1
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. JCI Insight 2023; 8:e174976. [PMID: 37934865 PMCID: PMC10795829 DOI: 10.1172/jci.insight.174976] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq) in profiling mouse autoantibodies. This library was validated using 7 genetically distinct mouse lines across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model nonspecific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate 3 distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities. Second, serum from nonobese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, was enriched in peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous autoantigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 carrying recessive mutations in AIRE. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity profiling.
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Affiliation(s)
| | | | - Haleigh S. Miller
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | | | - David Yu
- Diabetes Center, School of Medicine
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics
- Diabetes Center, School of Medicine
| | | | - Clare L. Abram
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | | | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | | | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics
- Chan Zuckerberg Biohub, San Francisco, California, USA
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2
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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3
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik C, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities. bioRxiv 2023:2023.04.07.535899. [PMID: 37066405 PMCID: PMC10104109 DOI: 10.1101/2023.04.07.535899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq), to profile mouse autoantibodies. This system and library were validated using seven genetic mouse models across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model non-specific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor (BCR)-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate three distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities, lending support to the hypothesis that apoptosis is a shared origin of these antigens. Second, serum from non-obese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, enriched peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous auto-antigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 (APS1) carrying recessive mutations in AIRE. Among these were peptides derived from Perilipin-1, a validated autoimmune biomarker of generalized acquired lipodystrophy in humans. Autoreactivity to Perilipin-1 correlated with lymphocyte infiltration in adipose tissue and underscores the approach in revealing previously unknown specificities. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity.
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Affiliation(s)
- Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - Irina Proekt
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Haleigh S. Miller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA USA
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA USA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - David Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Colin Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - Clare L. Abram
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Clifford A. Lowell
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, NY
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Mark S. Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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4
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Liu J, Laurie MT, Rubio L, Vazquez SE, Sunshine S, Mitchell AM, Hapte-Selassie M, Mann SA, Pilarowski G, Black D, Marquez C, Rojas S, Lionakis MS, Petersen M, Whitman JD, Jain V, Anderson M, Havlir D, DeRisi J. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Dynamics and Immune Responses in a Household of Vaccinated Persons. Clin Infect Dis 2022; 75:e303-e306. [PMID: 35037050 PMCID: PMC8807302 DOI: 10.1093/cid/ciac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
While SARS-CoV-2 vaccines prevent severe disease effectively, postvaccination "breakthrough" COVID-19 infections and transmission among vaccinated individuals remain ongoing concerns. We present an in-depth characterization of transmission and immunity among vaccinated individuals in a household, revealing complex dynamics and unappreciated comorbidities, including autoimmunity to type 1 interferon in the presumptive index case.
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Affiliation(s)
- Jamin Liu
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, California, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Luis Rubio
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Sara E Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Anthea M Mitchell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Matthias Hapte-Selassie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Genay Pilarowski
- The Public Health Company, Oakland, California, USA
- Unidos en Salud, San Francisco, California, USA
| | - Douglas Black
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Carina Marquez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Maya Petersen
- Division of Biostatistics, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Vivek Jain
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Mark Anderson
- Department of Medicine, Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Diane Havlir
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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5
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Guastaferro K, Holloway JL, Trudeau J, Lipson LB, Sunshine S, Noll JG, Pulido ML. Virtual Delivery of A School-Based Child Sexual Abuse Prevention Program: A Pilot Study. J Child Sex Abus 2022; 31:577-592. [PMID: 35959797 PMCID: PMC9421613 DOI: 10.1080/10538712.2022.2112347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/06/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Universal child sexual abuse (CSA) prevention is a public health priority. The prevailing prevention strategy is school-based CSA prevention programming. School closures during the COVID-19 pandemic highlighted the need for flexible modes of delivery, including virtual programs. This pilot examined the virtual delivery of an evidence-based, school-based CSA prevention program, Safe Touches, designed to teach CSA-related knowledge and concepts. Using mixed methods, the pilot sought to determine the feasibility of the virtually delivered CSA prevention program. One school district that had previously received Safe Touches in-person participated. A total of 176 second grade students participated in the virtual workshop. Post-workshop survey responses from virtual (N = 37) and in-person workshops (N = 60) were compared descriptively. Mean item scores and response patterns from students who received the virtual workshop were nominally comparable to the student scores from the in-person workshop. Following the virtual workshop, one teacher notified the research team of a disclosure of CSA. Qualitative input from the facilitator and school staff was positive, indicating high student engagement. Results suggest the viability and feasibility of virtual school-based CSA preventive programs. Investment in virtual modes of delivery would ensure all students have access to CSA prevention programming in the future.
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Affiliation(s)
- Kate Guastaferro
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | | | - Jessica Trudeau
- The New York Society for the Prevention of Cruelty to Children, New York, NY, USA
| | - Lauren B Lipson
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | - S Sunshine
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | - Jennie G Noll
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | - Mary L Pulido
- The New York Society for the Prevention of Cruelty to Children, New York, NY, USA
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6
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Laurie MT, Liu J, Sunshine S, Peng J, Black D, Mitchell AM, Mann SA, Pilarowski G, Zorn KC, Rubio L, Bravo S, Marquez C, Sabatino JJ, Mittl K, Petersen M, Havlir D, DeRisi J. SARS-CoV-2 Variant Exposures Elicit Antibody Responses With Differential Cross-Neutralization of Established and Emerging Strains Including Delta and Omicron. J Infect Dis 2022; 225:1909-1914. [PMID: 34979030 PMCID: PMC8755395 DOI: 10.1093/infdis/jiab635] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
The wide spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of immune responses to different spike protein versions. Here, we compare neutralization of variants of concern, including B.1.617.2 (delta) and B.1.1.529 (omicron), in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure, and exposure to multiple spike variants increases breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies.
