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Kuo HC, Prupes J, Chou CW, Finkelstein IJ. Massively parallel profiling of RNA-targeting CRISPR-Cas13d. Nat Commun 2024; 15:498. [PMID: 38216559 PMCID: PMC10786891 DOI: 10.1038/s41467-024-44738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
CRISPR-Cas13d cleaves RNA and is used in vivo and for diagnostics. However, a systematic understanding of its RNA binding and cleavage specificity is lacking. Here, we describe an RNA Chip-Hybridized Association-Mapping Platform (RNA-CHAMP) for measuring the binding affinity for > 10,000 RNAs containing structural perturbations and other alterations relative to the CRISPR RNA (crRNA). Deep profiling of Cas13d reveals that it does not require a protospacer flanking sequence but is exquisitely sensitive to secondary structure within the target RNA. Cas13d binding is penalized by mismatches in the distal crRNA-target RNA region, while alterations in the proximal region inhibit nuclease activity. A biophysical model built from these data reveals that target recognition initiates in the distal end of the target RNA. Using this model, we design crRNAs that can differentiate between SARS-CoV-2 variants by modulating nuclease activation. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme.
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Brewer SM, Chen JS, Hankin AM, Clements ER, Chou CW, Wineland DJ, Hume DB, Leibrandt DR. Erratum: ^{27}Al^{+} Quantum-Logic Clock with a Systematic Uncertainty below 10^{-18} [Phys. Rev. Lett. 123, 033201 (2019)]. PHYSICAL REVIEW LETTERS 2023; 131:059901. [PMID: 37595250 DOI: 10.1103/physrevlett.131.059901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Indexed: 08/20/2023]
Abstract
This corrects the article DOI: 10.1103/PhysRevLett.123.033201.
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Kuo HC, Prupes J, Chou CW, Finkelstein IJ. Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534188. [PMID: 37034598 PMCID: PMC10081190 DOI: 10.1101/2023.03.27.534188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Type VI CRISPR enzymes cleave target RNAs and are widely used for gene regulation, RNA tracking, and diagnostics. However, a systematic understanding of their RNA binding specificity and cleavage activation is lacking. Here, we describe RNA chip-hybridized association-mapping platform (RNA-CHAMP), a massively parallel platform that repurposes next-generation DNA sequencing chips to measure the binding affinity for over 10,000 RNA targets containing structural perturbations, mismatches, insertions, and deletions relative to the CRISPR RNA (crRNA). Deep profiling of Cas13d, a compact and widely used RNA nuclease, reveals that it does not require a protospacer flanking sequence (PFS) but is exquisitely sensitive to secondary structure within the target RNA. Cas13d binding is strongly penalized by mismatches, insertions, and deletions in the distal crRNA-target RNA regions, while alterations in the proximal region inhibit nuclease activity without affecting binding. A biophysical model built from these data reveals that target recognition begins at the distal end of unstructured target RNAs and proceeds to the proximal end. Using this model, we designed a series of partially mismatched guide RNAs that modulate nuclease activity to detect single nucleotide polymorphisms (SNPs) in circulating SARS-CoV-2 variants. This work describes the key determinants of RNA targeting by a type VI CRISPR enzyme to improve CRISPR diagnostics and in vivo RNA editing. More broadly, RNA-CHAMP provides a quantitative platform for systematically measuring protein-RNA interactions.
