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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, King CR, 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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Braunack-Mayer L, Malinga J, Masserey T, Nekkab N, Sen S, Schellenberg D, Tchouatieu AM, Kelly SL, Penny MA. Design and selection of drug properties to increase the public health impact of next-generation seasonal malaria chemoprevention: a modelling study. Lancet Glob Health 2024; 12:e478-e490. [PMID: 38365418 PMCID: PMC10882206 DOI: 10.1016/s2214-109x(23)00550-8] [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: 04/16/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND Seasonal malaria chemoprevention (SMC) is recommended for disease control in settings with moderate to high Plasmodium falciparum transmission and currently depends on the administration of sulfadoxine-pyrimethamine plus amodiaquine. However, poor regimen adherence and the increased frequency of parasite mutations conferring sulfadoxine-pyrimethamine resistance might threaten the effectiveness of SMC. Guidance is needed to de-risk the development of drug compounds for malaria prevention. We aimed to provide guidance for the early prioritisation of new and alternative SMC drugs and their target product profiles. METHODS In this modelling study, we combined an individual-based malaria transmission model that has explicit parasite growth with drug pharmacokinetic and pharmacodynamic models. We modelled SMC drug attributes for several possible modes of action, linked to their potential public health impact. Global sensitivity analyses identified trade-offs between drug elimination half-life, maximum parasite killing effect, and SMC coverage, and optimisation identified minimum requirements to maximise malaria burden reductions. FINDINGS Model predictions show that preventing infection for the entire period between SMC cycles is more important than drug curative efficacy for clinical disease effectiveness outcomes, but similarly important for impact on prevalence. When children younger than 5 years receive four SMC cycles with high levels of coverage (ie, 69% of children receiving all cycles), drug candidates require a duration of protection half-life higher than 23 days (elimination half-life >10 days) to achieve reductions higher than 75% in clinical incidence and severe disease (measured over the intervention period in the target population, compared with no intervention across a range of modelled scenarios). High coverage is crucial to achieve these targets, requiring more than 60% of children to receive all SMC cycles and more than 90% of children to receive at least one cycle regardless of the protection duration of the drug. INTERPRETATION Although efficacy is crucial for malaria prevalence reductions, chemoprevention development should select drug candidates for their duration of protection to maximise burden reductions, with the duration half-life determining cycle timing. Explicitly designing or selecting drug properties to increase community uptake is paramount. FUNDING Bill & Melinda Gates Foundation and the Swiss National Science Foundation.
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Affiliation(s)
- Lydia Braunack-Mayer
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Josephine Malinga
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Thiery Masserey
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Narimane Nekkab
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Swapnoleena Sen
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - David Schellenberg
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sherrie L Kelly
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Melissa A Penny
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland; Telethon Kids Institute, Nedlands, WA, Australia; Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia.
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Giacobbe DR, Zhang Y, de la Fuente J. Explainable artificial intelligence and machine learning: novel approaches to face infectious diseases challenges. Ann Med 2023; 55:2286336. [PMID: 38010090 PMCID: PMC10836268 DOI: 10.1080/07853890.2023.2286336] [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: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
Artificial intelligence (AI) and machine learning (ML) are revolutionizing human activities in various fields, with medicine and infectious diseases being not exempt from their rapid and exponential growth. Furthermore, the field of explainable AI and ML has gained particular relevance and is attracting increasing interest. Infectious diseases have already started to benefit from explainable AI/ML models. For example, they have been employed or proposed to better understand complex models aimed at improving the diagnosis and management of coronavirus disease 2019, in the field of antimicrobial resistance prediction and in quantum vaccine algorithms. Although some issues concerning the dichotomy between explainability and interpretability still require careful attention, an in-depth understanding of how complex AI/ML models arrive at their predictions or recommendations is becoming increasingly essential to properly face the growing challenges of infectious diseases in the present century.
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Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
- Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Italy
| | - Yudong Zhang
- School of Computing and Mathematical Sciences, University of Leicester, Leicester, UK
- School of Computer Science and Engineering, Southeast University, Nanjing, China
| | - José de la Fuente
- SaBio (Health and Biotechnology), Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
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Nekkab N, Malinga J, Braunack-Mayer L, Kelly SL, Miller RS, Penny MA. Modelling to inform next-generation medical interventions for malaria prevention and treatment. COMMUNICATIONS MEDICINE 2023; 3:41. [PMID: 36966272 PMCID: PMC10039673 DOI: 10.1038/s43856-023-00274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Global progress against malaria has stagnated and novel medical interventions to prevent malaria are needed to fill gaps in existing tools and improve protection against infection and disease. Candidate selection for next-generation interventions should be supported by the best available evidence. Target product profiles and preferred product characteristics play a key role in setting selection criteria requirements and early endorsement by health authorities. While clinical evidence and expert opinion often inform product development decisions, integrating modelling evidence early and iteratively into this process provides an opportunity to link product characteristics with expected public health outcomes. Population models of malaria transmission can provide a better understanding of which, and at what magnitude, key intervention characteristics drive public health impact, and provide quantitative evidence to support selection of use-cases, transmission settings, and deployment strategies. We describe how modelling evidence can guide and accelerate development of new malaria vaccines, monoclonal antibodies, and chemoprevention.
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Affiliation(s)
- Narimane Nekkab
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Josephine Malinga
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Lydia Braunack-Mayer
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sherrie L Kelly
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Melissa A Penny
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
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Masserey T, Lee T, Golumbeanu M, Shattock AJ, Kelly SL, Hastings IM, Penny MA. The influence of biological, epidemiological, and treatment factors on the establishment and spread of drug-resistant Plasmodium falciparum. eLife 2022; 11:77634. [PMID: 35796430 PMCID: PMC9262398 DOI: 10.7554/elife.77634] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
The effectiveness of artemisinin-based combination therapies (ACTs) to treat Plasmodium falciparum malaria is threatened by resistance. The complex interplay between sources of selective pressure-treatment properties, biological factors, transmission intensity, and access to treatment-obscures understanding how, when, and why resistance establishes and spreads across different locations. We developed a disease modelling approach with emulator-based global sensitivity analysis to systematically quantify which of these factors drive establishment and spread of drug resistance. Drug resistance was more likely to evolve in low transmission settings due to the lower levels of (i) immunity and (ii) within-host competition between genotypes. Spread of parasites resistant to artemisinin partner drugs depended on the period of low drug concentration (known as the selection window). Spread of partial artemisinin resistance was slowed with prolonged parasite exposure to artemisinin derivatives and accelerated when the parasite was also resistant to the partner drug. Thus, to slow the spread of partial artemisinin resistance, molecular surveillance should be supported to detect resistance to partner drugs and to change ACTs accordingly. Furthermore, implementing more sustainable artemisinin-based therapies will require extending parasite exposure to artemisinin derivatives, and mitigating the selection windows of partner drugs, which could be achieved by including an additional long-acting drug.
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Affiliation(s)
- Thiery Masserey
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Tamsin Lee
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Monica Golumbeanu
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrew J Shattock
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Sherrie L Kelly
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Ian M Hastings
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Melissa A Penny
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
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