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Affiliation(s)
- Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, Berkeley, California, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - James Peng
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Douglas Black
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Anthea M Mitchell
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Genay Pilarowski
- The Public Health Company, Oakland, California, USA
- Unidos en Salud, San Francisco, California, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Luis Rubio
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sara Bravo
- Unidos en Salud, San Francisco, California, USA
| | - Carina Marquez
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, San Francisco, California, USA
| | - Kristen Mittl
- Weill Institute for Neurosciences, Department of Neurology, San Francisco, California, USA
| | - Maya Petersen
- Division of Biostatistics, University of California Berkeley, Berkeley, California, USA
| | - Diane Havlir
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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7
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Zinter MS, Versluys AB, Lindemans CA, Mayday MY, Reyes G, Sunshine S, Chan M, Fiorino EK, Cancio M, Prevaes S, Sirota M, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL. Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates. Sci Transl Med 2022; 14:eabm8646. [PMID: 35263147 PMCID: PMC9487170 DOI: 10.1126/scitranslmed.abm8646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Impaired baseline lung function is associated with mortality after pediatric allogeneic hematopoietic cell transplantation (HCT), yet limited knowledge of the molecular pathways that characterize pretransplant lung function has hindered the development of lung-targeted interventions. In this study, we quantified the association between bronchoalveolar lavage (BAL) metatranscriptomes and paired pulmonary function tests performed a median of 1 to 2 weeks before allogeneic HCT in 104 children in The Netherlands. Abnormal pulmonary function was recorded in more than half the cohort, consisted most commonly of restriction and impaired diffusion, and was associated with both all-cause and lung injury-related mortality after HCT. Depletion of commensal supraglottic taxa, such as Haemophilus, and enrichment of nasal and skin taxa, such as Staphylococcus, in the BAL microbiome were associated with worse measures of lung capacity and gas diffusion. In addition, BAL gene expression signatures of alveolar epithelial activation, epithelial-mesenchymal transition, and down-regulated immunity were associated with impaired lung capacity and diffusion, suggesting a postinjury profibrotic response. Detection of microbial depletion and abnormal epithelial gene expression in BAL enhanced the prognostic utility of pre-HCT pulmonary function tests for the outcome of post-HCT mortality. These findings suggest a potentially actionable connection between microbiome depletion, alveolar injury, and pulmonary fibrosis in the pathogenesis of pre-HCT lung dysfunction.
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Affiliation(s)
- Matt S Zinter
- School of Medicine, Department of Pediatrics, Division of Critical Care Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,School of Medicine, Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, San Francisco, CA 94143, USA
| | - A Birgitta Versluys
- University Medical Center Utrecht, Department of Pediatric Stem Cell Transplantation, Utrecht, 3584 CX, Netherlands.,Princess Maxima Center for Pediatric Oncology, Department of Hematopoietic Cell Transplantation, Utrecht 3584 CX, Netherlands
| | - Caroline A Lindemans
- University Medical Center Utrecht, Department of Pediatric Stem Cell Transplantation, Utrecht, 3584 CX, Netherlands.,Princess Maxima Center for Pediatric Oncology, Department of Hematopoietic Cell Transplantation, Utrecht 3584 CX, Netherlands
| | - Madeline Y Mayday
- Department of Pathology, Graduate Program in Experimental Pathology, and Yale Stem Cell Center, Yale University, New Haven, CT 06510, USA
| | - Gustavo Reyes
- School of Medicine, Department of Pediatrics, Division of Critical Care Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sara Sunshine
- School of Medicine, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marilynn Chan
- School of Medicine, Department of Pediatrics, Division of Pulmonology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elizabeth K Fiorino
- WC Medical College, Department of Pediatrics, Division of Pulmonology, Allergy and Immunology, Cornell University, New York City, NY 10065, USA
| | - Maria Cancio
- WC Medical College, Department of Pediatrics, Cornell University, New York City, NY 10065, USA.,Department of Pediatric Stem Cell Transplantation and Cellular Therapies, Memorial Sloan Kettering Cancer Center, New York City, NY 10065, USA
| | - Sabine Prevaes
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, 3584 CX, Netherlands
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,School of Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael A Matthay
- School of Medicine, Cardiovascular Research Institute, Departments of Medicine and Anesthesiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sandhya Kharbanda
- School of Medicine, Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christopher C Dvorak
- School of Medicine, Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jaap J Boelens
- WC Medical College, Department of Pediatrics, Cornell University, New York City, NY 10065, USA.,Department of Pediatric Stem Cell Transplantation and Cellular Therapies, Memorial Sloan Kettering Cancer Center, New York City, NY 10065, USA
| | - Joseph L DeRisi
- School of Medicine, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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8
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Peng J, Liu J, Mann SA, Mitchell AM, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, Jacobo J, Rojas S, Rojas S, Tulier-Laiwa V, Black D, Martinez J, Naso J, Schwab J, Petersen M, Havlir D, DeRisi J. Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco. Clin Infect Dis 2022; 74:32-39. [PMID: 33788923 PMCID: PMC8083548 DOI: 10.1093/cid/ciab283] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. METHODS SARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during 22 November to 1 December, 2020, and 10-29 January 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants. RESULTS A total of 12 124 tests were performed yielding 1099 positives. From these, 928 high-quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to the "California" or "West Coast" variants (B.1.427 and B.1.429) were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.36 vs 0.29, risk ratio [RR] = 1.28; 95% confidence interval [CI]: 1.00-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.3%). CONCLUSIONS The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants. Summary: We observed a growing prevalence and modestly elevated attack rate for "West Coast" severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.