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Javanmardi K, Segall-Shapiro TH, Chou CW, Boutz DR, Olsen RJ, Xie X, Xia H, Shi PY, Johnson CD, Annapareddy A, Weaver S, Musser JM, Ellington AD, Finkelstein IJ, Gollihar JD. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein. Cell Host Microbe 2022; 30:1242-1254.e6. [PMID: 35988543 PMCID: PMC9350683 DOI: 10.1016/j.chom.2022.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022]
Abstract
The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the repeated emergence of variants of concern. For the Omicron variant, sub-lineages BA.1 and BA.2, respectively, contain 33 and 29 nonsynonymous and indel spike protein mutations. These amino acid substitutions and indels are implicated in increased transmissibility and enhanced immune evasion. By reverting individual spike mutations of BA.1 or BA.2, we characterize the molecular effects of the Omicron spike mutations on expression, ACE2 receptor affinity, and neutralizing antibody recognition. We identified key mutations enabling escape from neutralizing antibodies at a variety of epitopes. Stabilizing mutations in the N-terminal and S2 domains of the spike protein can compensate for destabilizing mutations in the receptor binding domain, enabling the record number of mutations in Omicron. Our results provide a comprehensive account of the mutational effects in the Omicron spike protein and illustrate previously uncharacterized mechanisms of host evasion.
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Hsieh CL, Rush SA, Palomo C, Chou CW, Pickens W, Más V, McLellan JS. Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins. Nat Commun 2022; 13:1299. [PMID: 35288548 PMCID: PMC8921277 DOI: 10.1038/s41467-022-28931-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
The human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15 mg/L and has a melting temperature of 71.9 °C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies. The degree to which the conformation of the human metapneumovirus fusion (F) protein affects immunogenicity has been debated. Here, Hsieh et al. engineer prefusion-stabilized F variants with enhanced thermostability that elicit higher neutralizing antibody titers in mice than postfusion F.
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Javanmardi K, Chou CW, Terrace CI, Annapareddy A, Kaoud TS, Guo Q, Lutgens J, Zorkic H, Horton AP, Gardner EC, Nguyen G, Boutz DR, Goike J, Voss WN, Kuo HC, Dalby KN, Gollihar JD, Finkelstein IJ. Rapid characterization of spike variants via mammalian cell surface display. Mol Cell 2021; 81:5099-5111.e8. [PMID: 34919820 PMCID: PMC8675084 DOI: 10.1016/j.molcel.2021.11.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.
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Hsieh CL, Werner AP, Leist SR, Stevens LJ, Falconer E, Goldsmith JA, Chou CW, Abiona OM, West A, Westendorf K, Muthuraman K, Fritch EJ, Dinnon KH, Schäfer A, Denison MR, Chappell JD, Baric RS, Graham BS, Corbett KS, McLellan JS. Stabilized coronavirus spike stem elicits a broadly protective antibody. Cell Rep 2021; 37:109929. [PMID: 34710354 PMCID: PMC8519809 DOI: 10.1016/j.celrep.2021.109929] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 09/09/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
Current coronavirus (CoV) vaccines primarily target immunodominant epitopes in the S1 subunit, which are poorly conserved and susceptible to escape mutations, thus threatening vaccine efficacy. Here, we use structure-guided protein engineering to remove the S1 subunit from the Middle East respiratory syndrome (MERS)-CoV spike (S) glycoprotein and develop stabilized stem (SS) antigens. Vaccination with MERS SS elicits cross-reactive β-CoV antibody responses and protects mice against lethal MERS-CoV challenge. High-throughput screening of antibody-secreting cells from MERS SS-immunized mice led to the discovery of a panel of cross-reactive monoclonal antibodies. Among them, antibody IgG22 binds with high affinity to both MERS-CoV and severe acute respiratory syndrome (SARS)-CoV-2 S proteins, and a combination of electron microscopy and crystal structures localizes the epitope to a conserved coiled-coil region in the S2 subunit. Passive transfer of IgG22 protects mice against both MERS-CoV and SARS-CoV-2 challenge. Collectively, these results provide a proof of principle for cross-reactive CoV antibodies and inform the development of pan-CoV vaccines and therapeutic antibodies.
