1
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Verosloff MS, Shapiro SJ, Hawkins EM, Alpay E, Verma D, Stanfield EG, Kreindler L, Jain S, McKay B, Hubbell SA, Hendriks CG, Blizard BA, Broughton JP, Chen JS. CRISPR-Cas enzymes: The toolkit revolutionizing diagnostics. Biotechnol J 2021; 17:e2100304. [PMID: 34505742 DOI: 10.1002/biot.202100304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/11/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
The programmable nature of sequence-specific targeting by CRISPR-Cas nucleases has revolutionized a wide range of genomic applications and is now emerging as a method for nucleic acid detection. We explore how the diversity of CRISPR systems and their fundamental mechanisms have given rise to a wave of new methods for target recognition and readout. These cross-disciplinary advances found at the intersection of CRISPR biology and engineering have led to the ability to rapidly generate solutions for emerging global challenges like the COVID-19 pandemic. We further discuss the advances and potential for CRISPR-based detection to have an impact across a continuum of diagnostic applications.
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Affiliation(s)
| | | | | | - Emel Alpay
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | - Deepika Verma
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | | | | | - Sonal Jain
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | - Bridget McKay
- Mammoth Biosciences, Inc., Brisbane, California, USA
| | | | | | | | | | - Janice S Chen
- Mammoth Biosciences, Inc., Brisbane, California, USA
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2
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Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020; 38:870-874. [PMID: 32300245 PMCID: PMC9107629 DOI: 10.1038/s41587-020-0513-4] [Citation(s) in RCA: 1500] [Impact Index Per Article: 375.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 12/26/2022]
Abstract
An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with SARS-CoV-2 infection, rapidly spread to produce a global pandemic. We report development of a rapid (<40 min), easy-to-implement and accurate CRISPR-Cas12-based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated our method using contrived reference samples and clinical samples from patients in the United States, including 36 patients with COVID-19 infection and 42 patients with other viral respiratory infections. Our CRISPR-based DETECTR assay provides a visual and faster alternative to the US Centers for Disease Control and Prevention SARS-CoV-2 real-time RT-PCR assay, with 95% positive predictive agreement and 100% negative predictive agreement.
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Affiliation(s)
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jasmeet Singh
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Xin Miao
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Janice S Chen
- Mammoth Biosciences, Inc., South San Francisco, CA, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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3
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Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 2020; 38:870-874. [PMID: 32300245 PMCID: PMC9107629 DOI: 10.1038/s41587-020-0513-4,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 02/02/2024]
Abstract
An outbreak of betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with SARS-CoV-2 infection, rapidly spread to produce a global pandemic. We report development of a rapid (<40 min), easy-to-implement and accurate CRISPR-Cas12-based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated our method using contrived reference samples and clinical samples from patients in the United States, including 36 patients with COVID-19 infection and 42 patients with other viral respiratory infections. Our CRISPR-based DETECTR assay provides a visual and faster alternative to the US Centers for Disease Control and Prevention SARS-CoV-2 real-time RT-PCR assay, with 95% positive predictive agreement and 100% negative predictive agreement.
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Affiliation(s)
| | - Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jasmeet Singh
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Xin Miao
- Mammoth Biosciences, Inc., South San Francisco, CA, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Janice S Chen
- Mammoth Biosciences, Inc., South San Francisco, CA, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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4
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Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho SW, Mistry A, Longaker MT, Khavari PA, Batey RT, Wuttke DS, Chang HY. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. eLife 2020; 9:e54508. [PMID: 32379046 PMCID: PMC7282817 DOI: 10.7554/elife.54508] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen loss activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.
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Affiliation(s)
- Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Meagan Y Nakamoto
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Brian J Zarnegar
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - James P Broughton
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Ryan C Ransom
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Ankit Salhotra
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Surya D Nagaraja
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Seung-Woo Cho
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Anil Mistry
- Novartis Institute for Biomedical ResearchCambridgeUnited States
| | - Michael T Longaker
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Robert T Batey
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Deborah S Wuttke
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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5
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Broughton JP, Deng X, Yu G, Fasching CL, Singh J, Streithorst J, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY. Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay. medRxiv 2020:2020.03.06.20032334. [PMID: 32511449 PMCID: PMC7239074 DOI: 10.1101/2020.03.06.20032334] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (~30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.
