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Sundell GN, Tao SC. Phage immunoprecipitation and sequencing-a versatile technique for mapping the antibody reactome. Mol Cell Proteomics 2024:100831. [PMID: 39168282 DOI: 10.1016/j.mcpro.2024.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
Characterizing the antibody reactome for circulating antibodies provide insight into pathogen exposure, allergies and autoimmune diseases. This is important for biomarker discovery, clinical diagnosis, and prognosis of disease progression, as well as population-level insights into the immune system. The emerging technology phage display immunoprecipitation and sequencing (PhIP-seq) is a high-throughput method for identifying antigens/epitopes of the antibody reactome. In PhIP-seq, libraries with sequences of defined lengths and overlapping segments are bioinformatically designed using naturally occurring proteins and cloned into phage genomes to be displayed on the surface. These libraries are used in immunoprecipitation experiments of circulating antibodies. This can be done with parallel samples from multiple sources, and the DNA inserts from the bound phages are barcoded and subjected to next-generation sequencing for hit-determination. PhIP-seq is a powerful technique for characterizing the antibody reactome that has undergone rapid advances in recent years. In this review, we comprehensively describe the history of PhIP-seq and discuss recent advances in library design and applications.
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Affiliation(s)
- Gustav N Sundell
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.
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Amen A, Yoo R, Fabra-García A, Bolscher J, Stone WJR, Bally I, Dergan-Dylon S, Kucharska I, de Jong RM, de Bruijni M, Bousema T, Richter King C, MacGill RS, Sauerwein RW, Julien JP, Poignard P, Jore MM. Target-agnostic identification of human antibodies to Plasmodium falciparum sexual forms reveals cross stage recognition of glutamate-rich repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565335. [PMID: 37961136 PMCID: PMC10635103 DOI: 10.1101/2023.11.03.565335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Circulating sexual stages of Plasmodium falciparum (Pf) can be transmitted from humans to mosquitoes, thereby furthering the spread of malaria in the population. It is well established that antibodies (Abs) can efficiently block parasite transmission. In search for naturally acquired Ab targets on sexual stages, we established an efficient method for target-agnostic single B cell activation followed by high-throughput selection of human monoclonal antibodies (mAbs) reactive to sexual stages of Pf in the form of gamete and gametocyte extract. We isolated mAbs reactive against a range of Pf proteins including well-established targets Pfs48/45 and Pfs230. One mAb, B1E11K, was cross-reactive to various proteins containing glutamate-rich repetitive elements expressed at different stages of the parasite life cycle. A crystal structure of two B1E11K Fab domains in complex with its main antigen, RESA, expressed on asexual blood stages, showed binding of B1E11K to a repeating epitope motif in a head-to-head conformation engaging in affinity-matured homotypic interactions. Thus, this mode of recognition of Pf proteins, previously described only for PfCSP, extends to other repeats expressed across various stages. The findings augment our understanding of immune-pathogen interactions to repeating elements of the Plasmodium parasite proteome and underscore the potential of the novel mAb identification method used to provide new insights into the natural humoral immune response against Pf . Impact Statement A naturally acquired human monoclonal antibody recognizes proteins expressed at different stages of the Plasmodium falciparum lifecycle through affinity-matured homotypic interactions with glutamate-rich repeats.
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Williams KL, Guerrero S, Flores-Garcia Y, Kim D, Williamson KS, Siska C, Smidt P, Jepson SZ, Li K, Dennison SM, Mathis-Torres S, Chen X, Wille-Reece U, MacGill RS, Walker M, Jongert E, King CR, Ockenhouse C, Glanville J, Moon JE, Regules JA, Tan YC, Cavet G, Lippow SM, Robinson WH, Dutta S, Tomaras GD, Zavala F, Ketchem RR, Emerling DE. A candidate antibody drug for prevention of malaria. Nat Med 2024; 30:117-129. [PMID: 38167935 PMCID: PMC10803262 DOI: 10.1038/s41591-023-02659-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/20/2023] [Indexed: 01/05/2024]
Abstract
Over 75% of malaria-attributable deaths occur in children under the age of 5 years. However, the first malaria vaccine recommended by the World Health Organization (WHO) for pediatric use, RTS,S/AS01 (Mosquirix), has modest efficacy. Complementary strategies, including monoclonal antibodies, will be important in efforts to eradicate malaria. Here we characterize the circulating B cell repertoires of 45 RTS,S/AS01 vaccinees and discover monoclonal antibodies for development as potential therapeutics. We generated >28,000 antibody sequences and tested 481 antibodies for binding activity and 125 antibodies for antimalaria activity in vivo. Through these analyses we identified correlations suggesting that sequences in Plasmodium falciparum circumsporozoite protein, the target antigen in RTS,S/AS01, may induce immunodominant antibody responses that limit more protective, but subdominant, responses. Using binding studies, mouse malaria models, biomanufacturing assessments and protein stability assays, we selected AB-000224 and AB-007088 for advancement as a clinical lead and backup. We engineered the variable domains (Fv) of both antibodies to enable low-cost manufacturing at scale for distribution to pediatric populations, in alignment with WHO's preferred product guidelines. The engineered clone with the optimal manufacturing and drug property profile, MAM01, was advanced into clinical development.
