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Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D. Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Cell Rep 2023; 42:112621. [PMID: 37300832 PMCID: PMC10213294 DOI: 10.1016/j.celrep.2023.112621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/09/2022] [Revised: 04/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is eroding antibody responses elicited by prior vaccination and infection. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-COV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the AZD1061 (COV2-2130) mAb. Here, we show that this mutation remodels the receptor-binding site allosterically, thereby altering the epitopes recognized by these three mAbs and vaccine-elicited neutralizing antibodies while remaining functional. Our results demonstrate the spectacular structural and functional plasticity of the SARS-CoV-2 RBD, which is continuously evolving in emerging SARS-CoV-2 variants, including currently circulating strains that are accumulating mutations in the antigenic sites remodeled by the E406W substitution.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Tyler Starr
- Howard Hughes Medical Institute, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sasha W Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA 98195, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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2
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Sumstad D, Webber B, Growe M, Moriarity B, Kadidlo D, Starr T, Johnson M, Lou E, Choudhry M, McKenna, Jr. D. Gene Editing/Gene Therapies: CLINICAL MANUFACTURE OF CRISPR/CAS9-BASED CYTOKINE-INDUCED SH2 PROTEIN (CISH) KNOCK-OUT (KO) TUMOR-INFILTRATING LYMPHOCYTES (TIL) FOR GASTROINTESTINAL (GI) CANCERS. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00154-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Addetia A, Park YJ, Starr T, Greaney AJ, Sprouse KR, Bowen JE, Tiles SW, Van Voorhis WC, Bloom JD, Corti D, Walls AC, Veesler D. Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. bioRxiv 2022:2022.01.21.477288. [PMID: 35118471 PMCID: PMC8811904 DOI: 10.1101/2022.01.21.477288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-CoV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the cilgavimab (AZD1061) mAb. Here, we show that this residue substitution remodels the ACE2-binding site allosterically, thereby dampening receptor recognition severely and altering the epitopes recognized by these three mAbs. Although vaccine-elicited neutralizing antibody titers are decreased similarly against the E406 mutant and the Delta or Epsilon variants, broadly neutralizing sarbecovirus mAbs, including a clinical mAb, inhibit the E406W spike mutant.
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Affiliation(s)
- Amin Addetia
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Tyler Starr
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Sasha W. Tiles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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4
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Walls AC, Miranda MC, Schäfer A, Pham MN, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shirreff L, Ferrell DE, Bowen J, Brunette N, Kepl E, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Sprouse KR, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, Leist SR, Martinez DR, Clark M, Tisch R, O'Hagan DT, Van Der Most R, Van Voorhis WC, Corti D, McLellan JS, Kleanthous H, Sheahan TP, Smith KD, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric RS, King NP, Veesler D. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Cell 2021; 184:5432-5447.e16. [PMID: 34619077 PMCID: PMC8440233 DOI: 10.1016/j.cell.2021.09.015] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/18/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022]
Abstract
