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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Polster M, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. PLoS Comput Biol 2024; 20:e1012265. [PMID: 39058741 DOI: 10.1371/journal.pcbi.1012265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets.
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Affiliation(s)
- Gisela Gabernet
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Robert Bjornson
- Yale Center for Research Computing, New Haven, Connecticut, United States of America
| | | | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Edel Aron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Noah Y Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Cole Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - David Ladd
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Mark Polster
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Markus C Kowarik
- Department of Neurology and Stroke, Center for Neurology, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
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Planchais C, Fernández I, Chalopin B, Bruel T, Rosenbaum P, Beretta M, Dimitrov JD, Conquet L, Donati F, Prot M, Porrot F, Planas D, Staropoli I, Guivel-Benhassine F, Baquero E, van der Werf S, Haouz A, Simon-Lorière E, Montagutelli X, Maillère B, Rey FA, Guardado-Calvo P, Nozach H, Schwartz O, Mouquet H. Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2. iScience 2024; 27:110354. [PMID: 39071888 PMCID: PMC11277385 DOI: 10.1016/j.isci.2024.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024] Open
Abstract
Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.
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Affiliation(s)
- Cyril Planchais
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Timothée Bruel
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Pierre Rosenbaum
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Maxime Beretta
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
| | - Françoise Porrot
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Delphine Planas
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Isabelle Staropoli
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Florence Guivel-Benhassine
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Eduard Baquero
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Sylvie van der Werf
- CNRS UMR3569, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Cristallography Platform-C2RT, 75015 Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Félix A. Rey
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Olivier Schwartz
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
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Dallan B, Proietto D, De Laurentis M, Gallerani E, Martino M, Ghisellini S, Zurlo A, Volpato S, Govoni B, Borghesi M, Albanese V, Appay V, Bonnini S, Llewellyn-Lacey S, Pacifico S, Grumiro L, Brandolini M, Semprini S, Sambri V, Ladell K, Parry HM, Moss PAH, Price DA, Caputo A, Gavioli R, Nicoli F. Age differentially impacts adaptive immune responses induced by adenoviral versus mRNA vaccines against COVID-19. NATURE AGING 2024:10.1038/s43587-024-00644-w. [PMID: 38918602 DOI: 10.1038/s43587-024-00644-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 05/02/2024] [Indexed: 06/27/2024]
Abstract
Adenoviral and mRNA vaccines encoding the viral spike (S) protein have been deployed globally to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Older individuals are particularly vulnerable to severe infection, probably reflecting age-related changes in the immune system, which can also compromise vaccine efficacy. It is nonetheless unclear to what extent different vaccine platforms are impacted by immunosenescence. Here, we evaluated S protein-specific immune responses elicited by vaccination with two doses of BNT162b2 or ChAdOx1-S and subsequently boosted with a single dose of BNT162b2 or mRNA-1273, comparing age-stratified participants with no evidence of previous infection with SARS-CoV-2. We found that aging profoundly compromised S protein-specific IgG titers and further limited S protein-specific CD4+ and CD8+ T cell immunity as a probable function of progressive erosion of the naive lymphocyte pool in individuals vaccinated initially with BNT162b2. Our results demonstrate that primary vaccination with ChAdOx1-S and subsequent boosting with BNT162b2 or mRNA-1273 promotes sustained immunological memory in older adults and potentially confers optimal protection against coronavirus disease 2019.
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Affiliation(s)
- Beatrice Dallan
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Davide Proietto
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Martina De Laurentis
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Eleonora Gallerani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Mara Martino
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Sara Ghisellini
- Laboratory of Clinical Pathology, University Hospital St. Anna, Ferrara, Italy
| | - Amedeo Zurlo
- Department of Medical Sciences, University of Ferrara, Geriatrics Unit, University Hospital of Ferrara, Ferrara, Italy
| | - Stefano Volpato
- Department of Medical Sciences, University of Ferrara, Geriatrics Unit, University Hospital of Ferrara, Ferrara, Italy
| | - Benedetta Govoni
- Department of Medical Sciences, University of Ferrara, Geriatrics Unit, University Hospital of Ferrara, Ferrara, Italy
| | - Michela Borghesi
- Department of Economics and Management, University of Ferrara, Ferrara, Italy
| | - Valentina Albanese
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
| | - Victor Appay
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, Bordeaux, France
| | - Stefano Bonnini
- Department of Economics and Management, University of Ferrara, Ferrara, Italy
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Salvatore Pacifico
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Laura Grumiro
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Martina Brandolini
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Simona Semprini
- Unit of Microbiology, Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Vittorio Sambri
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Unit of Microbiology, Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Helen M Parry
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Paul A H Moss
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Antonella Caputo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Riccardo Gavioli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Francesco Nicoli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy.