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Schaub JM, Chou CW, Kuo HC, Javanmardi K, Hsieh CL, Goldsmith J, DiVenere AM, Le KC, Wrapp D, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Wang N, Lavinder JJ, Ippolito GC, Maynard JA, McLellan JS, Finkelstein IJ. Expression and characterization of SARS-CoV-2 spike proteins. Nat Protoc 2021; 16:5339-5356. [PMID: 34611365 PMCID: PMC9665560 DOI: 10.1038/s41596-021-00623-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/06/2021] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 spike protein is a critical component of coronavirus disease 2019 vaccines and diagnostics and is also a therapeutic target. However, the spike protein is difficult to produce recombinantly because it is a large trimeric class I fusion membrane protein that is metastable and heavily glycosylated. We recently developed a prefusion-stabilized spike variant, termed HexaPro for six stabilizing proline substitutions, that can be expressed with a yield of >30 mg/L in ExpiCHO cells. This protocol describes an optimized workflow for expressing and biophysically characterizing rationally engineered spike proteins in Freestyle 293 and ExpiCHO cell lines. Although we focus on HexaPro, this protocol has been used to purify over a hundred different spike variants in our laboratories. We also provide guidance on expression quality control, long-term storage, and uses in enzyme-linked immunosorbent assays. The entire protocol, from transfection to biophysical characterization, can be completed in 7 d by researchers with basic tissue cell culture and protein purification expertise.
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Voss WN, Hou YJ, Johnson NV, Delidakis G, Kim JE, Javanmardi K, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Chou CW, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye JM, Herbert AS, Finkelstein IJ, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science 2021; 372:1108-1112. [PMID: 33947773 PMCID: PMC8224265 DOI: 10.1126/science.abg5268] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.
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MESH Headings
- Animals
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/immunology
- COVID-19/prevention & control
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/immunology
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Mutation
- Protein Domains
- Proteomics
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020; 11:e02707-20. [PMID: 33127862 PMCID: PMC7642679 DOI: 10.1128/mbio.02707-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antibodies, Neutralizing/immunology
- Base Sequence
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus RNA-Dependent RNA Polymerase
- Genome, Viral
- Genotype
- Humans
- Machine Learning
- Models, Molecular
- Molecular Diagnostic Techniques
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Texas/epidemiology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.22.20199125. [PMID: 33024977 PMCID: PMC7536878 DOI: 10.1101/2020.09.22.20199125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.
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12
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020. [PMID: 32703906 DOI: 10.1126/science:abd0826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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13
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AG, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Lavinder JJ, Ippolito GC, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020; 369:1501-1505. [PMID: 32703906 PMCID: PMC7402631 DOI: 10.1126/science.abd0826] [Citation(s) in RCA: 793] [Impact Index Per Article: 198.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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14
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Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, Le KC, Wrapp D, Lee AGW, Liu Y, Chou CW, Byrne PO, Hjorth CK, Johnson NV, Ludes-Meyers J, Nguyen AW, Park J, Wang N, Amengor D, Maynard JA, Finkelstein IJ, McLellan JS. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.30.125484. [PMID: 32577660 PMCID: PMC7302215 DOI: 10.1101/2020.05.30.125484] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ~10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
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15
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Chou CW, Collopy AL, Kurz C, Lin Y, Harding ME, Plessow PN, Fortier T, Diddams S, Leibfried D, Leibrandt DR. Frequency-comb spectroscopy on pure quantum states of a single molecular ion. Science 2020; 367:1458-1461. [PMID: 32217722 PMCID: PMC10652508 DOI: 10.1126/science.aba3628] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/04/2020] [Indexed: 01/21/2023]
Abstract
Spectroscopy is a powerful tool for studying molecules and is commonly performed on large thermal molecular ensembles that are perturbed by motional shifts and interactions with the environment and one another, resulting in convoluted spectra and limited resolution. Here, we use quantum-logic techniques to prepare a trapped molecular ion in a single quantum state, drive terahertz rotational transitions with an optical frequency comb, and read out the final state nondestructively, leaving the molecule ready for further manipulation. We can resolve rotational transitions to 11 significant digits and derive the rotational constant of 40CaH+ to be B R = 142 501 777.9(1.7) kilohertz. Our approach is suited for a wide range of molecular ions, including polyatomics and species relevant for tests of fundamental physics, chemistry, and astrophysics.