Understanding vaccine-elicited protection against SARS-CoV-2 variants and other sarbecoviruses is key for guiding public health policies. We show that a clinical stage multivalent SARS-CoV-2 spike receptor-binding domain nanoparticle (RBD-NP) vaccine protects mice from SARS-CoV-2 challenge after a single immunization, indicating a potential dose-sparing strategy. We benchmarked serum neutralizing activity elicited by RBD-NPs in non-human primates against a lead prefusion-stabilized SARS-CoV-2 spike (HexaPro) using a panel of circulating mutants. Polyclonal antibodies elicited by both vaccines are similarly resilient to many RBD residue substitutions tested, although mutations at and surrounding position 484 have negative consequences for neutralization. Mosaic and cocktail nanoparticle immunogens displaying multiple sarbecovirus RBDs elicit broad neutralizing activity in mice and protect mice against SARS-CoV challenge even in the absence of SARS-CoV RBD in the vaccine. This study provides proof of principle that multivalent sarbecovirus RBD-NPs induce heterotypic protection and motivates advancing such broadly protective sarbecovirus vaccines to the clinic.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Allison Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Kenneth Rogers
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Megan A O'Connor
- Washington National Primate Research Center, Seattle, WA 98121, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lisa Shirreff
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Douglas E Ferrell
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tyler Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Matthew Clark
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Roland Tisch
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | | | | | - Wesley C Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kelly D Smith
- UW Medicine Department of Laboratory Medicine and Pathology, Seattle, WA 98195, USA
| | - Deborah H Fuller
- Washington National Primate Research Center, Seattle, WA 98121, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Francois Villinger
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Jesse Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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5
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Walls AC, Miranda MC, Pham MN, Schäfer A, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shireff L, Ferrell DE, Brunette N, Kepl E, Bowen J, Zepeda SK, Starr T, Hsieh CL, Fiala B, Wrenn S, Pettie D, Sydeman C, Johnson M, Blackstone A, Ravichandran R, Ogohara C, Carter L, Tilles SW, Rappuoli R, O'Hagan DT, Van Der Most R, Van Voorhis WC, McLellan JS, Kleanthous H, Sheahan TP, Fuller DH, Villinger F, Bloom J, Pulendran B, Baric R, King N, Veesler D. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. bioRxiv 2021:2021.03.15.435528. [PMID: 33758839 PMCID: PMC7986998 DOI: 10.1101/2021.03.15.435528] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the ability of SARS-CoV-2 vaccine-elicited antibodies to neutralize and protect against emerging variants of concern and other sarbecoviruses is key for guiding vaccine development decisions and public health policies. We show that a clinical stage multivalent SARS-CoV-2 receptor-binding domain nanoparticle vaccine (SARS-CoV-2 RBD-NP) protects mice from SARS-CoV-2-induced disease after a single shot, indicating that the vaccine could allow dose-sparing. SARS-CoV-2 RBD-NP elicits high antibody titers in two non-human primate (NHP) models against multiple distinct RBD antigenic sites known to be recognized by neutralizing antibodies. We benchmarked NHP serum neutralizing activity elicited by RBD-NP against a lead prefusion-stabilized SARS-CoV-2 spike immunogen using a panel of single-residue spike mutants detected in clinical isolates as well as the B.1.1.7 and B.1.351 variants of concern. Polyclonal antibodies elicited by both vaccines are resilient to most RBD mutations tested, but the E484K substitution has similar negative consequences for neutralization, and exhibit modest but comparable neutralization breadth against distantly related sarbecoviruses. We demonstrate that mosaic and cocktail sarbecovirus RBD-NPs elicit broad sarbecovirus neutralizing activity, including against the SARS-CoV-2 B.1.351 variant, and protect mice against severe SARS-CoV challenge even in the absence of the SARS-CoV RBD in the vaccine. This study provides proof of principle that sarbecovirus RBD-NPs induce heterotypic protection and enables advancement of broadly protective sarbecovirus vaccines to the clinic.
