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Saha A, Chakraborty T, Rahimikollu J, Xiao H, de Oliveira LBP, Hand TW, Handali S, Secor WE, A O Fraga L, Fairley JK, Das J, Sarkar A. Deep humoral profiling coupled to interpretable machine learning unveils diagnostic markers and pathophysiology of schistosomiasis. Sci Transl Med 2024; 16:eadk7832. [PMID: 39292803 DOI: 10.1126/scitranslmed.adk7832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/27/2024] [Accepted: 08/27/2024] [Indexed: 09/20/2024]
Abstract
Schistosomiasis, a highly prevalent parasitic disease, affects more than 200 million people worldwide. Current diagnostics based on parasite egg detection in stool detect infection only at a late stage, and current antibody-based tests cannot distinguish past from current infection. Here, we developed and used a multiplexed antibody profiling platform to obtain a comprehensive repertoire of antihelminth humoral profiles including isotype, subclass, Fc receptor (FcR) binding, and glycosylation profiles of antigen-specific antibodies. Using Essential Regression (ER) and SLIDE, interpretable machine learning methods, we identified latent factors (context-specific groups) that move beyond biomarkers and provide insights into the pathophysiology of different stages of schistosome infection. By comparing profiles of infected and healthy individuals, we identified modules with unique humoral signatures of active disease, including hallmark signatures of parasitic infection such as elevated immunoglobulin G4 (IgG4). However, we also captured previously uncharacterized humoral responses including elevated FcR binding and specific antibody glycoforms in patients with active infection, helping distinguish them from those without active infection but with equivalent antibody titers. This signature was validated in an independent cohort. Our approach also uncovered two distinct endotypes, nonpatent infection and prior infection, in those who were not actively infected. Higher amounts of IgG1 and FcR1/FcR3A binding were also found to be likely protective of the transition from nonpatent to active infection. Overall, we unveiled markers for antibody-based diagnostics and latent factors underlying the pathogenesis of schistosome infection. Our results suggest that selective antigen targeting could be useful in early detection, thus controlling infection severity.
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Affiliation(s)
- Anushka Saha
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Trirupa Chakraborty
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Integrative Systems Biology Program, Pittsburgh, PA 15213, USA
| | - Javad Rahimikollu
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Joint CMU-Pitt Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, USA
| | - Lorena B Pereira de Oliveira
- Programa Multicêntrico de Bioquímica e Biologia Molecular (PMBqBM), Federal University of Juiz de Fora, Campus Governador Valadares, Juiz de Fora, Minas Gerais 36036-900, Brazil
- University Vale do Rio Doce, Governador Valadares, Minas Gerais 36036-900, Brazil
| | - Timothy W Hand
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sukwan Handali
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - W Evan Secor
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lucia A O Fraga
- Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais 36036-900, Brazil
| | - Jessica K Fairley
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Aniruddh Sarkar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30309, USA
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2
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Walker IS, Dini S, Aitken EH, Damelang T, Hasang W, Alemu A, Jensen ATR, Rambhatla JS, Opi DH, Duffy MF, Takashima E, Harawa V, Tsuboi T, Simpson JA, Mandala W, Taylor TE, Seydel KB, Chung AW, Rogerson SJ. A systems serology approach to identifying key antibody correlates of protection from cerebral malaria in Malawian children. BMC Med 2024; 22:388. [PMID: 39267089 PMCID: PMC11396342 DOI: 10.1186/s12916-024-03604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) proteins are expressed on the surface of infected erythrocytes, mediating parasite sequestration in the vasculature. PfEMP1 is a major target of protective antibodies, but the features of the antibody response are poorly defined. METHODS In Malawian children with cerebral or uncomplicated malaria, we characterized the antibody response to 39 recombinant PfEMP1 Duffy binding like (DBL) domains or cysteine-rich interdomain regions (CIDRs) in detail, including measures of antibody classes, subclasses, and engagement with Fcγ receptors and complement. Using elastic net regularized logistic regression, we identified a combination of seven antibody targets and Fc features that best distinguished between children with cerebral and uncomplicated malaria. To confirm the role of the selected targets and Fc features, we measured antibody-dependent neutrophil and THP-1 cell phagocytosis of intercellular adhesion molecule-1 (ICAM-1) and endothelial protein C (EPCR) co-binding infected erythrocytes. RESULTS The selected features distinguished between children with cerebral and uncomplicated malaria with 87% accuracy (median, 80-96% interquartile range) and included antibody to well-characterized DBLβ3 domains and a less well-characterized CIDRγ12 domain. The abilities of antibodies to engage C1q and FcγRIIIb, rather than levels of IgG, correlated with protection. In line with a role of FcγRIIIb binding antibodies to DBLβ3 domains, antibody-dependent neutrophil phagocytosis of ICAM-1 and EPCR co-binding IE was higher in uncomplicated malaria (15% median, 8-38% interquartile range) compared to cerebral malaria (7%, 30-15%, p < 0.001). CONCLUSIONS Antibodies associated with protection from cerebral malaria target a subset of PfEMP1 domains. The Fc features of protective antibody response include engagement of FcγRIIIb and C1q, and ability to induce antibody-dependent neutrophil phagocytosis of infected erythrocytes. Identifying the targets and Fc features of protective immunity could facilitate the development of PfEMP1-based therapeutics for cerebral malaria.
