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Hannon ER, Marsit CJ, Dent AE, Embury P, Ogolla S, Midem D, Williams SM, Kazura JW. Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation. BioData Min 2024; 17:21. [PMID: 38992677 PMCID: PMC11241886 DOI: 10.1186/s13040-024-00374-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). METHODS Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. RESULTS Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. CONCLUSION Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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Affiliation(s)
- Emily R Hannon
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA.
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Arlene E Dent
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
- Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, Cleveland, OH, 44106, USA
| | - Paula Embury
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
| | | | - David Midem
- Chulaimbo Sub-county Hospital, Kisumu County, Kenya
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA
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Jackeline Pérez-Vega M, Manuel Corral-Ruiz G, Galán-Salinas A, Silva-García R, Mancilla-Herrera I, Barrios-Payán J, Fabila-Castillo L, Hernández-Pando R, Enid Sánchez-Torres L. Acute lung injury is prevented by monocyte locomotion inhibitory factor in an experimental severe malaria mouse model. Immunobiology 2024; 229:152823. [PMID: 38861873 DOI: 10.1016/j.imbio.2024.152823] [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: 08/29/2023] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024]
Abstract
Acute lung injury caused by severe malaria (SM) is triggered by a dysregulated immune response towards the infection with Plasmodium parasites. Postmortem analysis of human lungs shows diffuse alveolar damage (DAD), the presence of CD8 lymphocytes, neutrophils, and increased expression of Intercellular Adhesion Molecule 1 (ICAM-1). P. berghei ANKA (PbA) infection in C57BL/6 mice reproduces many SM features, including acute lung injury characterized by DAD, CD8+ T lymphocytes and neutrophils in the lung parenchyma, and tissular expression of proinflammatory cytokines and adhesion molecules, such as IFNγ, TNFα, ICAM, and VCAM. Since this is related to a dysregulated immune response, immunomodulatory agents are proposed to reduce the complications of SM. The monocyte locomotion inhibitory factor (MLIF) is an immunomodulatory pentapeptide isolated from axenic cultures of Entamoeba hystolitica. Thus, we evaluated if the MLIF intraperitoneal (i.p.) treatment prevented SM-induced acute lung injury. The peptide prevented SM without a parasiticidal effect, indicating that its protective effect was related to modifications in the immune response. Furthermore, peripheral CD8+ leukocytes and neutrophil proportions were higher in infected treated mice. However, the treatment prevented DAD, CD8+ cell infiltration into the pulmonary tissue and downregulated IFNγ. Moreover, VCAM-1 expression was abrogated. These results indicate that the MLIF treatment downregulated adhesion molecule expression, impeding cell migration and proinflammatory cytokine tissular production, preventing acute lung injury induced by SM. Our findings represent a potential novel strategy to avoid this complication in various events where a dysregulated immune response triggers lung injury.
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Affiliation(s)
- Martha Jackeline Pérez-Vega
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico; Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Gerardo Manuel Corral-Ruiz
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico; Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Adrian Galán-Salinas
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Raúl Silva-García
- Unidad de Investigación Médica en Inmunología, Hospital de Pediatría, CMN-Siglo XXI, IMSS, Ciudad de México, Mexico
| | - Ismael Mancilla-Herrera
- Departamento de Infectología e Inmunología, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | - Jorge Barrios-Payán
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico
| | | | - Rogelio Hernández-Pando
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, Mexico.
| | - Luvia Enid Sánchez-Torres
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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Prah DA, Laryea-Akrong E. Asymptomatic Low-Density Plasmodium falciparum Infections: Parasites Under the Host's Immune Radar? J Infect Dis 2024; 229:1913-1918. [PMID: 38349649 PMCID: PMC11175676 DOI: 10.1093/infdis/jiad581] [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: 09/25/2023] [Accepted: 12/18/2023] [Indexed: 06/15/2024] Open
Abstract
A large body of evidence suggests that low parasite carriage in Plasmodium falciparum asymptomatic infection is required for the maintenance of malaria immunity. However, the fact that treating such infections has little to no impact on subsequent clinical malaria is rarely noted. In this paper, we review data and argue that low-density parasite carriage in asymptomatic infection may not support host immune processes and that parasites are virtually under the host's immunological radar. We also discuss factors that may be constraining parasitemia in asymptomatic infections from reaching the threshold required to cause clinical symptoms. A thorough understanding of this infectious reservoir is essential for malaria control and eradication because asymptomatic infections contribute significantly to Plasmodium transmission.