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Affiliation(s)
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | | | - Jasmeet Singh
- Mammoth Biosciences, Inc., San Francisco, California, USA
| | - Jessica Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, San Francisco, California, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Janice S. Chen
- Mammoth Biosciences, Inc., San Francisco, California, USA
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California, USA
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6
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Chen YG, Chen R, Ahmad S, Verma R, Kasturi SP, Amaya L, Broughton JP, Kim J, Cadena C, Pulendran B, Hur S, Chang HY. N6-Methyladenosine Modification Controls Circular RNA Immunity. Mol Cell 2019; 76:96-109.e9. [PMID: 31474572 PMCID: PMC6778039 DOI: 10.1016/j.molcel.2019.07.016] [Citation(s) in RCA: 320] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 05/25/2019] [Accepted: 07/10/2019] [Indexed: 02/08/2023]
Abstract
Circular RNAs (circRNAs) are prevalent in eukaryotic cells and viral genomes. Mammalian cells possess innate immunity to detect foreign circRNAs, but the molecular basis of self versus foreign identity in circRNA immunity is unknown. Here, we show that N6-methyladenosine (m6A) RNA modification on human circRNAs inhibits innate immunity. Foreign circRNAs are potent adjuvants to induce antigen-specific T cell activation, antibody production, and anti-tumor immunity in vivo, and m6A modification abrogates immune gene activation and adjuvant activity. m6A reader YTHDF2 sequesters m6A-circRNA and is essential for suppression of innate immunity. Unmodified circRNA, but not m6A-modified circRNA, directly activates RNA pattern recognition receptor RIG-I in the presence of lysine-63-linked polyubiquitin chain to cause filamentation of the adaptor protein MAVS and activation of the downstream transcription factor IRF3. CircRNA immunity has considerable parallel to prokaryotic DNA restriction modification system that transforms nucleic acid chemical modification into organismal innate immunity.
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MESH Headings
- Adaptor Proteins, Signal Transducing/immunology
- Adaptor Proteins, Signal Transducing/metabolism
- Adenosine/administration & dosage
- Adenosine/analogs & derivatives
- Adenosine/immunology
- Adenosine/metabolism
- Adjuvants, Immunologic/administration & dosage
- Animals
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- DEAD Box Protein 58/immunology
- DEAD Box Protein 58/metabolism
- Female
- HEK293 Cells
- HeLa Cells
- Humans
- Immunity, Innate
- Immunization
- Interferon Regulatory Factor-3/immunology
- Interferon Regulatory Factor-3/metabolism
- Interferons/immunology
- Interferons/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/pathology
- Melanoma, Experimental/therapy
- Mice, Inbred C57BL
- Polyubiquitin/immunology
- Polyubiquitin/metabolism
- Protein Multimerization
- RNA, Circular/administration & dosage
- RNA, Circular/immunology
- RNA, Circular/metabolism
- RNA-Binding Proteins/immunology
- RNA-Binding Proteins/metabolism
- Receptors, Immunologic
- Ubiquitination
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Affiliation(s)
- Y Grace Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | - Robert Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Rohit Verma
- Institute for Immunity, Transplantation and Infection, Department of Pathology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Sudhir Pai Kasturi
- Emory Vaccine Center/Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Laura Amaya
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - James P Broughton
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeewon Kim
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Cristhian Cadena
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Department of Pathology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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7
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Aalto AP, Nicastro IA, Broughton JP, Chipman LB, Schreiner WP, Chen JS, Pasquinelli AE. Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging. PLoS Genet 2018; 14:e1007379. [PMID: 29927939 PMCID: PMC6013023 DOI: 10.1371/journal.pgen.1007379] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/25/2018] [Indexed: 01/08/2023] Open
Abstract