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Affiliation(s)
- Isobel S Walker
- Department of Medicine, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Saber Dini
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Elizabeth H Aitken
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Timon Damelang
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Wina Hasang
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Agersew Alemu
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Anja T R Jensen
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Janavi S Rambhatla
- Department of Medicine, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - D Herbert Opi
- Department of Medicine, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
- Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
- Department of Immunology, Monash University, Melbourne, VIC, Australia
| | - Michael F Duffy
- Department of Medicine, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Visopo Harawa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Takafumi Tsuboi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wilson Mandala
- Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo, Malawi
| | - Terrie E Taylor
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- College of Osteopathic Medicine, Michigan State University, East Lansing, USA
| | - Karl B Seydel
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
- College of Osteopathic Medicine, Michigan State University, East Lansing, USA
| | - Amy W Chung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Stephen J Rogerson
- Department of Medicine, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia.
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia.
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3
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Wang LT, Idris AH, Kisalu NK, Crompton PD, Seder RA. Monoclonal antibodies to the circumsporozoite proteins as an emerging tool for malaria prevention. Nat Immunol 2024; 25:1530-1545. [PMID: 39198635 DOI: 10.1038/s41590-024-01938-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/17/2024] [Indexed: 09/01/2024]
Abstract
Despite various public health strategies, malaria caused by Plasmodium falciparum parasites remains a major global health challenge that requires development of new interventions. Extended half-life human monoclonal antibodies targeting the P. falciparum circumsporozoite protein on sporozoites, the infective form of malaria parasites, prevent malaria in rodents and humans and have been advanced into clinical development. The protective epitopes on the circumsporozoite protein targeted by monoclonal antibodies have been defined. Cryogenic electron and multiphoton microscopy have enabled mechanistic structural and functional investigations of how antibodies bind to the circumsporozoite protein and neutralize sporozoites. Moreover, innovations in bioinformatics and antibody engineering have facilitated enhancement of antibody potency and durability. Here, we summarize the latest scientific advances in understanding how monoclonal antibodies to the circumsporozoite protein prevent malaria and highlight existing clinical data and future plans for how this emerging intervention can be used alone or alongside existing antimalarial interventions to control malaria across at-risk populations.
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Affiliation(s)
- Lawrence T Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Azza H Idris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
| | - Neville K Kisalu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- PATH's Center for Vaccine Innovation and Access, Washington, DC, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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4
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Duffy PE, Gorres JP, Healy SA, Fried M. Malaria vaccines: a new era of prevention and control. Nat Rev Microbiol 2024:10.1038/s41579-024-01065-7. [PMID: 39025972 DOI: 10.1038/s41579-024-01065-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2024] [Indexed: 07/20/2024]
Abstract
Malaria killed over 600,000 people in 2022, a death toll that has not improved since 2015. Additionally, parasites and mosquitoes resistant to existing interventions are spreading across Africa and other regions. Vaccines offer hope to reduce the mortality burden: the first licensed malaria vaccines, RTS,S and R21, will be widely deployed in 2024 and should substantially reduce childhood deaths. In this Review, we provide an overview of the malaria problem and the Plasmodium parasite, then describe the RTS,S and R21 vaccines (the first vaccines for any human parasitic disease), summarizing their benefits and limitations. We explore next-generation vaccines designed using new knowledge of malaria pathogenesis and protective immunity, which incorporate antigens and platforms to elicit effective immune responses against different parasite stages in human or mosquito hosts. We describe a decision-making process that prioritizes malaria vaccine candidates for development in a resource-constrained environment. Future vaccines might improve upon the protective efficacy of RTS,S or R21 for children, or address the wider malaria scourge by preventing pregnancy malaria, reducing the burden of Plasmodium vivax or accelerating malaria elimination.