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Affiliation(s)
| | | | - Yevel Flores-Garcia
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dongkyoon Kim
- Atreca, Inc., San Carlos, CA, USA
- Initium Therapeutics, Inc., Natick, MA, USA
| | | | | | | | | | - Kan Li
- Duke Center for Human Systems Immunology, Department of Surgery, Duke University, Durham, NC, USA
| | - S Moses Dennison
- Duke Center for Human Systems Immunology, Department of Surgery, Duke University, Durham, NC, USA
| | - Shamika Mathis-Torres
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Ulrike Wille-Reece
- BioNTech US, Inc., Cambridge, MA, USA
- PATH Center for Vaccine Innovation and Access, Washington DC, USA
| | | | | | | | - C Richter King
- PATH Center for Vaccine Innovation and Access, Washington DC, USA
| | | | | | - James E Moon
- Center for Enabling Capabilities, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason A Regules
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yann Chong Tan
- Atreca, Inc., San Carlos, CA, USA
- Nuevocor Pte. Ltd, Singapore, Singapore
| | - Guy Cavet
- Atreca, Inc., San Carlos, CA, USA
- Paramune, Inc., San Carlos, CA, USA
| | | | - William H Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sheetij Dutta
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Georgia D Tomaras
- Duke Center for Human Systems Immunology, Department of Surgery, Duke University, Durham, NC, USA
- Departments of Immunology, Molecular Genetics and Microbiology, Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Fidel Zavala
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Bolton JS, MacGill RS, Locke E, Regules JA, Bergmann-Leitner ES. Novel antibody competition binding assay identifies distinct serological profiles associated with protection. Front Immunol 2023; 14:1303446. [PMID: 38152401 PMCID: PMC10752609 DOI: 10.3389/fimmu.2023.1303446] [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: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023] Open
Abstract
Introduction Pre-erythrocytic malaria vaccines hold the promise of inducing sterile protection thereby preventing the morbidity and mortality associated with Plasmodium infection. The main surface antigen of P. falciparum sporozoites, i.e., the circumsporozoite protein (CSP), has been extensively explored as a target of such vaccines with significant success in recent years. Systematic adjuvant selection, refinements of the immunization regimen, and physical properties of the antigen may all contribute to the potential of increasing the efficacy of CSP-based vaccines. Protection appears to be dependent in large part on CSP antibodies. However due to a knowledge gap related to the exact correlates of immunity, there is a critical need to improve our ability to down select candidates preclinically before entering clinical trials including with controlled human malaria infections (CHMI). Methods We developed a novel multiplex competition assay based on well-characterized monoclonal antibodies (mAbs) that target crucial epitopes across the CSP molecule. This new tool assesses both, quality and epitope-specific concentrations of vaccine-induced antibodies by measuring their equivalency with a panel of well-characterized, CSP-epitope-specific mAbs. Results Applying this method to RTS,S-immune sera from a CHMI trial demonstrated a quantitative epitope-specificity profile of antibody responses that can differentiate between protected vs. nonprotected individuals. Aligning vaccine efficacy with quantitation of the epitope fine specificity results of this equivalency assay reveals the importance of epitope specificity. Discussion The newly developed serological equivalence assay will inform future vaccine design and possibly even adjuvant selection. This methodology can be adapted to other antigens and disease models, when a panel of relevant mAbs exists, and could offer a unique tool for comparing and down-selecting vaccine formulations.
