly impair its phosphorylation by GSK3 or binding to BTRC, the K335I or N387K substitutions increase signaling via reduced binding to APC. However, these mutant forms of β-catenin still interact with the TCF family of transcription factors in the nucleus. These findings show how these amino acid substitutions increase β-catenin signaling in cancer cells.
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Affiliation(s)
- Pengyu Liu
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam
| | - Binyong Liang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA,Hepatic Surgery Center, Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Menggang Liu
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam,Department of Hepatobiliary Surgery, Daping Hospital, The Third Military Medical University, 10 Changjiangzhilu Daping, Chongqing 400042, China
| | - Joyce H.G. Lebbink
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands,Department of Radiation Oncology, Erasmus MC, Rotterdam, the Netherlands
| | - Shan Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam
| | - Manning Qian
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA,The Clinical Medical Testing Laboratory, Northern Jiangsu People’s Hospital and Clinical Medical College of Yangzhou University, Yangzhou, 225001, China
| | - Marla Lavrijsen
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Ron Smits
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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14
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Lomov NA, Viushkov VS, Petrenko AP, Syrkina MS, Rubtsov MA. Methods of Evaluating the Efficiency of CRISPR/Cas Genome Editing. Mol Biol 2019. [DOI: 10.1134/s0026893319060116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Optical control of sphingosine-1-phosphate formation and function. Nat Chem Biol 2019; 15:623-631. [PMID: 31036923 PMCID: PMC7428055 DOI: 10.1038/s41589-019-0269-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
Abstract
Sphingosine-1-phosphate (S1P) plays important roles as a signaling lipid in a variety of physiological and pathophysiological processes. S1P signals via a family of G protein-coupled receptors (S1P1–5) and intracellular targets. Here, we report on photoswitchable analogs of S1P and its precursor sphingosine, respectively termed PhotoS1P and PhotoSph. PhotoS1P enables optical control of S1P1–3, shown through electrophysiology and Ca2+ mobilization assays. We evaluated PhotoS1Pin vivo, where it reversibly controlled S1P3-dependent pain hypersensitivity in mice. The hypersensitivity induced by PhotoS1P is comparable to that induced by S1P. PhotoS1P is uniquely suited for the study of S1P biology in cultured cells and in vivo because it exhibits prolonged metabolic stability compared to the rapidly metabolized S1P. Using lipid mass spectrometry analysis, we constructed a metabolic map of PhotoS1P and PhotoSph. The formation of these photoswitchable lipids was found to be light-dependent, providing a novel approach to optically probe sphingolipid biology.
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16
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Biswas S, Li R, Yuan Z, Zhang D, Zhao X, Shi J. Development of methods for effective identification of CRISPR/Cas9-induced indels in rice. PLANT CELL REPORTS 2019; 38:503-510. [PMID: 30783736 DOI: 10.1007/s00299-019-02392-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/02/2019] [Indexed: 05/07/2023]
Abstract
Two methods, PCR and amplicon labeling based, were developed and successfully applied to reliably detect CRISPR/Cas9 induced indels in rice. The use of CRISPR/Cas9 has emerged as a powerful nuclease-based genome editing tool in several model organisms including plants for mutagenesis by inducing precise gene editing through efficient double strand DNA breaks (DSBs) at the target site and subsequent error-prone non-homologous end joining (NHEJ) repair, leading to indel mutations. Different molecular methods including enzymatic mismatch cleavage (EMC), high-resolution melting curve analysis (HRMA) and conventional polymerase chain reaction (PCR) combined with ligation detection reaction (LDR) have been developed to quick identify CRISPR/Cas9 induced mutations. However, their intrinsic drawbacks limit their application in the identification of indel mutants in plants. Here we present two methods (one simple PCR based and the other amplicon labeling based) for effective and sensitive detection of CRISPR/Cas9 induced indels in rice. In PCR-based method, targets were amplified using two pairs of primers for each target locus and visualized on gel electrophoresis, while in amplicon labeling-based method, targets were amplified using tri-primers (with one a universal 6-FAM 5'-labelled) and detected by DNA capillary electrophoresis. Both methods can accurately define indel sizes down to ± 1 bp, and are amenable for high throughput analysis, therefore, will significantly facilitate the identification of indel mutants generated by CRISPR/Cas9 for further functional analysis and breeding in rice and other plants.
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Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Xiangxiang Zhao
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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17
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A refined two-step oligoribonucleotide interference-PCR method for precise discrimination of nucleotide differences. Sci Rep 2018; 8:17195. [PMID: 30464194 PMCID: PMC6249316 DOI: 10.1038/s41598-018-35479-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/06/2018] [Indexed: 11/09/2022] Open
Abstract
We previously developed oligoribonucleotide (ORN) interference-PCR (ORNi-PCR), in which an ORN hybridises with a complementary DNA sequence and inhibits PCR amplification across the sequence in a sequence-specific manner. Suppression of target amplification by ORNi-PCR can be used to detect nucleotide differences such as mutations in a target sequence. In the present study, we refined the ORNi-PCR method and established a detailed technical protocol to precisely discriminate single-nucleotide differences. We first revealed that a two-step (denaturing and annealing plus elongation) rather than a standard three-step (denaturing, annealing and elongation) method is more suitable for stably hybridising an ORN to its target DNA sequence for sequence-specific suppression of target amplification. We then optimised the ORNi-PCR method using two-step cycles and established a step-by-step technical protocol. The optimised Two-Step ORNi-PCR method could discriminate single-nucleotide differences in genomic DNA or cDNA introduced by genome editing or mutations in cancer cells. In addition, we showed that Two-Step ORNi-PCR can detect the cancer cells possessing a single nucleotide mutation in a target locus mixed with a large number of cells harboring wild-type sequences in the locus so that the number of the cancer cells is only 0.2% of the total cell number. Two-Step ORNi-PCR is useful for simple, precise, cost-effective and positive detection of nucleotide differences in a wide range of molecular biology and medical applications.