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4
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Zhang J, Askenase P, Jaenisch R, Crumpacker CS. Approaches to pandemic prevention - the chromatin vaccine. Front Immunol 2023; 14:1324084. [PMID: 38143744 PMCID: PMC10739501 DOI: 10.3389/fimmu.2023.1324084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Developing effective vaccines against viral infections have significant impacts on development, prosperity and well-being of human populations. Thus, successful vaccines such as smallpox and polio vaccines, have promoted global societal well-being. In contrast, ineffective vaccines may fuel arguments that retard scientific progress. We aim to stimulate a multilevel discussion on how to develop effective vaccines against recent and future pandemics by focusing on acquired immunodeficiency syndrome (AIDS), coronavirus disease (COVID) and other viral infections. We appeal to harnessing recent achievements in this field specifically towards a cure for current pandemics and prevention of the next pandemics. Among these, we propose to apply the HIV DNA in chromatin format - an end product of aborted HIV integration in episomal forms, i.e., the chromatin vaccines (cVacc), to elicit the epigenetic silencing and memory that prevent viral replication and infection.
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Affiliation(s)
- Jielin Zhang
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Philip Askenase
- Allergy & Clinical Immunology, Yale School of Medicine, New Haven, CT, United States
| | - Rudolf Jaenisch
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Clyde S. Crumpacker
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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Siles N, Schuler M, Maguire C, Amengor D, Nguyen A, Wilen R, Rogers J, Bazzi S, Caslin B, DiPasquale C, Abigania M, Olson E, Creaturo J, Hurley K, Triplett TA, Rousseau JF, Strakowski SM, Wylie D, Maynard J, Ehrlich LIR, Melamed E. SARS-CoV-2 Humoral Immune Responses in Convalescent Individuals Over 12 Months Reveal Severity-Dependent Antibody Dynamics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.05.23299462. [PMID: 38106077 PMCID: PMC10723498 DOI: 10.1101/2023.12.05.23299462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background Understanding the kinetics and longevity of antibody responses to SARS-CoV-2 is critical to informing strategies toward reducing Coronavirus disease 2019 (COVID-19) reinfections, and improving vaccination and therapy approaches. Methods We evaluated antibody titers against SARS-CoV-2 nucleocapsid (N), spike (S), and receptor binding domain (RBD) of spike in 98 convalescent participants who experienced asymptomatic, mild, moderate or severe COVID-19 disease and in 17 non-vaccinated, non-infected controls, using four different antibody assays. Participants were sampled longitudinally at 1, 3, 6, and 12 months post-SARS-CoV-2 positive PCR test. Findings Increasing acute COVID-19 disease severity correlated with higher anti-N and anti-RBD antibody titers throughout 12 months post-infection. Anti-N and anti-RBD titers declined over time in all participants, with the exception of increased anti-RBD titers post-vaccination, and the decay rates were faster in hospitalized compared to non-hospitalized participants. <50% of participants retained anti-N titers above control levels at 12 months, with non-hospitalized participants falling below control levels sooner. Nearly all hospitalized and non-hospitalized participants maintained anti-RBD titers above controls for up to 12 months, suggesting longevity of protection against severe reinfections. Nonetheless, by 6 months, few participants retained >50% of their 1-month anti-N or anti-RBD titers. Vaccine-induced increases in anti-RBD titers were greater in non-hospitalized relative to hospitalized participants. Early convalescent antibody titers correlated with age, but no association was observed between Post-Acute Sequelae of SARS-CoV-2 infection (PASC) status or acute steroid treatment and convalescent antibody titers. Interpretation Hospitalized participants developed higher anti-SARS-CoV-2 antibody titers relative to non-hospitalized participants, a difference that persisted throughout 12 months, despite the faster decline in titers in hospitalized participants. In both groups, while anti-N titers fell below control levels for at least half of the participants, anti-RBD titers remained above control levels for almost all participants over 12 months, demonstrating generation of long-lived antibody responses known to correlate with protection from severe disease across COVID-19 severities. Overall, our findings contribute to the evolving understanding of COVID-19 antibody dynamics. Funding Austin Public Health, NIAAA, Babson Diagnostics, Dell Medical School Startup.
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Affiliation(s)
- Nadia Siles
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Maisey Schuler
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Cole Maguire
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Dzifa Amengor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas
| | - Annalee Nguyen
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Rebecca Wilen
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Jacob Rogers
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Sam Bazzi
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Blaine Caslin
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | | | | | | | - Janelle Creaturo
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Kerin Hurley
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas; Dell Seton Medical Center at the University of Texas, Austin, Texas
| | - Todd A Triplett
- Department of Oncology Dell Medical School, University of Texas at Austin, Austin, Texas; Department of Immunotherapeutics & Biotechnology, School of Pharmacy, Texas Tech University Health Sciences Center, Abilene, TX, USA
| | - Justin F Rousseau
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas; Department of Population Health, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Stephen M Strakowski
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis; Department of Psychiatry, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Dennis Wylie
- Center for Biomedical Research Support, University of Texas at Austin, Austin Texas
| | - Jennifer Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Lauren I R Ehrlich
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas
| | - Esther Melamed
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas
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