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Affiliation(s)
- James Peng
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, California, USA
| | - Sabrina A Mann
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Anthea M Mitchell
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Genay Pilarowski
- Department of Pathology, Stanford University, Stanford, California, USA
| | | | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Carina Marquez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Robert Nakamura
- California Department of Public Health, Richmond, California, USA
| | - Luis Rubio
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Diane Jones
- Unidos en Salud, San Francisco, California, USA
| | - Jon Jacobo
- Unidos en Salud, San Francisco, California, USA
| | | | - Susy Rojas
- Unidos en Salud, San Francisco, California, USA
| | | | - Douglas Black
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Jamie Naso
- Unidos en Salud, San Francisco, California, USA
| | - Joshua Schwab
- Division of Biostatistics, University of California, Berkeley, Berkeley, California, USA
| | - Maya Petersen
- Division of Biostatistics, University of California, Berkeley, Berkeley, California, USA
| | - Diane Havlir
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - IDseq Team
- Chan Zuckerberg Initiative, Redwood City, CaliforniaUSA
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9
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Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Detweiler A, Jones NG, Wu B, Darmanis S, Lynch SV, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. medRxiv 2021:2021.03.23.21253487. [PMID: 33791731 PMCID: PMC8010763 DOI: 10.1101/2021.03.23.21253487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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10
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Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CB, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. Cell Rep Med 2021; 2:100288. [PMID: 33969321 PMCID: PMC8091032 DOI: 10.1016/j.xcrm.2021.100288] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [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: 12/08/2020] [Revised: 03/03/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022]
Abstract
Individuals with coronavirus disease 2019 (COVID-19) frequently develop neurological symptoms, but the biological underpinnings of these phenomena are unknown. Through single-cell RNA sequencing (scRNA-seq) and cytokine analyses of cerebrospinal fluid (CSF) and blood from individuals with COVID-19 with neurological symptoms, we find compartmentalized, CNS-specific T cell activation and B cell responses. All affected individuals had CSF anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies whose target epitopes diverged from serum antibodies. In an animal model, we find that intrathecal SARS-CoV-2 antibodies are present only during brain infection and not elicited by pulmonary infection. We produced CSF-derived monoclonal antibodies from an individual with COVID-19 and found that these monoclonal antibodies (mAbs) target antiviral and antineural antigens, including one mAb that reacted to spike protein and neural tissue. CSF immunoglobulin G (IgG) from 5 of 7 patients showed antineural reactivity. This immune survey reveals evidence of a compartmentalized immune response in the CNS of individuals with COVID-19 and suggests a role of autoimmunity in neurologic sequelae of COVID-19.
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Affiliation(s)
- Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Christopher M. Bartley
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan D. Chow
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Ruoyi Jiang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Ravi Dandekar
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P. Loudermilk
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- University of California, Berkeley—University of California, San Francisco Gradate Program in Bioengineering, Berkeley, CA, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Isobel A. Hawes
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Bonny D. Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Trung Huynh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Lindsay McAlpine
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Nur-Taz Rahman
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Bertie Geng
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | | | - Benjamin Goldman-Israelow
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale University School of Medicine, New Haven, CT, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Brett S. Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Jessa R. Alexander
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Juan A. Gallego
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Todd Lencz
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Hannah Walsh
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Anne E. Wapniarski
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Subhasis Mohanty
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jieun Oh
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Albert I. Ko
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Steven H. Kleinstein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - John Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Shelli F. Farhadian
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
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11
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Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. Res Sq 2021:rs.3.rs-380803. [PMID: 34013247 PMCID: PMC8132240 DOI: 10.21203/rs.3.rs-380803/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing (scRNA-seq) we assessed lower respiratory tract immune responses and microbiome dynamics in 28 COVID-19 patients, 15 of whom developed VAP, and eight critically ill uninfected controls. Two days before VAP onset we observed a transcriptional signature of bacterial infection. Two weeks prior to VAP onset, following intubation, we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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Affiliation(s)
- Alexandra Tsitsiklis
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Catherine Devoe
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Sophia Levan
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Rajani Ghale
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alejandra Jauregui
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aartik Sarma
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Thomas J. Deiss
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sidney Carrillo
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - K. Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Aleksandra Leligdowicz
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Norman Jones
- Department of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Bing Wu
- Genentech, Inc. San Francisco, CA, USA
| | | | - Michael A. Matthay
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Susan V. Lynch
- Department of Gastroenterology, University of California, San Francisco, CA, USA
- Benioff Center for Microbiome Medicine, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Carolyn M. Hendrickson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten N. Kangelaris
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - David J. Erle
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Lung Biology Center, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Oren Rosenberg
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles R. Langelier
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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12
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Pilarowski G, Lebel P, Sunshine S, Liu J, Crawford E, Marquez C, Rubio L, Chamie G, Martinez J, Peng J, Black D, Wu W, Pak J, Laurie MT, Jones D, Miller S, Jacobo J, Rojas S, Rojas S, Nakamura R, Tulier-Laiwa V, Petersen M, Havlir DV, DeRisi J. Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco. J Infect Dis 2021; 223:1139-1144. [PMID: 33394052 PMCID: PMC7799021 DOI: 10.1093/infdis/jiaa802] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/27/2020] [Indexed: 12/04/2022] Open
Abstract
We evaluated the performance of the Abbott BinaxNOW rapid antigen test for coronavirus disease 2019 (Binax-CoV2) to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured severe acute respiratory syndrome coronavirus 2 yielded a human observable threshold between 1.6 × 104-4.3 × 104 viral RNA copies (cycle threshold [Ct], 30.3–28.8). Among 878 subjects tested, 3% (26 of 878) were positive by reverse-transcription polymerase chain reaction, of whom 15 of 26 had a Ct <30, indicating high viral load; of these, 40% (6 of 15) were asymptomatic. Using this Ct threshold (<30) for Binax-CoV2 evaluation, the sensitivity of Binax-CoV2 was 93.3% (95% confidence interval, 68.1%–99.8%) (14 of 15) and the specificity was 99.9% (99.4%–99.9%) (855 of 856).