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Affiliation(s)
- Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - J Patrick Gorres
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sara A Healy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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5
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Rahimikollu J, Xiao H, Rosengart A, Rosen ABI, Tabib T, Zdinak PM, He K, Bing X, Bunea F, Wegkamp M, Poholek AC, Joglekar AV, Lafyatis RA, Das J. SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains. Nat Methods 2024; 21:835-845. [PMID: 38374265 DOI: 10.1038/s41592-024-02175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
Modern multiomic technologies can generate deep multiscale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make analyses and integration of high-dimensional omic datasets challenging. Here we present Significant Latent Factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, and has rigorous false discovery rate control. Using SLIDE on single-cell and spatial omic datasets, we uncovered significant interacting latent factors underlying a range of molecular, cellular and organismal phenotypes. SLIDE outperforms/performs at least as well as a wide range of state-of-the-art approaches, including other latent factor approaches. More importantly, it provides biological inference beyond prediction that other methods do not afford. Thus, SLIDE is a versatile engine for biological discovery from modern multiomic datasets.
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Affiliation(s)
- Javad Rahimikollu
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - AnnaElaine Rosengart
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron B I Rosen
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul M Zdinak
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kun He
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xin Bing
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Florentina Bunea
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Marten Wegkamp
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
- Department of Mathematics, Cornell University, Ithaca, NY, USA
| | - Amanda C Poholek
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Alok V Joglekar
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Robert A Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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6
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Barrett JR, Silk SE, Mkindi CG, Kwiatkowska KM, Hou MM, Lias AM, Kalinga WF, Mtaka IM, McHugh K, Bardelli M, Davies H, King LDW, Edwards NJ, Chauhan VS, Mukherjee P, Rwezaula S, Chitnis CE, Olotu AI, Minassian AM, Draper SJ, Nielsen CM. Analyses of human vaccine-specific circulating and bone marrow-resident B cell populations reveal benefit of delayed vaccine booster dosing with blood-stage malaria antigens. Front Immunol 2024; 14:1193079. [PMID: 38299155 PMCID: PMC10827869 DOI: 10.3389/fimmu.2023.1193079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 12/11/2023] [Indexed: 02/02/2024] Open
Abstract
We have previously reported primary endpoints of a clinical trial testing two vaccine platforms for the delivery of Plasmodium vivax malaria DBPRII: viral vectors (ChAd63, MVA), and protein/adjuvant (PvDBPII with 50µg Matrix-M™ adjuvant). Delayed boosting was necessitated due to trial halts during the pandemic and provides an opportunity to investigate the impact of dosing regimens. Here, using flow cytometry - including agnostic definition of B cell populations with the clustering tool CITRUS - we report enhanced induction of DBPRII-specific plasma cell and memory B cell responses in protein/adjuvant versus viral vector vaccinees. Within protein/adjuvant groups, delayed boosting further improved B cell immunogenicity compared to a monthly boosting regimen. Consistent with this, delayed boosting also drove more durable anti-DBPRII serum IgG. In an independent vaccine clinical trial with the P. falciparum malaria RH5.1 protein/adjuvant (50µg Matrix-M™) vaccine candidate, we similarly observed enhanced circulating B cell responses in vaccinees receiving a delayed final booster. Notably, a higher frequency of vaccine-specific (putatively long-lived) plasma cells was detected in the bone marrow of these delayed boosting vaccinees by ELISPOT and correlated strongly with serum IgG. Finally, following controlled human malaria infection with P. vivax parasites in the DBPRII trial, in vivo growth inhibition was observed to correlate with DBPRII-specific B cell and serum IgG responses. In contrast, the CD4+ and CD8+ T cell responses were impacted by vaccine platform but not dosing regimen and did not correlate with in vivo growth inhibition in a challenge model. Taken together, our DBPRII and RH5 data suggest an opportunity for protein/adjuvant dosing regimen optimisation in the context of rational vaccine development against pathogens where protection is antibody-mediated.
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Affiliation(s)
- Jordan R. Barrett
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Sarah E. Silk
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | - Mimi M. Hou
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Amelia M. Lias
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | - Kirsty McHugh
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Martino Bardelli
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Hannah Davies
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Lloyd D. W. King
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Nick J. Edwards
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Virander S. Chauhan
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | | | | | - Chetan E. Chitnis
- Unité de Biologie de Plasmodium et Vaccins, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Angela M. Minassian
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Simon J. Draper
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Carolyn M. Nielsen
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
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7
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Xiao H, Rosen A, Chhibbar P, Moise L, Das J. From bench to bedside via bytes: Multi-omic immunoprofiling and integration using machine learning and network approaches. Hum Vaccin Immunother 2023; 19:2282803. [PMID: 38100557 PMCID: PMC10730168 DOI: 10.1080/21645515.2023.2282803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
A significant surge in research endeavors leverages the vast potential of high-throughput omic technology platforms for broad profiling of biological responses to vaccines and cutting-edge immunotherapies and stem-cell therapies under development. These profiles capture different aspects of core regulatory and functional processes at different scales of resolution from molecular and cellular to organismal. Systems approaches capture the complex and intricate interplay between these layers and scales. Here, we summarize experimental data modalities, for characterizing the genome, epigenome, transcriptome, proteome, metabolome, and antibody-ome, that enable us to generate large-scale immune profiles. We also discuss machine learning and network approaches that are commonly used to analyze and integrate these modalities, to gain insights into correlates and mechanisms of natural and vaccine-mediated immunity as well as therapy-induced immunomodulation.