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Affiliation(s)
- Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Allison Greaney
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Kenneth Rogers
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Megan A O'Connor
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Lisa Shireff
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Douglas E Ferrell
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tyler Starr
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | - Wesley C Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Deborah H Fuller
- Washington National Primate Research Center, Seattle, WA 98121, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Francois Villinger
- New Iberia Research Center and Department of Biology, University of Louisiana at Lafayette, New Iberia, LA, 70560 USA
| | - Jesse Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Neil King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Talukdar S, Cepela J, Chang Z, Zhang Y, Mullany S, Nelson A, Starr T, Winterhoff B. Development of a predictive signatures for immune therapy in ovarian cancer: Whom to treat and whom not to treat? Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.06.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Thomaier L, Hagen J, Henzler C, LaRue R, Talukdar S, Chang Z, Munro S, Mullany S, Starr T, Nelson A, Winterhoff B. Identification of clinically relevant genomic alterations in ovarian cancer: A comparison of a focused cancer next generation sequencing (NGS) assay and whole exome sequencing. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chang Z, Lee W, Rivers Z, Uppendahl L, Grad A, Talukdar S, Aliferis C, Jacobson P, Starr T, Nelson A, Winterhoff B. Clinical and Germline Molecular Findings From an Ovarian Cancer Precision Medicine Initiative. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.04.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Schefter A, Uppendahl L, Zhang Y, Wang J, Shetty M, Clark C, Grad A, Mullany S, Winterhoff B, Starr T. Single cell RNA-sequencing identifies unique immune cell profiles across metastatic sites in a case of primary ovarian cancer. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Talukdar S, Cepela J, Chang Z, Zhang Y, Grad A, Mullany S, Starr T, Winterhoff B. Gene expression of programmed cell death (PD-1) and its ligand, PD-L1, in primary epithelial ovarian cancer. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Uppendahl L, Chang Z, Grad A, Lee W, Rivers Z, Munro S, Zhang Y, Baller J, Ma S, Shabaneh A, Woo J, Wang J, Jacobson P, Nelson A, Starr T, Mullany S, Winterhoff B. Development and implementation of a multidisciplinary precision medicine program in ovarian cancer: A new paradigm. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Chang Z, Bedell S, Uppendahl L, Zhang Y, Grad A, Wang J, Mullany S, Nelson A, Starr T, Winterhoff B. Comprehensive single cell analysis of a patient’s primary, recurrent, and xenograft ovarian cancer. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.03.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Bedell S, Chang Z, Zhang Y, Uppendahl L, Grad A, Talukdar S, Wilhite A, Zhang R, Wang J, Mullany S, Starr T, Winterhoff B. Single cell exome analysis of hereditary breast and gynecologic cancer loci. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Wilhite A, Uppendahl L, Zhang Y, Clark C, Shetty M, Ramesh S, Mullany S, Winterhoff B, Starr T, Starr T. A descriptive subgroup analysis of individual tumor cells from 4 patients with ovarian cancer. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Chang Z, Bedell S, Uppendahl L, Clark C, Shetty M, Ramesh S, Abrahante J, Nelson A, Starr T, Winterhoff B. Single cell exome sequencing reveals somatic BRCA1 heterogeneity in a patient with BRCA1 germline mutation. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Wilhite A, Uppendahl L, Zhang Y, Clark C, Shetty M, Ramesh S, Mullany S, Winterhoff B, Starr T. Single cell sequencing: A descriptive subgroup analysis of individual tumor cells from 4 patients with ovarian cancer. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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De Waele JJ, Lipman J, Akova M, Bassetti M, Dimopoulos G, Kaukonen M, Koulenti D, Martin C, Montravers P, Rello J, Rhodes A, Udy AA, Starr T, Wallis SC, Roberts JA. Erratum to: Risk factors for target non-attainment during empirical treatment with β-lactam antibiotics in critically ill patients. Intensive Care Med 2015; 41:969. [PMID: 25820545 DOI: 10.1007/s00134-015-3772-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan J De Waele
- Department of Critical Care Medicine, Ghent University Hospital, De Pintelaan 185, 9000, Ghent, Belgium,
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Koerte IK, Lin AP, Muehlmann M, Merugumala S, Liao H, Starr T, Kaufmann D, Mayinger M, Steffinger D, Fisch B, Karch S, Heinen F, Ertl-Wagner B, Reiser M, Stern RA, Zafonte R, Shenton ME. Altered Neurochemistry in Former Professional Soccer Players without a History of Concussion. J Neurotrauma 2015; 32:1287-93. [PMID: 25843317 DOI: 10.1089/neu.2014.3715] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soccer is played by more than 250 million people worldwide. Repeatedly heading the ball may place soccer players at high risk for repetitive subconcussive head impacts (RSHI). This study evaluates the long-term effects of RSHI on neurochemistry in athletes without a history of clinically diagnosed concussion, but with a high exposure to RSHI. Eleven former professional soccer players (mean age 52.0±6.8 years) and a comparison cohort of 14 age- and gender-matched, former non-contact sport athletes (mean age 46.9±7.9 years) underwent 3T magnetic resonance spectroscopy (MRS) and neurocognitive evaluation. In the soccer players a significant increase was observed in both choline (Cho), a membrane marker, and myo-inositol (ml), a marker of glial activation, compared with control athletes. Additionally, ml and glutathione (GSH) were significantly correlated with lifetime estimate of RSHI within the soccer group. There was no significant difference in neurocognitive tests between groups. Results of this study suggest an association between RSHI in soccer players and MRS markers of neuroinflammation, suggesting that even subconcussive head impacts affect the neurochemistry of the brain and may precede neurocognitive changes. Future studies will need to determine the role of neuroinflammation in RSHI and the effect on neurocognitive function.