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Affiliation(s)
- Genay Pilarowski
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Paul Lebel
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California
| | - Carina Marquez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Luis Rubio
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jackie Martinez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - James Peng
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Douglas Black
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - John Pak
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Diane Jones
- Unidos en Salud, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jon Jacobo
- Latino Task Force-COVID-19, San Francisco, California, USA
| | - Susana Rojas
- Latino Task Force-COVID-19, San Francisco, California, USA
| | - Susy Rojas
- Latino Task Force-COVID-19, San Francisco, California, USA
| | - Robert Nakamura
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | | | - Maya Petersen
- Division of Epidemiology and Biostatistics, University of California, Berkeley, Berkeley, California, USA
| | - Diane V Havlir
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Joseph DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
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13
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Zinter MS, Lindemans CA, Versluys BA, Mayday MY, Sunshine S, Reyes G, Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL. The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury. Blood 2021; 137:1679-1689. [PMID: 33512420 PMCID: PMC7995292 DOI: 10.1182/blood.2020009246] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Lung injury after pediatric allogeneic hematopoietic cell transplantation (HCT) is a common and disastrous complication that threatens long-term survival. To develop strategies to prevent lung injury, novel tools are needed to comprehensively assess lung health in HCT candidates. Therefore, this study analyzed biospecimens from 181 pediatric HCT candidates who underwent routine pre-HCT bronchoalveolar lavage (BAL) at the University Medical Center Utrecht between 2005 and 2016. BAL fluid underwent metatranscriptomic sequencing of microbial and human RNA, and unsupervised clustering and generalized linear models were used to associate microbiome gene expression data with the development of post-HCT lung injury. Microbe-gene correlations were validated using a geographically distinct cohort of 18 pediatric HCT candidates. The cumulative incidence of post-HCT lung injury varied significantly according to 4 pre-HCT pulmonary metatranscriptome clusters, with the highest incidence observed in children with pre-HCT viral enrichment and innate immune activation, as well as in children with profound microbial depletion and concomitant natural killer/T-cell activation (P < .001). In contrast, children with pre-HCT pulmonary metatranscriptomes containing diverse oropharyngeal taxa and lacking inflammation rarely developed post-HCT lung injury. In addition, activation of epithelial-epidermal differentiation, mucus production, and cellular adhesion were associated with fatal post-HCT lung injury. In a separate validation cohort, associations among pulmonary respiratory viral load, oropharyngeal taxa, and pulmonary gene expression were recapitulated; the association with post-HCT lung injury needs to be validated in an independent cohort. This analysis suggests that assessment of the pre-HCT BAL fluid may identify high-risk pediatric HCT candidates who may benefit from pathobiology-targeted interventions.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care Medicine and
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, CA
| | - Caroline A Lindemans
- Department of Pediatric Stem Cell Transplantation, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Hematopoietic Cell Transplantation, Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Birgitta A Versluys
- Department of Pediatric Stem Cell Transplantation, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Hematopoietic Cell Transplantation, Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Madeline Y Mayday
- Graduate Program in Experimental Pathology, and Yale Stem Cell Center, Department of Pathology, Yale University, New Haven, CT
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, School of Medicine
| | | | - Marina Sirota
- Bakar Computational Health Sciences Institute, and
- Department of Pediatrics, School of Medicine, University of California, San Francisco, CA
| | - Anil Sapru
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, University of California, Los Angeles, CA
| | - Michael A Matthay
- Department of Medicine and
- Department of Anesthesiology, Cardiovascular Research Institute, School of Medicine, University of California, San Francisco, CA
| | - Sandhya Kharbanda
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, CA
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, CA
| | - Jaap J Boelens
- Department of Pediatric Stem Cell Transplantation and Cellular Therapies, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, School of Medicine
- Chan Zuckerberg Biohub, San Francisco, CA
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14
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Peng J, Mann SA, Mitchell AM, Liu J, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Team ID, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, Jacobo J, Rojas S, Rojas S, Tulier-Laiwa V, Black D, Martinez J, Naso J, Schwab J, Petersen M, Havlir D, DeRisi J. Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. medRxiv 2021:2021.03.01.21252705. [PMID: 33688689 PMCID: PMC7941666 DOI: 10.1101/2021.03.01.21252705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Sequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. METHODS SARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants. RESULTS A total of 12,124 tests were performed yielding 1,099 positives. From these, 811 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to "West Coast" variants were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.357 vs 0.294, RR=1.29; 95% CI:1.01-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.1%). CONCLUSIONS The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants; however, additional laboratory and epidemiological studies are required to better understand differences between these variants. SUMMARY We observed a growing prevalence and elevated attack rate for "West Coast" SARS-CoV-2 variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.