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16
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Brewer SM, Chen JS, Hankin AM, Clements ER, Chou CW, Wineland DJ, Hume DB, Leibrandt DR. ^{27}Al^{+} Quantum-Logic Clock with a Systematic Uncertainty below 10^{-18}. PHYSICAL REVIEW LETTERS 2019; 123:033201. [PMID: 31386450 DOI: 10.1103/physrevlett.123.033201] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/17/2019] [Indexed: 06/10/2023]
Abstract
We describe an optical atomic clock based on quantum-logic spectroscopy of the ^{1}S_{0}↔^{3}P_{0} transition in ^{27}Al^{+} with a systematic uncertainty of 9.4×10^{-19} and a frequency stability of 1.2×10^{-15}/sqrt[τ]. A ^{25}Mg^{+} ion is simultaneously trapped with the ^{27}Al^{+} ion and used for sympathetic cooling and state readout. Improvements in a new trap have led to reduced secular motion heating, compared to previous ^{27}Al^{+} clocks, enabling clock operation with ion secular motion near the three-dimensional ground state. Operating the clock with a lower trap drive frequency has reduced excess micromotion compared to previous ^{27}Al^{+} clocks. Both of these improvements have led to a reduced time-dilation shift uncertainty. Other systematic uncertainties including those due to blackbody radiation and the second-order Zeeman effect have also been reduced.
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Okamoto H, Hamao S, Eguchi R, Goto H, Takabayashi Y, Yen PYH, Liang LU, Chou CW, Hoffmann G, Gohda S, Sugino H, Liao YF, Ishii H, Kubozono Y. Synthesis of the extended phenacene molecules, [10]phenacene and [11]phenacene, and their performance in a field-effect transistor. Sci Rep 2019; 9:4009. [PMID: 30850618 PMCID: PMC6408568 DOI: 10.1038/s41598-019-39899-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/05/2019] [Indexed: 11/23/2022] Open
Abstract
The [10]phenacene and [11]phenacene molecules have been synthesized using a simple repetition of Wittig reactions followed by photocyclization. Sufficient amounts of [10]phenacene and [11]phenacene were obtained, and thin-film FETs using these molecules have been fabricated with SiO2 and ionic liquid gate dielectrics. These FETs operated in p-channel. The averaged measurements of field-effect mobility, <μ>, were 3.1(7) × 10−2 and 1.11(4) × 10−1 cm2 V−1 s−1, respectively, for [10]phenacene and [11]phenacene thin-film FETs with SiO2 gate dielectrics. Furthermore, [10]phenacene and [11]phenacene thin-film electric-double-layer (EDL) FETs with ionic liquid showed low-voltage p-channel FET properties, with <μ> values of 3(1) and 1(1) cm2 V−1 s−1, respectively. This study also discusses the future utility of the extremely extended π-network molecules [10]phenacene and [11]phenacene as the active layer of FET devices, based on the experimental results obtained.
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Chen JS, Brewer SM, Chou CW, Wineland DJ, Leibrandt DR, Hume DB. Sympathetic Ground State Cooling and Time-Dilation Shifts in an ^{27}Al^{+} Optical Clock. PHYSICAL REVIEW LETTERS 2017; 118:053002. [PMID: 28211723 DOI: 10.1103/physrevlett.118.053002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 06/06/2023]
Abstract
We report on Raman sideband cooling of ^{25}Mg^{+} to sympathetically cool the secular modes of motion in a ^{25}Mg^{+}-^{27}Al^{+} two-ion pair to near the three-dimensional (3D) ground state. The evolution of the Fock-state distribution during the cooling process is studied using a rate-equation simulation, and various heating sources that limit the efficiency of 3D sideband cooling in our system are discussed. We characterize the residual energy and heating rates of all of the secular modes of motion and estimate a secular motion time-dilation shift of -(1.9±0.1)×10^{-18} for an ^{27}Al^{+} clock at a typical clock probe duration of 150 ms. This is a 50-fold reduction in the secular motion time-dilation shift uncertainty in comparison with previous ^{27}Al^{+} clocks.