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Affiliation(s)
- Jessica S. Bolton
- Biologics Research & Development, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
| | - Randall S. MacGill
- Center for Vaccine Innovation and Access, PATH, Washington, DC, United States
| | - Emily Locke
- Center for Vaccine Innovation and Access, PATH, Washington, DC, United States
| | - Jason A. Regules
- Biologics Research & Development, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
| | - Elke S. Bergmann-Leitner
- Biologics Research & Development, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. JCI Insight 2023; 8:e174976. [PMID: 37934865 PMCID: PMC10795829 DOI: 10.1172/jci.insight.174976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq) in profiling mouse autoantibodies. This library was validated using 7 genetically distinct mouse lines across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model nonspecific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate 3 distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities. Second, serum from nonobese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, was enriched in peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous autoantigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 carrying recessive mutations in AIRE. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity profiling.
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Affiliation(s)
| | | | - Haleigh S. Miller
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | | | - David Yu
- Diabetes Center, School of Medicine
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics
- Diabetes Center, School of Medicine
| | | | - Clare L. Abram
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | | | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | | | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Hassan I, Kanoi BN, Nagaoka H, Sattabongkot J, Udomsangpetch R, Tsuboi T, Takashima E. High-Throughput Antibody Profiling Identifies Targets of Protective Immunity against P. falciparum Malaria in Thailand. Biomolecules 2023; 13:1267. [PMID: 37627332 PMCID: PMC10452476 DOI: 10.3390/biom13081267] [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: 06/12/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Malaria poses a significant global health challenge, resulting in approximately 600,000 deaths each year. Individuals living in regions with endemic malaria have the potential to develop partial immunity, thanks in part to the presence of anti-plasmodium antibodies. As efforts are made to optimize and implement strategies to reduce malaria transmission and ultimately eliminate the disease, it is crucial to understand how these interventions impact naturally acquired protective immunity. To shed light on this, our study focused on assessing antibody responses to a carefully curated library of P. falciparum recombinant proteins (n = 691) using samples collected from individuals residing in a low-malaria-transmission region of Thailand. We conducted the antibody assays using the AlphaScreen system, a high-throughput homogeneous proximity-based bead assay that detects protein interactions. We observed that out of the 691 variable surface and merozoite stage proteins included in the library, antibodies to 268 antigens significantly correlated with the absence of symptomatic malaria in an univariate analysis. Notably, the most prominent antigens identified were P. falciparum erythrocyte membrane protein 1 (PfEMP1) domains. These results align with our previous research conducted in Uganda, suggesting that similar antigens like PfEMP1s might play a pivotal role in determining infection outcomes in diverse populations. To further our understanding, it remains critical to conduct functional characterization of these identified proteins, exploring their potential as correlates of protection or as targets for vaccine development.
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Affiliation(s)
- Ifra Hassan
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama 790-8577, Japan; (I.H.); (H.N.)
| | - Bernard N. Kanoi
- Centre for Malaria Elimination, Institute of Tropical Medicine, Mount Kenya University, Thika 01000, Kenya;
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama 790-8577, Japan; (I.H.); (H.N.)
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Rachanee Udomsangpetch
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand;
| | - Takafumi Tsuboi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama 790-8577, Japan;
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama 790-8577, Japan; (I.H.); (H.N.)
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Murdoch J, Baum J. A sting in the tail-are antibodies against the C-terminus of Plasmodium falciparum circumsporozoite protein protective? EMBO Mol Med 2023:e17556. [PMID: 37082835 DOI: 10.15252/emmm.202317556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023] Open
Abstract
Malaria remains a huge burden on global public health. Annually there are more than 200 million cases with > 600,000 deaths worldwide, the vast majority of which occur within Sub-Saharan Africa (WHO; World Malaria Report, 2021). Malaria disease is the consequence of infection by a protozoan parasite from the genus Plasmodium with most morbidity and mortality caused by P. falciparum. With rates of infection plateauing and rebounding in some areas (in particular, as a result of the disruption caused by the COVID-19 pandemic), there have been increasing calls for new initiatives that can reduce malaria incidence towards local elimination or the hoped for goal of global eradication. In 2021, the World Health Organisation approved the first malaria vaccine RTS,S/AS01 (also called Mosquirix™), indicating it to be safe for use in young children and advocating its integration into routine immunisation programmes. Approval of this vaccine clearly represents a major landmark in global efforts towards malaria control and eradication aspirations. RTS,S modest efficacy, however, points at the need to better understand immune responses to the parasite if we hope to design next generation malaria vaccines with increased potency.
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Affiliation(s)
- Jem Murdoch
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Jake Baum
- School of Biomedical Sciences, UNSW Sydney, Kensington, NSW, Australia
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