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Affiliation(s)
- Inga K Koerte
- 1 Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany .,3 Department of Child and Adolescent Psychiatry, Psychosomatic, and Psychotherapy, Ludwig-Maximilian-University , Munich, Germany
| | - Alexander P Lin
- 1 Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,4 Department of Radiology, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts
| | - Marc Muehlmann
- 1 Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany .,3 Department of Child and Adolescent Psychiatry, Psychosomatic, and Psychotherapy, Ludwig-Maximilian-University , Munich, Germany
| | - Sai Merugumala
- 4 Department of Radiology, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts
| | - Huijun Liao
- 4 Department of Radiology, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts
| | - Tyler Starr
- 4 Department of Radiology, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts
| | - David Kaufmann
- 2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany .,5 Department of Radiology, Charité Berlin , Berlin, Germany
| | - Michael Mayinger
- 1 Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany
| | - Denise Steffinger
- 2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany
| | - Barbara Fisch
- 2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany
| | - Susanne Karch
- 6 Department of Psychiatry, Ludwig-Maximilian-University , Munich, Germany
| | - Florian Heinen
- 7 Department of Pediatric Neurology, Dr. von Hauner Children's Hospital, Ludwig-Maximilian-University , Munich, Germany
| | - Birgit Ertl-Wagner
- 2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany
| | - Maximilian Reiser
- 2 Institute for Clinical Radiology, Ludwig-Maximilian-University , Munich, Germany
| | - Robert A Stern
- 8 Departments of Neurology, Neurosurgery, and Anatomy and Neurobiology, Boston University Alzheimer's Disease Center, Boston University School of Medicine , Boston, Massachusetts
| | - Ross Zafonte
- 9 Spaulding Rehabilitation Hospital, Massachusetts General Hospital, Brigham and Women's Hospital, Department of Physical Medicine and Rehabilitation, Harvard Medical School , Boston, Massachusetts
| | - Martha E Shenton
- 1 Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,4 Department of Radiology, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,10 Department of Psychiatry, Brigham and Women's Hospital, and Harvard Medical School , Boston, Massachusetts.,11 VA Boston Healthcare System , Boston, Massachusetts
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De Waele JJ, Lipman J, Akova M, Bassetti M, Dimopoulos G, Kaukonen M, Koulenti D, Martin C, Montravers P, Rello J, Rhodes A, Udy AA, Starr T, Wallis SC, Roberts JA. Risk factors for target non-attainment during empirical treatment with β-lactam antibiotics in critically ill patients. Intensive Care Med 2014; 40:1340-51. [PMID: 25053248 DOI: 10.1007/s00134-014-3403-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/10/2014] [Indexed: 12/27/2022]
Abstract
PURPOSE Risk factors for β-lactam antibiotic underdosing in critically ill patients have not been described in large-scale studies. The objective of this study was to describe pharmacokinetic/pharmacodynamic (PK/PD) target non-attainment envisioning empirical dosing in critically ill patients and considering a worst-case scenario as well as to identify patient characteristics that are associated with target non-attainment. METHODS This analysis uses data from the DALI study, a prospective, multi-centre pharmacokinetic point-prevalence study. For this analysis, we assumed that these were the concentrations that would be reached during empirical dosing, and calculated target attainment using a hypothetical target minimum inhibitory concentration (MIC), namely the susceptibility breakpoint of the least susceptible organism for which that antibiotic is commonly used. PK/PD targets were free drug concentration maintained above the MIC of the suspected pathogen