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Wei TT, Lin YC, Lin PH, Shih JY, Chou CW, Huang WJ, Yang YC, Hsiao PW, Chen CC. Induction of c-Cbl contributes to anti-cancer effects of HDAC inhibitor in lung cancer. Oncotarget 2016; 6:12481-92. [PMID: 25980579 PMCID: PMC4494952 DOI: 10.18632/oncotarget.3489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/04/2015] [Indexed: 11/30/2022] Open
Abstract
Here we found loss of c-Cbl, an E3 ligase, expression in non-small cell lung cancer (NSCLC) compared with its adjacent normal tissue in patient specimens. HDAC inhibition by WJ or knockdown of HDAC 1, HDAC2, HDAC3 or HDAC6 all induced c-Cbl. Ectopic expression of c-Cbl induced decreased EGFR, inhibited growth in NSCLC cells. Knockdown of EGFR inhibited NSCLC growth. Mutation of EGFR at Y1045 decreased WJ-induced growth inhibition as well as in vivo anti-cancer effect and EGFR degradation mediated by WJ. Time-lapse confocal analysis showed co-localization of c-Cbl and EGFR after WJ treatment. Furthermore, WJ inhibited lung tumor growth through c-Cbl induction in orthotopic and tail vein injected models. C-Cbl up-regulation induced by HDACi is a potential strategy for NSCLC treatment.
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Ching-Chow C, Wei TT, Lin YC, Lin PH, Shih JY, Chou CW. Abstract LB-250: Induction of c-Cbl is a novel mechanism for the anti-cancer effect of HDAC inhibitor in lung cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Here we found loss of c-Cbl, an E3 ligase, expression in Non-small cell lung cancer (NSCLC) compared with its adjacent normal tissue in patient specimens. HDAC inhibition by WJ or knockdown of HDAC 1, HDAC2, HDAC3 or HDAC6 all induced c-Cbl. Ectopic expression of c-Cbl induced decreased EGFR, inhibited growth in NSCLC cells. Knockdown of EGFR inhibited NSCLC growth. Mutation of EGFR at Y1045 decreased WJ-induced growth inhibition as well as in vivo anti-cancer effect and EGFR degradation mediated by WJ. Time-lapse confocal analysis showed co-localization of c-Cbl and EGFR after WJ treatment. Furthermore, WJ inhibited lung tumor growth through c-Cbl induction in orthotopic and tail vein injected models. C-Cbl up-regulation induced by HDACi is a potential strategy for NSCLC treatment.
Citation Format: Chen Ching-Chow, Tzu-Tang Wei, Yu-Chin Lin, Pei-Hua Lin, Jin-Yuan Shih, Chia-Wei Chou. Induction of c-Cbl is a novel mechanism for the anti-cancer effect of HDAC inhibitor in lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-250. doi:10.1158/1538-7445.AM2015-LB-250
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Yang CY, Chou CW, Hao LJ. Malignant solitary fibrous tumor with hypoglycemia (Doege-Potter syndrome). J Postgrad Med 2013; 59:64-6. [PMID: 23525065 DOI: 10.4103/0022-3859.109503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Chou CW, Liu LC, Wu CY. A MedRadio-band low-energy-per-bit 4-Mbps CMOS OOK receiver for implantable medical devices. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:5171-5174. [PMID: 24110900 DOI: 10.1109/embc.2013.6610713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A 4-Mbps 400-MHz On-Off Keying (OOK) receiver implemented in 0.18-um CMOS technology for implantable epilepsy sense-and-stimulation devices is presented. The proposed receiver is composed of a new current-mode full-wave envelope detector and differential cascaded gain amplifiers which is operated at MedRadio band. The fabricated receiver has power consumption of 0.27 mW and energy consumption of 0.07 nJ per bit at 4-Mbps. The sensitivity of receiver is -45.67 dBm.