Argonaute (AGO) proteins partner with microRNAs (miRNAs) to target specific genes for post-transcriptional regulation. During larval development in Caenorhabditis elegans, Argonaute-Like Gene 1 (ALG-1) is the primary mediator of the miRNA pathway, while the related ALG-2 protein is largely dispensable. Here we show that in adult C. elegans these AGOs are differentially expressed and, surprisingly, work in opposition to each other; alg-1 promotes longevity, whereas alg-2 restricts lifespan. Transcriptional profiling of adult animals revealed that distinct miRNAs and largely non-overlapping sets of protein-coding genes are misregulated in alg-1 and alg-2 mutants. Interestingly, many of the differentially expressed genes are downstream targets of the Insulin/ IGF-1 Signaling (IIS) pathway, which controls lifespan by regulating the activity of the DAF-16/ FOXO transcription factor. Consistent with this observation, we show that daf-16 is required for the extended lifespan of alg-2 mutants. Furthermore, the long lifespan of daf-2 insulin receptor mutants, which depends on daf-16, is strongly reduced in animals lacking alg-1 activity. This work establishes an important role for AGO-mediated gene regulation in aging C. elegans and illustrates that the activity of homologous genes can switch from complementary to antagonistic, depending on the life stage. Tiny non-coding RNAs called microRNAs (miRNAs) are broadly conserved across animal species and have established roles in regulating development, metabolism and behavior. In humans, aberrant expression or function of specific miRNAs has been associated with a wide variety of diseases, underscoring the critical role of these molecules in organismal viability. Argonaute (AGO) proteins are essential co-factors for miRNAs to regulate the expression of target genes. In C. elegans nematodes, two highly related AGOs (ALG-1 and ALG-2; Argonaute-Like Genes) play largely overlapping roles in the miRNA pathway during development. Here we report that the activities of these two AGOs diverge in aging animals, as loss of ALG-1 shortens lifespan, while loss of ALG-2 extends it. These opposite longevity phenotypes are associated with differential regulation of specific miRNAs and protein-coding genes that act in the Insulin/ IGF-1 Signaling (IIS) pathway. Furthermore, we present genetic evidence that alg-1 and alg-2 operate within this pathway to impact aging. In sum, our findings reveal that two related AGOs function antagonistically within the conserved insulin signaling pathway that regulates longevity.
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Affiliation(s)
- Antti P. Aalto
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Ian A. Nicastro
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - James P. Broughton
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Laura B. Chipman
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - William P. Schreiner
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Jerry S. Chen
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Amy E. Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
- * E-mail:
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8
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Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA. m 6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 2017; 548:338-342. [PMID: 28792938 PMCID: PMC5729908 DOI: 10.1038/nature23450] [Citation(s) in RCA: 584] [Impact Index Per Article: 83.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
N6 -methyladenosine (m6A) is the most common and abundant messenger RNA modification, modulated by ‘writers’, ‘erasers’ and ‘readers’ of this mark 1,2. In vitro data have shown that m6A influences all fundamental aspects of mRNA metabolism, mainly mRNA stability, to determine stem cell fates 3,4. However, its in vivo physiological function in mammals and adult mammalian cells is still unknown. Here we show that deletion of m6A ‘writer’ protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation. In a lymphopenic mouse adoptive transfer model, naive Mettl3 deficient T cells failed to undergo homeostatic expansion and remarkably remained in the naïve state up through 12 weeks, thereby preventing colitis. Consistent with these observations, the mRNAs of SOCS family genes encoding STAT- signaling inhibitory proteins, Socs1, Socs3 and Cish, were marked by m6A, exhibited slower mRNA decay and increased mRNAs and protein expression levels in Mettl3 deficient naïve T cells. This increased SOCS family activity consequently inhibited IL-7 mediated STAT5 activation and T cell homeostatic proliferation and differentiation. We also found that m6A plays important roles for inducible degradation of Socs mRNAs in response to IL-7 signaling in order to reprogram Naïve T cells for proliferation and differentiation. Our study elucidates for the first time the in vivo biological role of m6A modification in T cell mediated pathogenesis and reveals a novel mechanism of T cell homeostasis and signal-dependent induction of mRNA degradation.