for at least 50 % and 100 % of the dosing interval respectively (50 % and 100 % f T (>MIC)). Multivariable analysis was performed to identify factors associated with inadequate antibiotic exposure. RESULTS A total of 343 critically ill patients receiving eight different β-lactam antibiotics were included. The median (interquartile range) age was 60 (47-73) years, APACHE II score was 18 (13-24). In the hypothetical situation of empirical dosing, antibiotic concentrations remained below the MIC during 50 % and 100 % of the dosing interval in 66 (19.2 %) and 142 (41.4 %) patients respectively. The use of intermittent infusion was significantly associated with increased risk of non-attainment for both targets; creatinine clearance was independently associated with not reaching the 100 % f T( >MIC) target. CONCLUSIONS This study found that-in empirical dosing and considering a worst--case scenario--19 % and 41 % of the patients would not achieve antibiotic concentrations above the MIC during 50 % and 100 % of the dosing interval. The use of intermittent infusion (compared to extended and continuous infusion) was the main determinant of non-attainment for both targets; increasing creatinine clearance was also associated with not attaining concentrations above the MIC for the whole dosing interval. In the light of this study from 68 ICUs across ten countries, we believe current empiric dosing recommendations for ICU patients are inadequate to effectively cover a broad range of susceptible organisms and need to be reconsidered.
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Affiliation(s)
- Jan J De Waele
- Department of Critical Care Medicine, Ghent University Hospital, De Pintelaan 185, 9000, Ghent, Belgium,
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20
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Roberts JA, Stove V, De Waele JJ, Sipinkoski B, McWhinney B, Ungerer JPJ, Akova M, Bassetti M, Dimopoulos G, Kaukonen KM, Koulenti D, Martin C, Montravers P, Rello J, Rhodes A, Starr T, Wallis SC, Lipman J. Variability in protein binding of teicoplanin and achievement of therapeutic drug monitoring targets in critically ill patients: lessons from the DALI Study. Int J Antimicrob Agents 2014; 43:423-30. [PMID: 24630304 DOI: 10.1016/j.ijantimicag.2014.01.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 01/21/2014] [Accepted: 01/23/2014] [Indexed: 12/24/2022]
Abstract
The aims of this study were to describe the variability in protein binding of teicoplanin in critically ill patients as well as the number of patients achieving therapeutic target concentrations. This report is part of the multinational pharmacokinetic DALI Study. Patients were sampled on a single day, with blood samples taken both at the midpoint and the end of the dosing interval. Total and unbound teicoplanin concentrations were assayed using validated chromatographic methods. The lower therapeutic range of teicoplanin was defined as total trough concentrations from 10 to 20 mg/L and the higher range as 10-30 mg/L. Thirteen critically ill patients were available for analysis. The following are the median (interquartile range) total and free concentrations (mg/L): midpoint, total 13.6 (11.2-26.0) and free 1.5 (0.7-2.5); trough, total 11.9 (10.2-22.7) and free 1.8 (0.6-2.6). The percentage free teicoplanin for the mid-dose and trough time points was 6.9% (4.5-15.6%) and 8.2% (5.5-16.4%), respectively. The correlation between total and free antibiotic concentrations was moderate for both the midpoint (ρ = 0.79, P = 0.0021) and trough (ρ = 0.63, P = 0.027). Only 42% and 58% of patients were in the lower and higher therapeutic ranges, respectively. In conclusion, use of standard dosing for teicoplanin leads to inappropriate concentrations in a high proportion of critically ill patients. Variability in teicoplanin protein binding is very high, placing significant doubt on the validity of total concentrations for therapeutic drug monitoring in critically ill patients.