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Hume DB, Chou CW, Leibrandt DR, Thorpe MJ, Wineland DJ, Rosenband T. Trapped-ion state detection through coherent motion. PHYSICAL REVIEW LETTERS 2011; 107:243902. [PMID: 22243001 DOI: 10.1103/physrevlett.107.243902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 05/31/2023]
Abstract
We demonstrate a general method for state detection of trapped ions that can be applied to a large class of atomic and molecular species. We couple a spectroscopy ion (27Al+) to a control ion (25Mg+) in the same trap and perform state detection through off-resonant laser excitation of the spectroscopy ion that induces coherent motion. The motional amplitude, dependent on the spectroscopy ion state, is measured either by time-resolved photon counting or by resolved sideband excitations on the control ion. The first method provides a simplified way to distinguish clock states in 27Al+, which avoids ground-state cooling and sideband transitions. The second method reduces spontaneous emission and optical pumping on the spectroscopy ion, which we demonstrate by nondestructively distinguishing Zeeman sublevels in the (1)S0 ground state of 27Al+.
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Chou CW, Hume DB, Thorpe MJ, Wineland DJ, Rosenband T. Quantum coherence between two atoms beyond Q=10(15). PHYSICAL REVIEW LETTERS 2011; 106:160801. [PMID: 21599347 DOI: 10.1103/physrevlett.106.160801] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Indexed: 05/30/2023]
Abstract
We place two atoms in quantum superposition states and observe coherent phase evolution for 3.4×10(15) cycles. Correlation signals from the two atoms yield information about their relative phase even after the probe radiation has decohered. This technique allowed a frequency comparison of two (27)Al(+) ions with fractional uncertainty 3.7(-0.8)(+1.0)×10(-16)/√[τ/s]. Two measures of the Q factor are reported: The Q factor derived from quantum coherence is 3.4(-1.1)(+2.4)×10(16), and the spectroscopic Q factor for a Ramsey time of 3 s is 6.7×10(15). We demonstrate a method to detect the individual quantum states of two Al(+) ions in a Mg(+)-Al(+)-Al(+) linear ion chain without spatially resolving the ions.
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Chou CW, Wu MS, Huang WC, Chen CC. HDAC inhibition decreases the expression of EGFR in colorectal cancer cells. PLoS One 2011; 6:e18087. [PMID: 21464950 PMCID: PMC3064594 DOI: 10.1371/journal.pone.0018087] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 02/24/2011] [Indexed: 01/27/2023] Open
Abstract
Epidermal growth factor receptor (EGFR), a receptor tyrosine kinase which
promotes cell proliferation and survival, is abnormally overexpressed in
numerous tumors of epithelial origin, including colorectal cancer (CRC). EGFR
monoclonal antibodies have been shown to increase the median survival and are
approved for the treatment of colorectal cancer. Histone deacetylases (HDACs),
frequently overexpressed in colorectal cancer and several malignancies, are
another attractive targets for cancer therapy. Several inhibitors of HDACs
(HDACi) are developed and exhibit powerful antitumor abilities. In this study,
human colorectal cancer cells treated with HDACi exhibited reduced EGFR
expression, thereby disturbed EGF-induced ERK and Akt phosphorylation. HDACi
also decreased the expression of SGLT1, an active glucose transporter found to
be stabilized by EGFR, and suppressed the glucose uptake of cancer cells. HDACi
suppressed the transcription of EGFR and class I HDACs were proved to be
involved in this event. Chromatin immunoprecipitation analysis showed that HDACi
caused the dissociation of SP1, HDAC3 and CBP from EGFR promoter. Our data
suggested that HDACi could serve as a single agent to block both EGFR and HDAC,
and may bring more benefits to the development of CRC therapy.
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