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18
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Fujita T, Yuno M, Kitaura F, Fujii H. Detection of genome-edited cells by oligoribonucleotide interference-PCR. DNA Res 2018; 25:395-407. [PMID: 29718217 PMCID: PMC6105111 DOI: 10.1093/dnares/dsy012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/05/2018] [Indexed: 01/20/2023] Open
Abstract
Genome editing by engineered sequence-specific nucleases, such as the clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for analysis of gene functions. Several techniques have been developed for detection of genome-edited cells, but simple, cost-effective, and positive detection methods remain limited. Recently, we developed oligoribonucleotide (ORN) interference-PCR (ORNi-PCR), in which hybridization of an ORN with a complementary DNA sequence inhibits amplification across the sequence. Here, we investigated whether ORNi-PCR can be used to detect genome-edited cells. First, we showed that ORNs that hybridize to a CRISPR target site in the THYN1 locus inhibited amplification across the target site, but no longer inhibited amplification after the target site was edited, resulting in mismatches. Importantly, ORNi-PCR could distinguish even single-nucleotide differences. These features of ORNi-PCR enabled detection of genome-edited cells by positive PCR amplification. In addition, ORNi-PCR was successful in discriminating genome-edited cells from wild-type cells, and multiplex ORNi-PCR simultaneously detected indel mutations at multiple loci. However, endpoint ORNi-PCR may not be able to distinguish between mono- and bi-allelic mutations, which may limit its utility. Taken together, these results demonstrate the potential utility of ORNi-PCR for the screening of genome-edited cells.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Fusako Kitaura
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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19
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Feng S, Harayama T, Montessuit S, David FP, Winssinger N, Martinou JC, Riezman H. Mitochondria-specific photoactivation to monitor local sphingosine metabolism and function. eLife 2018; 7:34555. [PMID: 29376826 PMCID: PMC5819948 DOI: 10.7554/elife.34555] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 01/24/2018] [Indexed: 12/20/2022] Open
Abstract
Photoactivation ('uncaging’) is a powerful approach for releasing bioactive small-molecules in living cells. Current uncaging methods are limited by the random distribution of caged molecules within cells. We have developed a mitochondria-specific photoactivation method, which permitted us to release free sphingosine inside mitochondria and thereafter monitor local sphingosine metabolism by lipidomics. Our results indicate that sphingosine was quickly phosphorylated into sphingosine 1-phosphate (S1P) driven by sphingosine kinases. In time-course studies, the mitochondria-specific uncaged sphingosine demonstrated distinct metabolic patterns compared to globally-released sphingosine, and did not induce calcium spikes. Our data provide direct evidence that sphingolipid metabolism and signaling are highly dependent on the subcellular location and opens up new possibilities to study the effects of lipid localization on signaling and metabolic fate. Fatty or oily molecules called lipids are essential components of the membranes of cells and important signaling molecules too. They are made in specific compartments of the cell, but most are found in all membranes, albeit in varying amounts. Their widespread distribution suggests that there are extensive networks for transporting lipids within cells. Yet scientists know little about lipid transport inside living cells because it is difficult to detect their movements. Mitochondria are cellular compartments that are often referred to as the “powerhouses of the cell”. Many lipids are found in mitochondria including one called sphingosine, which is a common component of many other cell membranes too. Sphingosine can increase the concentration of calcium ions inside the cells, and when converted to a molecule called sphingosine 1 phosphate it forms a signaling molecule that regulates fundamental processes like cell survival and migration. However, it was not known if sphingosine localized in the mitochondria was processed differently to the same molecule elsewhere in the cell, or if its signaling activity was affected by its location. In the laboratory, Feng et al. synthesized an inactive sphingosine-like molecule that would only localize to mitochondria and which could be activated with a flash of light. By adding this molecule to human cells, they showed that sphingosine could be converted to sphingosine 1 phosphate within the mitochondria, before being exported rapidly to another compartment in the cell. The experiments allowed Feng et al. to observe the process in enough detail to to conclude that, despite its rapid transport, when localized only inside mitochondria, sphingosine could not trigger its normal signaling response. This new light-activated lipid molecule will be a useful tool for many researchers studying both metabolism and signaling. In principle, a similar tool could be developed for many compounds and it should also be possible to localize the compound to different locations within the cell. This new generation of compounds would give scientists a better understanding of mitochondria biology. They could be applied to the study of diseases where the mitochondria do not function as they should, for example Barth syndrome, where a mitochondria specific lipid called cardiolipin is not properly synthesized.
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Affiliation(s)
- Suihan Feng
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Takeshi Harayama
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Sylvie Montessuit
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Fabrice Pa David
- Gene Expression Core Facility, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicolas Winssinger
- National Centre of Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland
| | | | - Howard Riezman
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
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