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Affiliation(s)
- J A Roberts
- Burns, Trauma and Critical Care Research Centre, The University of Queensland, Brisbane, Queensland, Australia; Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
| | - V Stove
- Ghent University Hospital, Ghent, Belgium
| | | | - B Sipinkoski
- Queensland Pathology, Brisbane, Queensland, Australia
| | - B McWhinney
- Queensland Pathology, Brisbane, Queensland, Australia
| | - J P J Ungerer
- Queensland Pathology, Brisbane, Queensland, Australia
| | - M Akova
- Hacettepe University, School of Medicine, Ankara, Turkey
| | - M Bassetti
- Azienda Ospedaliera-Universitaria 'Santa Maria della Misericordia', Udine, Italy
| | | | - K-M Kaukonen
- Helsinki University Central Hospital, Helsinki, Finland; Australian and New Zealand Intensive Care Research Centre (ANZIC RC), Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - D Koulenti
- Burns, Trauma and Critical Care Research Centre, The University of Queensland, Brisbane, Queensland, Australia; 'Attikon' University Hospital, Athens, Greece
| | - C Martin
- Hôpital Nord, Marseille, France; AzuRea Group, France
| | - P Montravers
- Centre Hospitalier Universitaire Bichat-Claude Bernard, AP-HP, Université Paris VII, Paris, France
| | - J Rello
- CIBERES, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Rhodes
- St George's Healthcare NHS Trust and St George's University of London, London, UK
| | - T Starr
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - S C Wallis
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - J Lipman
- Burns, Trauma and Critical Care Research Centre, The University of Queensland, Brisbane, Queensland, Australia; Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
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21
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Edelman P, Sparks P, Starr T. Litigation-related Research. Environ Health Perspect 1994; 102:512-4. [PMID: 17539106 PMCID: PMC1569683 DOI: 10.1289/ehp.94102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
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22
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Abstract
Essential genes have been identified in the 1.5 map unit (m.u.) dpy-14-unc-29 region of chromosome 1 in Caenorhabditis elegans. Previous work defined nine genes with visible mutant phenotypes and nine genes with lethal mutant phenotypes. In this study, we have identified an additional 28 essential genes with 97 lethal mutations. The mutations were mapped using eleven duplication breakpoints, eight deficiencies and three-factor recombination experiments. Genes required for the early stages of development were common, with 24 of the 37 essential genes having mutant phenotypes arresting at an early larval stage. Most mutants of a gene have the same time of arrest; only four of the 20 essential genes with multiple alleles have alleles with different phenotypes. From the analysis of complementing alleles of let-389, alleles with the same time-of-arrest phenotype were classified as either hypomorphic or amorphic. Mutants of let-605, let-534 and unc-37 have both uncoordinated and lethal phenotypes, suggesting that these genes are required for the coordination of movement and for viability. The physical and genetic maps in the dpy-14 region were linked by positioning two N2/BO polymorphisms with respect to duplications in the region, and by localizing the right breakpoint of the deficiency hDf8 on the physical map. Using cross-species hybridization to C. briggsae, ten regions of homology have been identified, eight of which are known to be coding regions, based on Northern analysis and/or the isolation of cDNA clones.
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Affiliation(s)
- K S McKim
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Starr T, Gertler MM. Shortened method for the determination of euglobulin lysis time employing Malayan pit viper venom. Thromb Res 1989; 54:511-7. [PMID: 2772869 DOI: 10.1016/0049-3848(89)90222-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- T Starr
- Cardiovascular Research Division, Rusk Institute of Rehabilitation Medicine, New York University Medical Center, New York 10016
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Starr T, Howell AM, McDowall J, Peters K, Rose AM. Isolation and mapping of DNA probes within the linkage group I gene cluster of Caenorhabditis elegans. Genome 1989; 32:365-72. [PMID: 2744447 DOI: 10.1139/g89-456] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have isolated probes for DNA polymorphisms across the linkage group I gene cluster in Caenorhabditis elegans, using Tc1-linkage selection. The probes detect strain polymorphism between the wild-type strains of var. Bristol and var. Bergerac. As a result of mapping the sites hP4, hP5, hP6, hP7, hP9, and sPl, more than 1000 kilobases (kb) of cloned cosmid DNA has been positioned on the genetic map. We found there is more DNA per map unit in the center of the gene cluster than expected on the basis of the genomic average. Furthermore, the amount is not constant across the entire region but reaches a peak in the hP9 unc-13 interval. To find the coding regions, we examined DNA cross-homology between two species, Caenorhabditis elegans and Caenorhabditis briggsae. Approximately one-third of the DNA in the hP5 hP9 interval was examined for coding regions and 21 sequences were identified within 318 kb of DNA.