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Affiliation(s)
- Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron Rosen
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Prabal Chhibbar
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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8
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Ouaked N, Demoitié MA, Godfroid F, Mortier MC, Vanloubbeeck Y, Temmerman ST. Non-clinical evaluation of local and systemic immunity induced by different vaccination strategies of the candidate tuberculosis vaccine M72/AS01. Tuberculosis (Edinb) 2023; 143:102425. [PMID: 38180028 DOI: 10.1016/j.tube.2023.102425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 01/06/2024]
Abstract
A new efficacious tuberculosis vaccine targeting adolescents/adults represents an urgent medical need. The M72/AS01E vaccine candidate protected half of the latently-infected adults against progression to pulmonary tuberculosis in a Phase IIb trial (NCT01755598). We report that three immunizations of mice, two weeks apart, with AS01-adjuvanted M72 induced polyfunctional, Th1-cytokine-expressing M72-specific CD4+/CD8+ T cells in blood and lungs, with the highest frequencies in lungs. Antigen-dose reductions across the three vaccinations skewed pulmonary CD4+ T-cell profiles towards IL-17 expression. In blood, reducing antigen and adjuvant doses of only the third injection (to 1/5th or 1/25th of those of the first injections) did not significantly alter CD4+ T-cell/antibody responses; applying a 10-week delay for the fractional third dose enhanced antibody titers. Delaying a full-dose booster enhanced systemic CD4+ T-cell and antibody responses. Cross-reactivity with PPE and non-PPE proteins was assessed, as Mycobacterium tuberculosis (Mtb) virulence factors and evasion mechanisms are often associated with PE/PPE proteins, to which Mtb39a (contained in M72) belongs. In silico/in vivo analyses revealed that M72/AS01 induced cross-reactive systemic CD4+ T-cell responses to epitopes in a non-vaccine antigen (putative latency-associated Mtb protein PPE24/Rv1753c). These preclinical data describing novel mechanisms of M72/AS01-induced immunity could guide future clinical development of the vaccine.
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Affiliation(s)
- Nadia Ouaked
- GSK, Rue de l'Institut 89, 1330, Rixensart, Belgium
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9
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Berkowitz JS, Tabib T, Xiao H, Sadej GM, Khanna D, Fuschiotti P, Lafyatis RA, Das J. Cell Type-Specific Biomarkers of Systemic Sclerosis Disease Severity Capture Cell-Intrinsic and Cell-Extrinsic Circuits. Arthritis Rheumatol 2023; 75:1819-1830. [PMID: 37096444 PMCID: PMC10543405 DOI: 10.1002/art.42536] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/04/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is a multifactorial autoimmune fibrotic disorder involving complex rewiring of cell-intrinsic and cell-extrinsic signaling coexpression networks involving a range of cell types. However, the rewired circuits as well as corresponding cell-cell interactions remain poorly understood. To address this, we used a predictive machine learning framework to analyze single-cell RNA-sequencing data from 24 SSc patients across the severity spectrum as quantified by the modified Rodnan skin score (MRSS). METHODS We used a least absolute shrinkage and selection operator (LASSO)-based predictive machine learning approach on the single-cell RNA-sequencing data set to identify predictive biomarkers of SSc severity, both across and within cell types. The use of L1 regularization helps prevent overfitting on high-dimensional data. Correlation network analyses were coupled to the LASSO model to identify cell-intrinsic and cell-extrinsic co-correlates of the identified biomarkers of SSc severity. RESULTS We found that the uncovered cell type-specific predictive biomarkers of MRSS included previously implicated genes in fibroblast and myeloid cell subsets (e.g., SFPR2+ fibroblasts and monocytes), as well as novel gene biomarkers of MRSS, especially in keratinocytes. Correlation network analyses revealed novel cross-talk between immune pathways and implicated keratinocytes in addition to fibroblast and myeloid cells as key cell types involved in SSc pathogenesis. We then validated the uncovered association of key gene expression and protein markers in keratinocytes, KRT6A and S100A8, with SSc skin disease severity. CONCLUSION Our global systems analyses reveal previously uncharacterized cell-intrinsic and cell-extrinsic signaling coexpression networks underlying SSc severity that involve keratinocytes, myeloid cells, and fibroblasts.