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Affiliation(s)
- James Peng
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sabrina A Mann
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Anthea M Mitchell
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA 94720, USA
| | - Matthew T. Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Genay Pilarowski
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Lucy M. Li
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Eric D. Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - IDseq Team
- Chan Zuckerberg Initiative, Redwood City, CA 94063, USA
| | - Carina Marquez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert Nakamura
- California Department of Public Health, Richmond, CA 94804, USA
| | - Luis Rubio
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane Jones
- Unidos en Salud, San Francisco, CA 94143, USA
| | - Jon Jacobo
- Unidos en Salud, San Francisco, CA 94143, USA
| | | | - Susy Rojas
- Unidos en Salud, San Francisco, CA 94143, USA
| | | | - Douglas Black
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Jamie Naso
- Unidos en Salud, San Francisco, CA 94143, USA
| | - Joshua Schwab
- Division of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maya Petersen
- Division of Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diane Havlir
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
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15
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Samuel RM, Majd H, Richter MN, Ghazizadeh Z, Zekavat SM, Navickas A, Ramirez JT, Asgharian H, Simoneau CR, Bonser LR, Koh KD, Garcia-Knight M, Tassetto M, Sunshine S, Farahvashi S, Kalantari A, Liu W, Andino R, Zhao H, Natarajan P, Erle DJ, Ott M, Goodarzi H, Fattahi F. Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. Cell Stem Cell 2020; 27:876-889.e12. [PMID: 33232663 PMCID: PMC7670929 DOI: 10.1016/j.stem.2020.11.009] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/17/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 infection has led to a global health crisis, and yet our understanding of the disease and potential treatment options remains limited. The infection occurs through binding of the virus with angiotensin converting enzyme 2 (ACE2) on the cell membrane. Here, we established a screening strategy to identify drugs that reduce ACE2 levels in human embryonic stem cell (hESC)-derived cardiac cells and lung organoids. Target analysis of hit compounds revealed androgen signaling as a key modulator of ACE2 levels. Treatment with antiandrogenic drugs reduced ACE2 expression and protected hESC-derived lung organoids against SARS-CoV-2 infection. Finally, clinical data on COVID-19 patients demonstrated that prostate diseases, which are linked to elevated androgen, are significant risk factors and that genetic variants that increase androgen levels are associated with higher disease severity. These findings offer insights on the mechanism of disproportionate disease susceptibility in men and identify antiandrogenic drugs as candidate therapeutics for COVID-19.
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Affiliation(s)
- Ryan M Samuel
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Homa Majd
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Mikayla N Richter
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Zaniar Ghazizadeh
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale School of Medicine, New Haven, CT 06510, USA
| | - Seyedeh Maryam Zekavat
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program of Computational Biology & Bioinformatics, Yale University, New Haven, CT 06510, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Jonathan T Ramirez
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Hosseinali Asgharian
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | | | - Luke R Bonser
- Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kyung Duk Koh
- Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Sina Farahvashi
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Ali Kalantari
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Wei Liu
- Program of Computational Biology & Bioinformatics, Yale University, New Haven, CT 06510, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hongyu Zhao
- Program of Computational Biology & Bioinformatics, Yale University, New Haven, CT 06510, USA; Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David J Erle
- Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94158, USA.
| | - Faranak Fattahi
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; Program in Craniofacial Biology, University of California, San Francisco, CA 94110, USA.
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16
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Pilarowski G, Lebel P, Sunshine S, Liu J, Crawford E, Marquez C, Rubio L, Chamie G, Martinez J, Peng J, Black D, Wu W, Pak J, Laurie MT, Jones D, Miller S, Jacobo J, Rojas S, Rojas S, Nakamura R, Tulier-Laiwa V, Petersen M, Havlir DV, DeRisi J. Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco. medRxiv 2020:2020.11.02.20223891. [PMID: 33173911 PMCID: PMC7654907 DOI: 10.1101/2020.11.02.20223891] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We evaluated the performance of the Abbott BinaxNOW™ Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6×104-4.3×104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.