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Affiliation(s)
- Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
- Faculty of Applied Sciences, Department of Science Laboratory Technology, Accra Technical University, Accra, Ghana
| | - Elizabeth Laryea-Akrong
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
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Asmah RH, Squire DS, Adupko S, Adedia D, Kyei-Baafour E, Aidoo EK, Ayeh-Kumi PF. Host-parasite interaction in severe and uncomplicated malaria infection in ghanaian children. Eur J Clin Microbiol Infect Dis 2024; 43:915-926. [PMID: 38472520 DOI: 10.1007/s10096-024-04804-z] [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: 12/21/2023] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
PURPOSE During malarial infection, both parasites and host red blood cells (RBCs) come under severe oxidative stress due to the production of free radicals. The host system responds in protecting the RBCs against the oxidative damage caused by these free radicals by producing antioxidants. In this study, we investigated the antioxidant enzyme; superoxide dismutase (SOD) activity and cytokine interactions with parasitaemia in Ghanaian children with severe and uncomplicated malaria. METHODOLOGY One hundred and fifty participants aged 0-12 years were administered with structured questionnaires. Active case finding approach was used in participating hospitals to identify and interview cases before treatment was applied. Blood samples were taken from each participant and used to quantify malaria parasitaemia, measure haematological parameters and SOD activity. Cytokine levels were measured by commercial ELISA kits. DNA comet assay was used to evaluate the extent of parasite DNA damage due to oxidative stress. RESULTS Seventy - Nine (79) and Twenty- Six (26) participants who were positive with malaria parasites were categorized as severe (56.75 × 103 ± 57.69 parasites/µl) and uncomplicated malaria (5.87 × 103 ± 2.87 parasites/µl) respectively, showing significant difference in parasitaemia (p < 0.0001). Significant negative correlation was found between parasitaemia and SOD activity levels among severe malaria study participants (p = 0.0428). Difference in cytokine levels (IL-10) amongst the control, uncomplicated and severe malaria groups was significant (p < 0.0001). The IFN-γ/IL-10 /TNF-α/IL-10 ratio differed significantly between the malaria infected and non- malaria infected study participants. DNA comet assay revealed damage to Plasmodium parasite DNA. CONCLUSION Critical roles played by SOD activity and cytokines as anti-parasitic defense during P. falciparum malaria infection in children were established.
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Affiliation(s)
- Richard H Asmah
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - Daniel Sai Squire
- Department of Medical Laboratory Science, School of Allied Health Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana.
| | - Selorme Adupko
- Department of Pharmaceutics and Microbiology, School of Pharmacy, University of Ghana, Accra, Ghana
| | - David Adedia
- Department of Basic Sciences, School of Basic and Biomedical Sciences, University of University of Health and Allied Sciences, Ho, Ghana
| | - Eric Kyei-Baafour
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ebenezer K Aidoo
- Department of Medical Laboratory Technology, Accra Technical University, Accra, Ghana
| | - Patrick F Ayeh-Kumi
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
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Hannon ER, Marsit CJ, Dent AE, Embury P, Ogolla S, Midem D, Williams SM, Kazura JW. Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation. RESEARCH SQUARE 2024:rs.3.rs-3992113. [PMID: 38645047 PMCID: PMC11030537 DOI: 10.21203/rs.3.rs-3992113/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs). Methods Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively. Results Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils. Conclusion Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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6
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Du X, Ren B, Li C, Li Q, Kan S, Wang X, Bai W, Wu C, Kassegne K, Yan H, Niu X, Yan M, Xu W, Wassmer SC, Wang J, Chen G, Wang Z. PRL2 regulates neutrophil extracellular trap formation which contributes to severe malaria and acute lung injury. Nat Commun 2024; 15:881. [PMID: 38286811 PMCID: PMC10825202 DOI: 10.1038/s41467-024-45210-5] [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: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
Excessive host immune responses contribute to severe malaria with high mortality. Here, we show that PRL2 in innate immune cells is highly related to experimental malaria disease progression, especially the development of murine severe malaria. In the absence of PRL2 in myeloid cells, Plasmodium berghei infection results in augmented lung injury, leading to significantly increased mortality. Intravital imaging revealed greater neutrophilic inflammation and NET formation in the lungs of PRL2 myeloid conditional knockout mice. Depletion of neutrophils prior to the onset of severe disease protected mice from NETs associated lung injury, and eliminated the difference between WT and PRL2 CKO mice. PRL2 regulates neutrophil activation and NET accumulation via the Rac-ROS pathway, thus contributing to NETs associated ALI. Hydroxychloroquine, an inhibitor of PRL2 degradation alleviates NETs associated tissue damage in vivo. Our findings suggest that PRL2 serves as an indicator of progression to severe malaria and ALI. In addition, our study indicated the importance of PRL2 in NET formation and tissue injury. It might open a promising path for adjunctive treatment of NET-associated disease.