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Affiliation(s)
- Jacob S Berkowitz
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gabrielle M. Sadej
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dinesh Khanna
- Division of Rheumatology, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Patrizia Fuschiotti
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A. Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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10
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Nziza N, Tran TM, DeRiso EA, Dolatshahi S, Herman JD, de Lacerda L, Junqueira C, Lieberman J, Ongoiba A, Doumbo S, Kayentao K, Traore B, Crompton PD, Alter G. Accumulation of Neutrophil Phagocytic Antibody Features Tracks With Naturally Acquired Immunity Against Malaria in Children. J Infect Dis 2023; 228:759-768. [PMID: 37150885 PMCID: PMC10503956 DOI: 10.1093/infdis/jiad115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/21/2023] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND Studies have demonstrated the protective role of antibodies against malaria. Young children are known to be particularly vulnerable to malaria, pointing to the evolution of naturally acquired clinical immunity over time. However, whether changes in antibody functionality track with the acquisition of naturally acquired malaria immunity remains incompletely understood. METHODS Using systems serology, we characterized sporozoite- and merozoite-specific antibody profiles of uninfected Malian children before the malaria season who differed in their ability to control parasitemia and fever following Plasmodium falciparum (Pf) infection. We then assessed the contributions of individual traits to overall clinical outcomes, focusing on the immunodominant sporozoite CSP and merozoite AMA1 and MSP1 antigens. RESULTS Humoral immunity evolved with age, with an expansion of both magnitude and functional quality, particularly within blood-stage phagocytic antibody activity. Moreover, concerning clinical outcomes postinfection, protected children had higher antibody-dependent neutrophil activity along with higher levels of MSP1-specific IgG3 and IgA and CSP-specific IgG3 and IgG4 prior to the malaria season. CONCLUSIONS These data point to the natural evolution of functional humoral immunity to Pf with age and highlight particular antibody Fc-effector profiles associated with the control of malaria in children, providing clues for the design of next-generation vaccines or therapeutics.
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Affiliation(s)
- Nadege Nziza
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
| | - Tuan M Tran
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Ryan White Center for Pediatric Infectious Disease and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elizabeth A DeRiso
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
| | - Sepideh Dolatshahi
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
| | - Jonathan D Herman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
| | - Luna de Lacerda
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
| | - Caroline Junqueira
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG, Brazil
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Aissata Ongoiba
- Malaria Research and Training Centre, Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- Malaria Research and Training Centre, Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boubacar Traore
- Malaria Research and Training Centre, Mali International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, USA
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11
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Purcell RA, Theisen RM, Arnold KB, Chung AW, Selva KJ. Polyfunctional antibodies: a path towards precision vaccines for vulnerable populations. Front Immunol 2023; 14:1183727. [PMID: 37600816 PMCID: PMC10433199 DOI: 10.3389/fimmu.2023.1183727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023] Open
Abstract
Vaccine efficacy determined within the controlled environment of a clinical trial is usually substantially greater than real-world vaccine effectiveness. Typically, this results from reduced protection of immunologically vulnerable populations, such as children, elderly individuals and people with chronic comorbidities. Consequently, these high-risk groups are frequently recommended tailored immunisation schedules to boost responses. In addition, diverse groups of healthy adults may also be variably protected by the same vaccine regimen. Current population-based vaccination strategies that consider basic clinical parameters offer a glimpse into what may be achievable if more nuanced aspects of the immune response are considered in vaccine design. To date, vaccine development has been largely empirical. However, next-generation approaches require more rational strategies. We foresee a generation of precision vaccines that consider the mechanistic basis of vaccine response variations associated with both immunogenetic and baseline health differences. Recent efforts have highlighted the importance of balanced and diverse extra-neutralising antibody functions for vaccine-induced protection. However, in immunologically vulnerable populations, significant modulation of polyfunctional antibody responses that mediate both neutralisation and effector functions has been observed. Here, we review the current understanding of key genetic and inflammatory modulators of antibody polyfunctionality that affect vaccination outcomes and consider how this knowledge may be harnessed to tailor vaccine design for improved public health.
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Affiliation(s)
- Ruth A. Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Robert M. Theisen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Amy W. Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Kevin J. Selva
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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12
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Nielsen CM, Barrett JR, Davis C, Fallon JK, Goh C, Michell AR, Griffin C, Kwok A, Loos C, Darko S, Laboune F, Tekman M, Diouf A, Miura K, Francica JR, Ransier A, Long CA, Silk SE, Payne RO, Minassian AM, Lauffenburger DA, Seder RA, Douek DC, Alter G, Draper SJ. Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine. JCI Insight 2023; 8:e163859. [PMID: 36692019 PMCID: PMC9977309 DOI: 10.1172/jci.insight.163859] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023] Open
Abstract
Modifications to vaccine delivery that increase serum antibody longevity are of great interest for maximizing efficacy. We have previously shown that a delayed fractional (DFx) dosing schedule (0-1-6 month) - using AS01B-adjuvanted RH5.1 malaria antigen - substantially improves serum IgG durability as compared with monthly dosing (0-1-2 month; NCT02927145). However, the underlying mechanism and whether there are wider immunological changes with DFx dosing were unclear. Here, PfRH5-specific Ig and B cell responses were analyzed in depth through standardized ELISAs, flow cytometry, systems serology, and single-cell RNA-Seq (scRNA-Seq). Data indicate that DFx dosing increases the magnitude and durability of circulating PfRH5-specific B cells and serum IgG1. At the peak antibody magnitude, DFx dosing was distinguished by a systems serology feature set comprising increased FcRn binding, IgG avidity, and proportion of G2B and G2S2F IgG Fc glycans, alongside decreased IgG3, antibody-dependent complement deposition, and proportion of G1S1F IgG Fc glycan. Concomitantly, scRNA-Seq data show a higher CDR3 percentage of mutation from germline and decreased plasma cell gene expression in circulating PfRH5-specific B cells. Our data, therefore, reveal a profound impact of DFx dosing on the humoral response and suggest plausible mechanisms that could enhance antibody longevity, including improved FcRn binding by serum Ig and a potential shift in the underlying cellular response from circulating short-lived plasma cells to nonperipheral long-lived plasma cells.