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Affiliation(s)
- Genay Pilarowski
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Paul Lebel
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, University of California San Francisco, CA 94143
| | - Carina Marquez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Luis Rubio
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel Chamie
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jackie Martinez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James Peng
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Douglas Black
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wesley Wu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - John Pak
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Matthew T. Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
| | - Diane Jones
- Unidos en Salud, San Francisco, CA 94143, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco CA 94131, USA
| | - Jon Jacobo
- Latino Task Force-COVID-19, San Francisco, CA 94110, USA
| | - Susana Rojas
- Latino Task Force-COVID-19, San Francisco, CA 94110, USA
| | - Susy Rojas
- Latino Task Force-COVID-19, San Francisco, CA 94110, USA
| | - Robert Nakamura
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, CA, 94804, USA
| | | | - Maya Petersen
- Division of Epidemiology and Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diane V. Havlir
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Joseph DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
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17
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Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL. Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. PLoS Pathog 2020; 16:e1008966. [PMID: 33112933 PMCID: PMC7592773 DOI: 10.1371/journal.ppat.1008966] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Emily D. Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Irene Acosta
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Erika C. Anderson
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shaun Arevalo
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel Asarnow
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Shannon Axelrod
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Patrick Ayscue
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Camillia S. Azimi
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Caleigh M. Azumaya
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Stefanie Bachl
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Iris Bachmutsky
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Aparna Bhaduri
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Jeremy Bancroft Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Astrid Behnert
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Ryan M. Boileau
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Saumya R. Bollam
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Alain R. Bonny
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - David Booth
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | | | - David Brown
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Bryan Buie
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Cassandra E. Burnett
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lauren E. Byrnes
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Katelyn A. Cabral
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
| | - Joana P. Cabrera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Saharai Caldera
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
| | - Gabriela Canales
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Agnes Protacio Chan
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Christopher R. Chang
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Arthur Charles-Orszag
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Carly Cheung
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Unseng Chio
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Eric D. Chow
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Y. Rose Citron
- University of California, Berkeley, California, United States of America
| | - Allison Cohen
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Lillian B. Cohn
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Experimental Medicine, San Francisco, California, United States of America
| | - Charles Chiu
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Mitchel A. Cole
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Daniel N. Conrad
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Angela Constantino
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Andrew Cote
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Spyros Darmanis
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Rebekah L. Dial
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Shen Dong
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Elias M. Duarte
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - David Dynerman
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Rebecca Egger
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Alison Fanton
- University of California, Berkeley, California, United States of America
| | - Stacey M. Frumm
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
- University of California San Francisco, Institute for Neurodegenerative Diseases, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Gladstone Institute, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Aileen W. Li
- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- eSix Development, Oakland, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Gladstone Institute, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | | | - Noelle Narez
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Division of Infectious Disease, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
| | - Peter Suslow
- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, Department of Laboratory Medicine, San Francisco, California, United States of America
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- Joint Bioengineering Graduate Program, University of California, Berkeley, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
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- University of California San Francisco, School of Medicine, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- University of California San Francisco, Department of Biochemistry and Biophysics, San Francisco, California, United States of America
- * E-mail:
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Vazquez SE, Ferré EMN, Scheel DW, Sunshine S, Miao B, Mandel-Brehm C, Quandt Z, Chan AY, Cheng M, German M, Lionakis M, DeRisi JL, Anderson MS. Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq. eLife 2020; 9:e55053. [PMID: 32410729 PMCID: PMC7228772 DOI: 10.7554/elife.55053] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to more common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from a cohort of people with APS1 and discovered multiple common antibody targets. These novel APS1 autoantigens exhibit tissue-restricted expression, including expression in enteroendocrine cells, pineal gland, and dental enamel. Using detailed clinical phenotyping, we find novel associations between autoantibodies and organ-restricted autoimmunity, including a link between anti-KHDC3L autoantibodies and premature ovarian insufficiency, and between anti-RFX6 autoantibodies and diarrheal-type intestinal dysfunction. Our study highlights the utility of PhIP-Seq for extensively interrogating antigenic repertoires in human autoimmunity and the importance of antigen discovery for improved understanding of disease mechanisms.
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Affiliation(s)
- Sara E Vazquez
- Medical Scientist Training Program, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Elise MN Ferré
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - David W Scheel
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Brenda Miao
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Zoe Quandt
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Alice Y Chan
- Department of Pediatrics, University of California, San FranciscoSan FranciscoUnited States
| | - Mickie Cheng
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
| | - Michael German
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Michail Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Mark S Anderson
- Diabetes Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Medicine, University of California, San FranciscoSan FranciscoUnited States
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Salani M, Urbina F, Brenner A, Morini E, Shetty R, Gallagher CS, Law EA, Sunshine S, Finneran DJ, Johnson G, Minor L, Slaugenhaupt SA. Development of a Screening Platform to Identify Small Molecules That Modify ELP1 Pre-mRNA Splicing in Familial Dysautonomia. SLAS Discov 2018; 24:57-67. [PMID: 30085848 DOI: 10.1177/2472555218792264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Familial dysautonomia (FD) is an autonomic and sensory neuropathy caused by a mutation in the splice donor site of intron 20 of the ELP1 gene. Variable skipping of exon 20 leads to a tissue-specific reduction in the level of ELP1 protein. We have shown that the plant cytokinin kinetin is able to increase cellular ELP1 protein levels in vivo and in vitro through correction of ELP1 splicing. Studies in FD patients determined that kinetin is not a practical therapy due to low potency and rapid elimination. To identify molecules with improved potency and efficacy, we developed a cell-based luciferase splicing assay by inserting renilla (Rluc) and firefly (Fluc) luciferase reporters into our previously well-characterized ELP1 minigene construct. Evaluation of the Fluc/Rluc signal ratio enables a fast and accurate way to measure exon 20 inclusion. Further, we developed a secondary assay that measures ELP1 splicing in FD patient-derived fibroblasts. Here we demonstrate the quality and reproducibility of our screening method. Development and implementation of this screening platform has allowed us to efficiently screen for new compounds that robustly and specifically enhance ELP1 pre-mRNA splicing.