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Affiliation(s)
- Xinyue Du
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Baiyang Ren
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500, P.R. China
| | - Chang Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500, P.R. China
| | - Qi Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Shuo Kan
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500, P.R. China
| | - Wenjuan Bai
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Chenyun Wu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Kokouvi Kassegne
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Huibo Yan
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Xiaoyin Niu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Min Yan
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500, P.R. China
| | - Wenyue Xu
- Department of Pathogenic Biology, Army Medical University (The Third Military Medical University), Chongqing, 400038, P.R. China
| | - Samuel C Wassmer
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Jing Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China.
| | - Guangjie Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China.
| | - Zhaojun Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China.
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China.
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Prah DA, Dunican C, Amoah LE, Marjaneh MM, Kaforou M, Nordgren A, Jones-Warner W, Aniweh Y, Awandare GA, Cunnington AJ, Hafalla JC. Asymptomatic Plasmodium falciparum infection evades triggering a host transcriptomic response. J Infect 2023; 87:259-262. [PMID: 37356628 DOI: 10.1016/j.jinf.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Affiliation(s)
- Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana; Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Claire Dunican
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mahdi Moradi Marjaneh
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, United Kingdom
| | - Asa Nordgren
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom
| | - William Jones-Warner
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, United Kingdom; Centre for Paediatrics and Child Health, Imperial College London, United Kingdom.
| | - Julius Clemence Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Malpartida-Cardenas K, Moser N, Ansah F, Pennisi I, Ahu Prah D, Amoah LE, Awandare G, Hafalla JCR, Cunnington A, Baum J, Rodriguez-Manzano J, Georgiou P. Sensitive Detection of Asymptomatic and Symptomatic Malaria with Seven Novel Parasite-Specific LAMP Assays and Translation for Use at Point-of-Care. Microbiol Spectr 2023; 11:e0522222. [PMID: 37158750 PMCID: PMC10269850 DOI: 10.1128/spectrum.05222-22] [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: 12/20/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
Human malaria is a life-threatening parasitic disease with high impact in the sub-Saharan Africa region, where 95% of global cases occurred in 2021. While most malaria diagnostic tools are focused on Plasmodium falciparum, there is a current lack of testing non-P. falciparum cases, which may be underreported and, if undiagnosed or untreated, may lead to severe consequences. In this work, seven species-specific loop-mediated isothermal amplification (LAMP) assays were designed and evaluated against TaqMan quantitative PCR (qPCR), microscopy, and enzyme-linked immunosorbent assays (ELISAs). Their clinical performance was assessed with a cohort of 164 samples of symptomatic and asymptomatic patients from Ghana. All asymptomatic samples with a parasite load above 80 genomic DNA (gDNA) copies per μL of extracted sample were detected with the Plasmodium falciparum LAMP assay, reporting 95.6% (95% confidence interval [95% CI] of 89.9 to 98.5) sensitivity and 100% (95% CI of 87.2 to 100) specificity. This assay showed higher sensitivity than microscopy and ELISA, which were 52.7% (95% CI of 39.7 to 67%) and 67.3% (95% CI of 53.3 to 79.3%), respectively. Nine samples were positive for P. malariae, indicating coinfections with P. falciparum, which represented 5.5% of the tested population. No samples were detected as positive for P. vivax, P. ovale, P. knowlesi, or P. cynomolgi by any method. Furthermore, translation to the point-of-care was demonstrated with a subcohort of 18 samples tested locally in Ghana using our handheld lab-on-chip platform, Lacewing, showing comparable results to a conventional fluorescence-based instrument. The developed molecular diagnostic test could detect asymptomatic malaria cases, including submicroscopic parasitemia, and it has the potential to be used for point-of-care applications. IMPORTANCE The spread of Plasmodium falciparum parasites with Pfhrp2/3 gene deletions presents a major threat to reliable point-of-care diagnosis with current rapid diagnostic tests (RDTs). Novel molecular diagnostics based on nucleic acid amplification are needed to address this liability. In this work, we overcome this challenge by developing sensitive tools for the detection of Plasmodium falciparum and non-P. falciparum species. Furthermore, we evaluate these tools with a cohort of symptomatic and asymptomatic malaria patients and test a subcohort locally in Ghana. The findings of this work could lead to the implementation of DNA-based diagnostics to fight against the spread of malaria and provide reliable, sensitive, and specific diagnostics at the point of care.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Nicolas Moser
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Julius Clemence R. Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- School of Biomedical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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9