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Affiliation(s)
- T Starr
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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25
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Starr T, Wood S. A restriction-fragment-length difference detected by the anonymous probe DXS199 exhibits non-Mendelian inheritance. Am J Hum Genet 1988; 42:267-70. [PMID: 2893545 PMCID: PMC1715271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Anonymous DNA probes were isolated from an X chromosome-enriched flow-sorted library. One of these probes, DXS199, identified a restriction-fragment difference that failed to show Mendelian segregation. All normal females were found to have two AvaII fragments of 6.5 kb and 6.0 kb, whereas all normal males had only the 6.5-kb fragment. DNA from a 49,XXXXY male was found to have both 6.0- and 6.5-kb AvaII fragments, in the same 3:1 ratio as seen in the inactive:active number of X chromosomes. This variant, which reflects a structural difference between active and inactive X chromosomes, is likely to be due to a methylation site on the active X chromosome.
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Affiliation(s)
- T Starr
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Starr T, Wood S, Riddell DC, Hamerton JL. Two RFLPs identified by an anonymous sequence (D7S19) (pTS119) from chromosome 7. Nucleic Acids Res 1987; 15:2784. [PMID: 2882481 PMCID: PMC340694 DOI: 10.1093/nar/15.6.2784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Starr T, Wood S. Isolation and characterization of DNA probes from the short arm of the human X chromosome that detect restriction fragment length polymorphisms. Genome 1987; 29:201-5. [PMID: 2884168 DOI: 10.1139/g87-034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have isolated 30 X chromosome specific probes from a flow-sorted library enriched for the human X chromosome. Hybridization to somatic cell hybrids containing different regions of the X chromosome localized nine of these probes to Xp. After testing 185 probe-enzyme combinations, three of the Xp probes were found to detect restriction fragment length polymorphisms.
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Pal PK, Starr T, Gertler MM. Catalytic and regulatory functions of N-bromosuccinimide-modified bovine thrombin. Thromb Res 1984; 36:293-303. [PMID: 6523442 DOI: 10.1016/0049-3848(84)90320-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
At pH 4.1, bovine thrombin reacts rapidly with N-bromo-succinimide to yield modified enzyme containing oxidized tryptophan residue. Both fibrinogen clotting activity and esterase activity are reduced considerably when three moles of tryptophan residues per mole of thrombin are oxidized, but the Michaelis constants for synthetic substrates are not appreciably altered. Reaction of NBS also results in a decrease in the affinity of thrombin for heparin. The dissociation constant for heparin-thrombin complex is increased by 2.6-fold due to the modification of one tryptophan residue. However, the magnitude of the increase in the dissociation constant remains the same for modified enzymes containing approximately two or three oxidized tryptophan residues. The rate constant for the inactivation of thrombin by antithrombin III is increased by 2.5-fold due to the modification of a single tryptophan residue. This increase in rate constant is not further amplified when more than one tryptophan residue is oxidized. In contrast, in the presence of heparin the rate of inactivation of modified and unmodified thrombins by antithrombin III are not significantly different. Thus, the heparin-sensitized inactivation of thrombin by antithrombin III is affected by the modification of one tryptophan residue. Spectrophotometric titrations of the phenolic hydroxyl groups suggest that the structural environments of tyrosyl groups for both unmodified and modified thrombin containing one oxidized tryptophan residue, are similar. The temperature for half loss of catalytic activity of control and NBS-modified thrombin, containing one oxidized tryptophan, are 52 and 51.5 degrees C respectively. It appears that the one tryptophan residue of thrombin is situated at or close to the binding site of heparin.