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Affiliation(s)
- Monica Salani
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Fabio Urbina
- 2 Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony Brenner
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Elisabetta Morini
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA.,3 Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Ranjit Shetty
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - C Scott Gallagher
- 3 Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Emily A Law
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Sara Sunshine
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Dylan J Finneran
- 4 Byrd Alzheimer's Institute College of Medicine Department of Molecular Pharmacology & Physiology, University of South Florida, Tampa, FL, USA
| | | | - Lisa Minor
- 6 In Vitro Strategies LLC, Flemington, NJ, USA
| | - Susan A Slaugenhaupt
- 1 Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Boston, MA, USA.,3 Department of Neurology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
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Seferovic MD, San Martin CS, Tamhankar M, Li T, Hu M, Blackman M, Martyn C, Sunshine S, Suter M, Tardif S, Chiu C, Patterson J, Aagaard K. 871: Primary Placental Trophoblasts from Primate Species are Permissive for Zika Virus (ZIKV) Replication. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2017.11.408] [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: 11/25/2022]
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Bekyarova E, Davis M, Burch T, Itkis ME, Zhao B, Sunshine S, Haddon RC. Chemically Functionalized Single-Walled Carbon Nanotubes as Ammonia Sensors. J Phys Chem B 2004. [DOI: 10.1021/jp0471857] [Citation(s) in RCA: 304] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Bekyarova
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
| | - M. Davis
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
| | - T. Burch
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
| | - M. E. Itkis
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
| | - B. Zhao
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
| | - S. Sunshine
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
| | - R. C. Haddon
- Carbon Solutions Inc., Riverside, CA; Smiths Detection, Pasadena, California, and Center for Nanoscale Science and Engineering, Departments of Chemistry and Chemical & Environmental Engineering, University of California, Riverside, California 92521-0403
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22
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Abstract
OBJECTIVE To compare the pattern of injury between men and women in seven collegiate sports to determine if gender-specific factors exist which could be modified to reduce the risk of injury to female athletes. DESIGN Retrospective cohort study of injury reports compiled by certified athletic trainers between Fall 1980 and Spring 1995. SETTING An NCAA division III College. PARTICIPANTS Eighteen to 22 year-old male and female college athletes competing in seven like sports (basketball, cross-country running, soccer, swimming, tennis, track and water polo) at the intercollegiate level, playing similar number of contests and using the same facilities. MAIN OUTCOME MEASURES Analyses of injury patterns, classified by sport and anatomic location, for men and women in seven like sports. RESULTS A total of 3,767 participants were included in the study, with 1874 sports-related injuries reported among the men and women's teams. Of these injuries, 856 (45.7%) were sustained by female and 1018 (54.3%) by male athletes. Overall, no statistically significant gender difference was found for injuries per 100 participant-years (52.5 for female athlete versus 47.7 for males). A statistically significant gender difference in injury incidence (p < 0.001) was seen for two sports: swimming and water polo. Female swimmers reported more back/neck, shoulder, hip, knee and foot injuries: and female water polo players reported more shoulder injuries. When evaluating all sports concurrently, female athletes reported a higher rate of hip, lower-leg and shoulder injuries, while male athletes reported a higher rate of thigh injuries. CONCLUSION Except for some minor gender differences in total injuries for two sports and several differences in total injuries by anatomic location, our data suggest very little difference in the pattern of injury between men and women competing in comparable sports. The increased rate of shoulder injury among female swimmers probably resulted from the more rigorous training philosophy of their coach. Thus, no gender-specific recommendations can be suggested for decreasing the incidence of injury to female athletes competing in these sports.
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Affiliation(s)
- R E Sallis
- Department of Family Medicine, Kaiser Permanente Medical Center, Fontana, Californa, USA.
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Sallis RE, Wang Q, Sunshine S, Jones K. THE ANNUAL INCIDENCE OF CONCUSSION IN HIGH SCHOOL FOOTBALL PLAYERS. Med Sci Sports Exerc 2001. [DOI: 10.1097/00005768-200105001-00821] [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: 11/25/2022]
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Abstract
We present a case of pyomyositis in an otherwise healthy 5-year-old child that underscores the potential for serious, life-threatening complications. Pyomyositis of the gluteal, psoas, and iliacus muscles was associated with osteomyelitis, septic arthritis, a large inferior vena cava thrombus, septic pulmonary emboli, and eventual pneumonia. Primary pyomyositis is a purulent infection of striated muscle thought to be caused by seeding from a transient bacteremia. The focal infection typically forms an abscess that generally responds to intravenous antibiotics and occasionally requires adjunctive computed tomography-guided aspiration and drainage. This localized infectious process rarely produces further sequelae unless treatment is delayed. Pyomyositis is rare in healthy individuals and requires a high clinical suspicion in patients who present with fever, leukocytosis, and localized pain.
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Affiliation(s)
- S Romeo
- Department of Family Practice, Kaiser Permanente, Fontana, Calif 92335, USA
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25
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Aviv JE, Kim T, Thomson JE, Sunshine S, Kaplan S, Close LG. Fiberoptic endoscopic evaluation of swallowing with sensory testing (FEESST) in healthy controls. Dysphagia 1998; 13:87-92. [PMID: 9513302 DOI: 10.1007/pl00009561] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The purpose of this study was to introduce a new method of bedside assessment of both the motor and sensory components of swallowing called fiberoptic endoscopic evaluation of swallowing with sensory testing (FEESST). This approach combines the established bedside endoscopic swallowing evaluation with a more recently described technique that allows objective determination of laryngopharyngeal (LP) sensory discrimination thresholds by delivering air pulse stimuli to the mucosa innervated by the superior laryngeal nerve via a flexible endoscope. A prospective study was conducted of FEESST in 20 healthy control subjects, mean age of 34 +/- 11 years. LP sensory thresholds were defined as either normal (< 4.0 mmHg air pulse pressure [APP]), moderate deficit (4.0-6.0 mmHg APP), or severe deficits (> 6.0 mmHg APP). Subsequent to LP sensory testing, food of varying consistencies, mixed with green food coloring, was given and attention was paid to spillage, laryngeal penetration, pharyngeal residue, aspiration, and reflux. Therapeutic maneuvers such as postural changes and airway protection techniques were performed on each subject to determine if the assessed swallowing parameters were affected by maneuvers. All patients completed the study; all had normal LP sensory discrimination thresholds (2.9 +/- 0.7 mmHg APP). There were no instances of spillage, laryngeal penetration, or aspiration. Two of 20 subjects had pharyngeal residue and 2 of 20 had reflux. Institution of therapeutic maneuvers resulted in a predictable change in the endoscopic view of the laryngopharyngeal anatomy. FEESST provides comprehensive, objective sensory and motor information about deglutition in the bedside setting and might have implications for the bedside diagnosis and management of patients with dysphagia.