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Affiliation(s)
| | | | - Christine Davis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Jonathan K. Fallon
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
| | - Cyndi Goh
- University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ashlin R. Michell
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
| | - Catherine Griffin
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Andrew Kwok
- University of Oxford, Oxford, Oxfordshire, United Kingdom
- Wellcome Center for Human Genetics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Carolin Loos
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
| | - Samuel Darko
- Vaccine Research Center, NIAID/NIH, Bethesda, Maryland, USA
| | - Farida Laboune
- Vaccine Research Center, NIAID/NIH, Bethesda, Maryland, USA
| | - Mehmet Tekman
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, Maryland, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, Maryland, USA
| | | | - Amy Ransier
- Vaccine Research Center, NIAID/NIH, Bethesda, Maryland, USA
| | - Carole A. Long
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, Maryland, USA
| | - Sarah E. Silk
- University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ruth O. Payne
- University of Oxford, Oxford, Oxfordshire, United Kingdom
| | | | | | | | | | - Galit Alter
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
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13
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Niaré K, Chege T, Rosenkranz M, Mwai K, Saßmannshausen Z, Odera D, Nyamako L, Tuju J, Alfred T, Waitumbi JN, Ogutu B, Sirima SB, Awandare G, Kouriba B, Rayner JC, Osier FHA. Characterization of a novel Plasmodium falciparum merozoite surface antigen and potential vaccine target. Front Immunol 2023; 14:1156806. [PMID: 37122725 PMCID: PMC10140549 DOI: 10.3389/fimmu.2023.1156806] [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: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Detailed analyses of genetic diversity, antigenic variability, protein localization and immunological responses are vital for the prioritization of novel malaria vaccine candidates. Comprehensive approaches to determine the most appropriate antigen variants needed to provide broad protection are challenging and consequently rarely undertaken. Methods Here, we characterized PF3D7_1136200, which we named Asparagine-Rich Merozoite Antigen (ARMA) based on the analysis of its sequence, localization and immunogenicity. We analyzed IgG and IgM responses against the common variants of ARMA in independent prospective cohort studies in Burkina Faso (N = 228), Kenya (N = 252) and Mali (N = 195) using a custom microarray, Div-KILCHIP. Results We found a marked population structure between parasites from Africa and Asia. African isolates shared 34 common haplotypes, including a dominant pair although the overall selection pressure was directional (Tajima's D = -2.57; Fu and Li's F = -9.69; P < 0.02). ARMA was localized to the merozoite surface, IgG antibodies induced Fc-mediated degranulation of natural killer cells and strongly inhibited parasite growth in vitro. We found profound serological diversity, but IgG and IgM responses were highly correlated and a hierarchical clustering analysis identified only three major serogroups. Protective IgG and IgM antibodies appeared to target both cross-reactive and distinct epitopes across variants. However, combinations of IgG and IgM antibodies against selected variants were associated with complete protection against clinical episodes of malaria. Discussion Our systematic strategy exploits genomic data to deduce the handful of antigen variants with the strongest potential to induce broad protection and may be broadly applicable to other complex pathogens for which effective vaccines remain elusive.