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Affiliation(s)
- Hua-Bing Li
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Shu Zhu
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Pedro J Batista
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Erin E Duffy
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Guangchao Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yuanyuan Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Institute of Surgical Research, Daping Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Geng Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - James P Broughton
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Y Grace Chen
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Howard Y Chang
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Zhinan Yin
- The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
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9
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Broughton JP, Lovci MT, Huang JL, Yeo GW, Pasquinelli AE. Pairing beyond the Seed Supports MicroRNA Targeting Specificity. Mol Cell 2016; 64:320-333. [PMID: 27720646 DOI: 10.1016/j.molcel.2016.09.004] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/01/2016] [Accepted: 08/31/2016] [Indexed: 12/31/2022]
Abstract
To identify endogenous miRNA-target sites, we isolated AGO-bound RNAs from Caenorhabditis elegans by individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP), which fortuitously also produced miRNA-target chimeric reads. Through the analysis of thousands of reproducible chimeras, pairing to the miRNA seed emerged as the predominant motif associated with functional interactions. Unexpectedly, we discovered that additional pairing to 3' sequences is prevalent in the majority of target sites and leads to specific targeting by members of miRNA families. By editing an endogenous target site, we demonstrate that 3' pairing determines targeting by specific miRNA family members and that seed pairing is not always sufficient for functional target interactions. Finally, we present a simplified method, chimera PCR (ChimP), for the detection of specific miRNA-target interactions. Overall, our analysis revealed that sequences in the 5' as well as the 3' regions of a miRNA provide the information necessary for stable and specific miRNA-target interactions in vivo.
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Affiliation(s)
- James P Broughton
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Michael T Lovci
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California, San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Jessica L Huang
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California, San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA.
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10
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Abstract
In animals, a functional interaction between a microRNA (miRNA) and its target RNA requires only partial base pairing. The limited number of base pair interactions required for miRNA targeting provides miRNAs with broad regulatory potential and also makes target prediction challenging. Computational approaches to target prediction have focused on identifying miRNA target sites based on known sequence features that are important for canonical targeting and may miss non-canonical targets. Current state-of-the-art experimental approaches, such as CLIP-seq (cross-linking immunoprecipitation with sequencing), PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), and iCLIP (individual-nucleotide resolution CLIP), require inference of which miRNA is bound at each site. Recently, the development of methods to ligate miRNAs to their target RNAs during the preparation of sequencing libraries has provided a new tool for the identification of miRNA target sites. The chimeric, or hybrid, miRNA-target reads that are produced by these methods unambiguously identify the miRNA bound at a specific target site. The information provided by these chimeric reads has revealed extensive non-canonical interactions between miRNAs and their target mRNAs, and identified many novel interactions between miRNAs and noncoding RNAs.
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Affiliation(s)
- James P Broughton
- Division of Biology, University of California, San Diego, La Jolla, CA, 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA, 92093-0349, USA.
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11
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Jones SA, O'Donnell VB, Wood JD, Broughton JP, Hughes EJ, Jones OT. Expression of phagocyte NADPH oxidase components in human endothelial cells. Am J Physiol 1996; 271:H1626-34. [PMID: 8897960 DOI: 10.1152/ajpheart.1996.271.4.h1626] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Low-level generation of reactive oxygen species (ROS) by endothelial cells in response to a variety of stimuli has been observed; however, the enzyme system responsible is unknown. Using a variety of techniques, we examined for components of the phagocyte superoxide-generating NADPH oxidase to elucidate whether this enzyme could be a source of endothelial-derived ROS. Superoxide generation on addition of 100 microM NAD(P)H to human umbilical vein endothelial cell (HUVEC) sonicates (using lucigenin-enhanced chemiluminescence) was partially inhibited on addition of the flavoenzyme inhibitor diphenyliodonium (IDP). Reverse transcriptase-polymerase chain reaction (RT-PCR) demonstrated expression of gp91phox, p22phox, p67phox, and p47phox in four independent HUVEC isolates. Expression of p22phox was also confirmed by Northern blotting. RT-PCR for tumor necrosis factor-alpha was negative, indicating an absence of mononuclear cell contamination (a potential source of NADPH oxidase). Immunoperoxidase staining, using anti-p47phox (JW-1)- and anti-p67phox (JW-2)-specific antibodies, showed protein expression of these cytosolic components. However, heme spectroscopy failed to indicate the presence of the low-potential cytochrome b558. These data indicate that cultured human endothelial cells express both mRNA and protein for cytosolic components of the phagocyte superoxide-generating NADPH oxidase. However, because the cytochrome b558 heme could not be conclusively demonstrated, a contribution of the phagocyte NADPH oxidase to endothelial oxidant generation may be unlikely.
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Affiliation(s)
- S A Jones
- Department of Biochemistry, School of Medical Sciences, University of Bristol, United Kingdom
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