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Affiliation(s)
- J E Aviv
- Department of Otolaryngology-Head and Neck Surgery, Columbia-Presbyterian Medical Center, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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Aviv JE, Sacco RL, Mohr JP, Thompson JL, Levin B, Sunshine S, Thomson J, Close LG. Laryngopharyngeal sensory testing with modified barium swallow as predictors of aspiration pneumonia after stroke. Laryngoscope 1997; 107:1254-60. [PMID: 9292613 DOI: 10.1097/00005537-199709000-00018] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Improved diagnostic tests that can accurately identify subjects at high risk for aspiration pneumonia (AP) are needed. One measure of this accuracy is the false-negative rate (FNR), which determines the failure of a test to identify a group at high risk. This study compares FNRs for AP among dysphagic stroke patients for two prognostic techniques: modified barium swallow (MBS) alone and MBS combined with laryngopharyngeal sensory discrimination testing (MBS + LPSDT). MBS and LPSDT were performed within 4 weeks of stroke in 20 subjects who were prospectively followed for at least 2 years to identify the frequency of AP. MBS identified 10 patients as not at risk based on the finding of no aspiration on initial MBS; four of these patients developed AP (FNR = 40%). MBS + LPSDT identified five patients as not at risk based on the findings of neither aspiration nor bilateral sensory deficits; none of these patients developed AP (FNR = 0%). The combination of MBS criterion (aspiration) with the LPSDT criterion (bilateral sensory deficits) improves prognostication of outcome in dysphagic stroke patients by identifying a subgroup at high risk for developing AP (nonaspirators with bilateral deficits).
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Affiliation(s)
- J E Aviv
- Department of Otolaryngology-Head and Neck Surgery, Columbia-Presbyterian Medical Center College of Physicians and Surgeons, Columbia University, New York, New York 10032, U.S.A
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Abstract
1. Following injection of trehalose into the bloodstream, no trehalose was found in urine of rabbits until the concentration of trehalose in blood exceeded 0.6 mg/ml. 2. Absence of trehalose in urine of the rabbit when the concentration of the sugar in blood is elevated supports the hypothesis that renal trehalase functions as a digestive enzyme in kidney. 3. The rat does not possess renal trehalase, and excretion of trehalose was in direct relation to the concentration of trehalose in blood. 4. There are differences in expression of the disaccharidases in kidney and intestine although they share many structural and enzymatic characteristics.
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Affiliation(s)
- J Riby
- Department of Nutritional Sciences, University of California, Berkeley 94720
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Mandich ML, DeSantolo AM, Fleming RM, Marsh P, Nakahara S, Sunshine S, Kwo J, Hong M, Boone T, Kometani TY, Martinez-Miranda L. Superconducting properties of a 27-A. Phys Rev B Condens Matter 1988; 38:5031-5034. [PMID: 9946908 DOI: 10.1103/physrevb.38.5031] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Grader GS, Gyorgy EM, Gallagher PK, O'Bryan HM, Johnson DW, Sunshine S, Zahurak SM, Jin S, Sherwood RC. Crystallographic, thermodynamic, and transport properties of the Bi2Sr3-xCaxCu2O8+ delta superconductor. Phys Rev B Condens Matter 1988; 38:757-760. [PMID: 9945247 DOI: 10.1103/physrevb.38.757] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Eibschutz M, Murphy DW, Sunshine S, Zahurak SM, Grodkiewicz AW. Electronic structure of Eu in the high-Tc superconductor Ba2EuCu. Phys Rev B Condens Matter 1987; 35:8714-8715. [PMID: 9941231 DOI: 10.1103/physrevb.35.8714] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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31
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Batlogg B, Cava RJ, Jayaraman A, Kourouklis GA, Sunshine S, Murphy DW, Rupp LW, Chen HS, White A, Short KT, Mujsce AM, Rietman EA. Isotope effect in the high-Tc superconductors Ba2YCu3O7 and Ba2EuCu3O7. Phys Rev Lett 1987; 58:2333-2336. [PMID: 10034718 DOI: 10.1103/physrevlett.58.2333] [Citation(s) in RCA: 144] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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32
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Murphy DW, Sunshine S, Cava RJ, Batlogg B, Zahurak SM, Schneemeyer LF. New superconducting cuprate perovskites. Phys Rev Lett 1987; 58:1888-1890. [PMID: 10034564 DOI: 10.1103/physrevlett.58.1888] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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33
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Siegrist T, Sunshine S, Murphy DW, Cava RJ, Zahurak SM. Crystal structure of the high-Tc superconductor Ba2YCu3O9- delta. Phys Rev B Condens Matter 1987; 35:7137-7139. [PMID: 9940981 DOI: 10.1103/physrevb.35.7137] [Citation(s) in RCA: 230] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Cava RJ, Batlogg B, Murphy DW, Sunshine S, Siegrist T, Remeika JP, Rietman EA, Zahurak S, Espinosa GP. Bulk superconductivity at 91 K in single-phase oxygen-deficient perovskite Ba2YCu. Phys Rev Lett 1987; 58:1676-1679. [PMID: 10034505 DOI: 10.1103/physrevlett.58.1676] [Citation(s) in RCA: 423] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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