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Affiliation(s)
- Karamoko Niaré
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
- Malaria Research and Training Centre (MRTC), Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
- *Correspondence: Karamoko Niaré, ; Faith H. A. Osier,
| | - Timothy Chege
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
| | - Micha Rosenkranz
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kennedy Mwai
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
- Epidemiology and Biostatistics Division, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Zoe Saßmannshausen
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Odera
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Lydia Nyamako
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
| | - James Tuju
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
| | - Tiono Alfred
- Public Health Department, Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso
| | - John N. Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate-Africa/Kenya Medical Research Institute, Kisumu, Kenya
| | - Bernhards Ogutu
- Kenya Medical Research Institute, Centre for Clinical Research, Nairobi, Kenya
| | | | - Gordon Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Bourema Kouriba
- Malaria Research and Training Centre (MRTC), Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- Centre d’Infectiologie Charles Mérieux-Mali, Bamako, Mali
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Faith H. A. Osier
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research—Coast, Kilifi, Kenya
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
- *Correspondence: Karamoko Niaré, ; Faith H. A. Osier,
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14
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Ray A, Das J, Wenzel SE. Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning. Cell Rep Med 2022; 3:100857. [PMID: 36543110 PMCID: PMC9798025 DOI: 10.1016/j.xcrm.2022.100857] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/24/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
There is unprecedented opportunity to use machine learning to integrate high-dimensional molecular data with clinical characteristics to accurately diagnose and manage disease. Asthma is a complex and heterogeneous disease and cannot be solely explained by an aberrant type 2 (T2) immune response. Available and emerging multi-omics datasets of asthma show dysregulation of different biological pathways including those linked to T2 mechanisms. While T2-directed biologics have been life changing for many patients, they have not proven effective for many others despite similar biomarker profiles. Thus, there is a great need to close this gap to understand asthma heterogeneity, which can be achieved by harnessing and integrating the rich multi-omics asthma datasets and the corresponding clinical data. This article presents a compendium of machine learning approaches that can be utilized to bridge the gap between predictive biomarkers and actual causal signatures that are validated in clinical trials to ultimately establish true asthma endotypes.
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Affiliation(s)
- Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, 3459 Fifth Avenue, MUH 628 NW, Pittsburgh, PA 15213, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Jishnu Das
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Center for Systems Immunology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sally E Wenzel
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, 3459 Fifth Avenue, MUH 628 NW, Pittsburgh, PA 15213, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Environmental Medicine and Occupational Health, School of Public Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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15
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Duffy PE. Current approaches to malaria vaccines. Curr Opin Microbiol 2022; 70:102227. [PMID: 36343566 PMCID: PMC11127243 DOI: 10.1016/j.mib.2022.102227] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The complex Plasmodium life cycle offers different vaccine approaches with distinct parasitological and clinical effects. The approaches and their rationales were established decades ago: vaccines targeting pre-erythrocytic (sporozoite and liver-stage) parasites prevent infection, those to blood-stage parasites reduce disease, and those to sexual-stage parasites or mosquito vector reduce transmission and eliminate malaria through herd immunity. The pre-erythrocytic RTS,S vaccine (Mosquirix, GlaskoSmithKline (GSK)), recommended by WHO in 2021, reduces clinical malaria in children. Knowledge of parasite biology, host-parasite interactions, and immune mechanisms is informing new concepts to improve on RTS,S and to target other parasite stages. This review emphasizes vaccine approaches and candidates currently in the clinic or likely to enter clinical testing soon.
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Affiliation(s)
- Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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16
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Bell GJ, Goel V, Essone P, Dosoo D, Adu B, Mensah BA, Gyaase S, Wiru K, Mougeni F, Osei M, Minsoko P, Sinai C, Niaré K, Juliano JJ, Hudgens M, Ghansah A, Kamthunzi P, Mvalo T, Agnandji ST, Bailey JA, Asante KP, Emch M. Malaria Transmission Intensity Likely Modifies RTS, S/AS01 Efficacy Due to a Rebound Effect in Ghana, Malawi, and Gabon. J Infect Dis 2022; 226:1646-1656. [PMID: 35899811 PMCID: PMC10205900 DOI: 10.1093/infdis/jiac322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND RTS,S/AS01 is the first malaria vaccine to be approved and recommended for widespread implementation by the World Health Organization (WHO). Trials reported lower vaccine efficacies in higher-incidence sites, potentially due to a "rebound" in malaria cases in vaccinated children. When naturally acquired protection in the control group rises and vaccine protection in the vaccinated wanes concurrently, malaria incidence can become greater in the vaccinated than in the control group, resulting in negative vaccine efficacies. METHODS Using data from the 2009-2014 phase III trial (NCT00866619) in Lilongwe, Malawi; Kintampo, Ghana; and Lambaréné, Gabon, we evaluate this hypothesis by estimating malaria incidence in each vaccine group over time and in varying transmission settings. After estimating transmission intensities using ecological variables, we fit models with 3-way interactions between vaccination, time, and transmission intensity. RESULTS Over time, incidence decreased in the control group and increased in the vaccine group. Three-dose efficacy in the lowest-transmission-intensity group (0.25 cases per person-year [CPPY]) decreased from 88.2% to 15.0% over 4.5 years, compared with 81.6% to -27.7% in the highest-transmission-intensity group (3 CPPY). CONCLUSIONS These findings suggest that interventions, including the fourth RTS,S dose, that protect vaccinated individuals during the potential rebound period should be implemented for high-transmission settings.