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Mooney JP, DonVito SM, Jahateh M, Bittaye H, Bottomley C, D'Alessandro U, Riley EM. Dry season prevalence of Plasmodium falciparum in asymptomatic gambian children, with a comparative evaluation of diagnostic methods. Malar J 2022; 21:171. [PMID: 35672850 PMCID: PMC9172138 DOI: 10.1186/s12936-022-04184-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/10/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Subclinical infection with Plasmodium falciparum remains highly prevalent, yet diagnosing these often low-density infections remains a challenge. Infections can be subpatent, falling below the limit of detection for conventional thick-film microscopy and rapid diagnostic testing (RDT). In this study, the prevalence of subclinical P. falciparum infections in school-aged children was characterised at the start of the dry season in the Upper River Region of The Gambia in 2017/2018, with a goal to also compare the utility of different diagnostic tools. METHODS In a cross-sectional survey of children living in 29 villages on the south bank of the Gambia river (median age of 10 years), matched microscopy, rapid diagnostic test (RDT, detecting histidine-rich protein 2) and polymerase chain reaction (PCR, targeting either 18S rRNA or var gene acidic terminal sequence) were used to determine the prevalence of patent and subpatent infections and to compare the performance of the different diagnostic methods. RESULTS The prevalence of var gene acidic terminal sequence (varATS) qPCR-detectable infections was 10.2% (141/1381) with a median density of 3.12 parasites/µL. Malaria prevalence was highly heterogeneous across the region, ranging from < 1% to ~ 40% prevalence in different village clusters. Compared to varATS, 18S rRNA PCR detected fewer low-density infections, with an assay sensitivity of 50% and specificity of 98.8%. Parasite prevalence in the cohort was 2.9% by microscopy and 1.5% by RDT. Compared to varATS qPCR, microscopy and RDT had sensitivities of 11.5% and 9.2%, respectively, although both methods were highly specific (> 98%). Samples that were positive by all three tests (varATS qPCR, RDT and microscopy) had significantly higher parasite densities (median = 1705 parasites/µL) than samples that were positive by varATS qPCR only (median = 2.4 parasites/µL). CONCLUSIONS The majority of subclinical malaria infections in school-aged children were of extremely low parasite density and detectable only by ultra-sensitive PCR analysis. Understanding the duration of these low density infections, their physiological impact and their contribution to sustained parasite transmission is necessary to inform malaria elimination strategies.
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Affiliation(s)
- Jason P Mooney
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Rd, Edinburgh, EH9 3FL, UK.
| | - Sophia M DonVito
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Rd, Edinburgh, EH9 3FL, UK
| | - Maimuna Jahateh
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Haddy Bittaye
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Umberto D'Alessandro
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Eleanor M Riley
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, Kings Buildings, Charlotte Auerbach Rd, Edinburgh, EH9 3FL, UK
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Mooney JP, DonVito SM, Jahateh M, Bittaye H, Keith M, Galloway LJ, Ndow M, Cunnington AJ, D'Alessandro U, Bottomley C, Riley EM. 'Bouncing Back' From Subclinical Malaria: Inflammation and Erythrocytosis After Resolution of P. falciparum Infection in Gambian Children. Front Immunol 2022; 13:780525. [PMID: 35154104 PMCID: PMC8831762 DOI: 10.3389/fimmu.2022.780525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Recent malaria is associated with an increased risk of systemic bacterial infection. The aetiology of this association is unclear but malaria-related haemolysis may be one contributory factor. To characterise the physiological consequences of persistent and recently resolved malaria infections and associated haemolysis, 1650 healthy Gambian children aged 8-15 years were screened for P. falciparum infection (by 18sRNA PCR) and/or anaemia (by haematocrit) at the end of the annual malaria transmission season (t1). P. falciparum-infected children and children with moderate or severe anaemia (haemoglobin concentration < 11g/dl) were age matched to healthy, uninfected, non-anaemic controls and screened again 2 months later (t2). Persistently infected children (PCR positive at t1 and t2) had stable parasite burdens and did not differ significantly haematologically or in terms of proinflammatory markers from healthy, uninfected children. However, among persistently infected children, IL-10 concentrations were positively correlated with parasite density suggesting a tolerogenic response to persistent infection. By contrast, children who naturally resolved their infections (positive at t1 and negative at t2) exhibited mild erythrocytosis and concentrations of pro-inflammatory markers were raised compared to other groups of children. These findings shed light on a 'resetting' and potential overshoot of the homeostatic haematological response following resolution of malaria infection. Interestingly, the majority of parameters tested were highly heterogeneous in uninfected children, suggesting that some may be harbouring cryptic malaria or other infections.
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Affiliation(s)
- Jason P Mooney
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sophia M DonVito
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Maimuna Jahateh
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Haddy Bittaye
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Marianne Keith
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lauren J Galloway
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Mortala Ndow
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Umberto D'Alessandro
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Christian Bottomley
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eleanor M Riley
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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