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Starr T. The baby at birth. Nursing 1984; 2:608-11. [PMID: 6560300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Abstract
The neutralization of heparin by histone and its subfractions has been systematically studied by measuring the effect of heparin on the esterolytic and proteolytic activity of thrombin. These results were compared with protamine sulfate, a most commonly used heparin-neutralizing agent. This study reveals that potencies of different fractions of histone are not similar. The antiheparin potency is in the order: lysine-rich histone greater than crude histone greater than arginine-rich histone. Histone binds strongly to heparin - Sepharose gel. The ability of histone to bind heparin can be utilized to fractionate heparin. By affinity chromatography on histone - Sepharose gel commercial heparin has been fractionated into components having a wide range of anticoagulant activities. The highest activity fraction, eluted around 1.0 NaCl, has 66% higher anticoagulant activity than the commercial heparin used.
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Abstract
Methacholine challenge testing was performed in 20 patients with pulmonary sarcoidosis and 13 normal control subjects. Increased methacholine responsiveness was demonstrated in 10 of 20 patients with sarcoidosis. Sarcoidosis patients with increased reactivity differed from those with normal reactivity in that they had more airway obstruction, smaller vital capacities, and lower single breath diffusing capacities for carbon monoxide. Responders tended to be more symptomatic with wheezing and cough and to have a longer duration of disease, although these differences did not reach statistical significance.
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Yue RH, Starr T, Gertler MM. Separation of heparin into subfractions by DEAE-cellulose chromatography. Thromb Haemost 1980; 42:1452-9. [PMID: 7368152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Commercial porcine heparin can be separated into three distinct subfractions by using DEAE-cellulose chromatography and a stepped salt gradient. Gram quantities of heparin can be fractionated by this technique. All three heparin subfractions can accelerate the inhibition of thrombin by antithrombin III with different efficiency. The specific activities of the high activity heparin, intermediate activity heparin and low activity heparin are 228 units/mg, 142 units/mg and 95 units/mg, respectively. Both the uronic acid content and the quantity of N-SO4 for all three heparin subfractions have been evaluated. The high activity heparin has the lowest uronic acid and N-SO4 content. The successful separation of commercial heparin into three distinct subfractions by means of ion-exchange chromatography suggests that the net charge on these three heparin components will serve as a model system in the elucidation of the structure and activity relationship to the biological function of heparin.
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Yue RH, Gertler MM, Starr T, Koutrouby R. Alteration of plasma antithrombin III levels in ischemic heart disease. Thromb Haemost 1976; 35:598-606. [PMID: 989967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The amount of antithrombin III in plasma was determined quantitatively in 218 males between 45-60 years of age. The mean antithrombin III value was found to be low in the group with low risk for ischemic heart disease, intermediate in the group with high risk for ischemic heart disease and highest in the group with acute myocardial infarction. Concomitant study of kaolin-activated partial thromboplastin time revealed a sharp decrease in its mean value in the group with acute myocardial infarction. The high correlation between antithrombin III and kaolin-activated partial thromboplastin time for the entire population suggests that the development of ischemic heart disease is a gradual process and that failure of the damping mechanism results as an acute event. These findings may be useful in the determination of the coagulation state of these patients.
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Yue RH, Starr T, Gertler MM. The rivanol method for the quantitative determination of antithrombin III in plasma. Thromb Diath Haemorrh 1974; 31:439-51. [PMID: 4423843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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35
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Yue RH, Starr T, Gertler MM. Quantitative determination of total antithrombin 3 in plasma. Thromb Diath Haemorrh 1973; 30:84-92. [PMID: 4788755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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