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Affiliation(s)
- Griffin J Bell
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Paulin Essone
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - David Dosoo
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | | | - Kenneth Wiru
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Fabrice Mougeni
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Musah Osei
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Pamela Minsoko
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Cyrus Sinai
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael Hudgens
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | | | - Selidji Todagbe Agnandji
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | | | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
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17
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Feng G, Kurtovic L, Agius PA, Aitken EH, Sacarlal J, Wines BD, Hogarth PM, Rogerson SJ, Fowkes FJI, Dobaño C, Beeson JG. Induction, decay, and determinants of functional antibodies following vaccination with the RTS,S malaria vaccine in young children. BMC Med 2022; 20:289. [PMID: 36002841 PMCID: PMC9402280 DOI: 10.1186/s12916-022-02466-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/06/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND RTS,S is the first malaria vaccine recommended for implementation among young children at risk. However, vaccine efficacy is modest and short-lived. Antibodies play the major role in vaccine-induced immunity, but knowledge on the induction, decay, and determinants of antibody function is limited, especially among children. Antibodies that promote opsonic phagocytosis and other cellular functions appear to be important contributors to RTS,S immunity. METHODS We studied a phase IIb trial of RTS,S/AS02 conducted in young children in malaria-endemic regions of Mozambique. We evaluated the induction of antibodies targeting the circumsporozoite protein (CSP, vaccine antigen) that interact with Fcγ-receptors (FcRγs) and promote phagocytosis (neutrophils, monocytes, THP-1 cells), antibody-dependent respiratory burst (ADRB) by neutrophils, and natural killer (NK) cell activity, as well as the temporal kinetics of responses over 5 years of follow-up (ClinicalTrials.gov registry number NCT00197041). RESULTS RTS,S vaccination induced CSP-specific IgG with FcγRIIa and FcγRIII binding activity and promoted phagocytosis by neutrophils, THP-1 monocytes, and primary human monocytes, neutrophil ADRB activity, and NK cell activation. Responses were highly heterogenous among children, and the magnitude of neutrophil phagocytosis by antibodies was relatively modest, which may reflect modest vaccine efficacy. Induction of functional antibodies was lower among children with higher malaria exposure. Functional antibody magnitude and the functional activity of antibodies largely declined within a year post-vaccination, and decay were highest in the first 6 months, consistent with the decline in vaccine efficacy over that time. Decay rates varied for different antibody parameters and decay was slower for neutrophil phagocytosis. Biostatistical modelling suggested IgG1 and IgG3 contribute in promoting FcγR binding and phagocytosis, and IgG targeting the NANP-repeat and C-terminal regions CSP were similarly important for functional activities. CONCLUSIONS Results provide new insights to understand the modest and time-limited efficacy of RTS,S in children and the induction of antibody functional activities. Improving the induction and maintenance of antibodies that promote phagocytosis and cellular functions, and combating the negative effect of malaria exposure on vaccine responses are potential strategies for improving RTS,S efficacy and longevity.
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Affiliation(s)
- Gaoqian Feng
- Burnet Institute, Melbourne, Australia.,Department of Medicine, The University of Melbourne, Melbourne, Australia
| | - Liriye Kurtovic
- Burnet Institute, Melbourne, Australia.,Central Clinical School, Monash University, Melbourne, Australia
| | - Paul A Agius
- Burnet Institute, Melbourne, Australia.,Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia.,Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Elizabeth H Aitken
- Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Jahit Sacarlal
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.,Faculdade de Medicina, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Bruce D Wines
- Burnet Institute, Melbourne, Australia.,Central Clinical School, Monash University, Melbourne, Australia.,Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - P Mark Hogarth
- Burnet Institute, Melbourne, Australia.,Central Clinical School, Monash University, Melbourne, Australia.,Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Stephen J Rogerson
- Department of Medicine, The University of Melbourne, Melbourne, Australia.,Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Freya J I Fowkes
- Burnet Institute, Melbourne, Australia.,Department of Epidemiology and Preventative Medicine, Monash University, Melbourne, Australia.,Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Carlota Dobaño
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique.,ISGlobal, Hospital Clínic Universitat de Barcelona, Barcelona, Catalonia, Spain.,CIBER de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - James G Beeson
- Burnet Institute, Melbourne, Australia. .,Department of Medicine, The University of Melbourne, Melbourne, Australia. .,Department of Microbiology, Monash University, Clayton, Australia.
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18
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Abstract
Last month, the World Health Organization (WHO) recommended widespread use of RTS,S/AS01 vaccine to prevent malaria in young African children, noting its 30% reduction in deadly severe malaria. In a recent report, Das et al. describe antibody effector functions that may contribute to RTS,S efficacy and thereby guide vaccine improvements.
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Affiliation(s)
- Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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