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Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2024:gkae585. [PMID: 38966997 DOI: 10.1093/nar/gkae585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.
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Affiliation(s)
- Victoria A Bonnell
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Yuning Zhang
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan S Brown
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - John Horton
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Gaisser KD, Skloss SN, Brettner LM, Paleologu L, Roco CM, Rosenberg AB, Hirano M, DePaolo RW, Seelig G, Kuchina A. High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding. Nat Protoc 2024:10.1038/s41596-024-01007-w. [PMID: 38886529 DOI: 10.1038/s41596-024-01007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
Abstract
Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. The standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.
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Affiliation(s)
| | | | - Leandra M Brettner
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Luana Paleologu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - Matthew Hirano
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - R William DePaolo
- Center for Microbiome Sciences and Therapeutics, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Gastroenterology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Anna Kuchina
- Institute for Systems Biology, Seattle, WA, USA.
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA.
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
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3
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Chou RT, Ouattara A, Adams M, Berry AA, Takala-Harrison S, Cummings MP. Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum. NPJ Syst Biol Appl 2024; 10:44. [PMID: 38678051 PMCID: PMC11055854 DOI: 10.1038/s41540-024-00365-1] [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: 06/14/2023] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Malaria vaccine development is hampered by extensive antigenic variation and complex life stages of Plasmodium species. Vaccine development has focused on a small number of antigens, many of which were identified without utilizing systematic genome-level approaches. In this study, we implement a machine learning-based reverse vaccinology approach to predict potential new malaria vaccine candidate antigens. We assemble and analyze P. falciparum proteomic, structural, functional, immunological, genomic, and transcriptomic data, and use positive-unlabeled learning to predict potential antigens based on the properties of known antigens and remaining proteins. We prioritize candidate antigens based on model performance on reference antigens with different genetic diversity and quantify the protein properties that contribute most to identifying top candidates. Candidate antigens are characterized by gene essentiality, gene ontology, and gene expression in different life stages to inform future vaccine development. This approach provides a framework for identifying and prioritizing candidate vaccine antigens for a broad range of pathogens.
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Affiliation(s)
- Renee Ti Chou
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea A Berry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Michael P Cummings
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
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4
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van Schuijlenburg R, Azargoshasb S, de Korne CM, Sijtsma JC, Bezemer S, van der Ham AJ, Baalbergen E, Geurten F, de Bes-Roeleveld LM, Chevalley-Maurel SC, van Oosterom MN, van Leeuwen FWB, Franke-Fayard B, Roestenberg M. Ageing of Plasmodium falciparum malaria sporozoites alters their motility, infectivity and reduces immune activation in vitro. Malar J 2024; 23:111. [PMID: 38641838 PMCID: PMC11027264 DOI: 10.1186/s12936-024-04946-7] [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: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Sporozoites (SPZ), the infective form of Plasmodium falciparum malaria, can be inoculated into the human host skin by Anopheline mosquitoes. These SPZ migrate at approximately 1 µm/s to find a blood vessel and travel to the liver where they infect hepatocytes and multiply. In the skin they are still low in number (50-100 SPZ) and vulnerable to immune attack by antibodies and skin macrophages. This is why whole SPZ and SPZ proteins are used as the basis for most malaria vaccines currently deployed and undergoing late clinical testing. Mosquitoes typically inoculate SPZ into a human host between 14 and 25 days after their previous infective blood meal. However, it is unknown whether residing time within the mosquito affects SPZ condition, infectivity or immunogenicity. This study aimed to unravel how the age of P. falciparum SPZ in salivary glands (14, 17, or 20 days post blood meal) affects their infectivity and the ensuing immune responses. METHODS SPZ numbers, viability by live/dead staining, motility using dedicated sporozoite motility orienting and organizing tool software (SMOOT), and infectivity of HC-04.j7 liver cells at 14, 17 and 20 days after mosquito feeding have been investigated. In vitro co-culture assays with SPZ stimulated monocyte-derived macrophages (MoMɸ) and CD8+ T-cells, analysed by flow cytometry, were used to investigate immune responses. RESULTS SPZ age did not result in different SPZ numbers or viability. However, a markedly different motility pattern, whereby motility decreased from 89% at day 14 to 80% at day 17 and 71% at day 20 was observed (p ≤ 0.0001). Similarly, infectivity of day 20 SPZ dropped to ~ 50% compared with day 14 SPZ (p = 0.004). MoMɸ were better able to take up day 14 SPZ than day 20 SPZ (from 7.6% to 4.1%, p = 0.03) and displayed an increased expression of pro-inflammatory CD80, IL-6 (p = 0.005), regulatory markers PDL1 (p = 0.02), IL-10 (p = 0.009) and cytokines upon phagocytosis of younger SPZ. Interestingly, co-culture of these cells with CD8+ T-cells revealed a decreased expression of activation marker CD137 and cytokine IFNγ compared to their day 20 counterparts. These findings suggest that older (day 17-20) P. falciparum SPZ are less infectious and have decreased immune regulatory potential. CONCLUSION Overall, this data is a first step in enhancing the understanding of how mosquito residing time affects P. falciparum SPZ and could impact the understanding of the P. falciparum infectious reservoir and the potency of whole SPZ vaccines.
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Affiliation(s)
- Roos van Schuijlenburg
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Samaneh Azargoshasb
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Clarize M de Korne
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen C Sijtsma
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Sascha Bezemer
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Alwin J van der Ham
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Els Baalbergen
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Fiona Geurten
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Laura M de Bes-Roeleveld
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Severine C Chevalley-Maurel
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Matthias N van Oosterom
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Fijs W B van Leeuwen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Blandine Franke-Fayard
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands
| | - Meta Roestenberg
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands.
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5
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Sollelis L, Howick VM, Marti M. Revisiting the determinants of malaria transmission. Trends Parasitol 2024; 40:302-312. [PMID: 38443304 DOI: 10.1016/j.pt.2024.02.001] [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: 12/20/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Malaria parasites have coevolved with humans over thousands of years, mirroring their migration out of Africa. They persist to this day, despite continuous elimination efforts worldwide. These parasites can adapt to changing environments during infection of human and mosquito, and when expanding the geographical range by switching vector species. Recent studies in the human malaria parasite, Plasmodium falciparum, identified determinants governing the plasticity of sexual conversion rates, sex ratio, and vector competence. Here we summarize the latest literature revealing environmental, epigenetic, and genetic determinants of malaria transmission.
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Affiliation(s)
- Lauriane Sollelis
- Wellcome Center for Integrative Parasitology, Institute of Infection and Immunity University of Glasgow, Glasgow, UK; Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Virginia M Howick
- Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland; Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Center for Integrative Parasitology, Institute of Infection and Immunity University of Glasgow, Glasgow, UK; Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland.
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6
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Hazzard B, Sá JM, Bogale HN, Pascini TV, Ellis AC, Amin S, Armistead JS, Adams JH, Wellems TE, Serre D. Single-cell analyses of polyclonal Plasmodium vivax infections and their consequences on parasite transmission. RESEARCH SQUARE 2024:rs.3.rs-3888175. [PMID: 38410426 PMCID: PMC10896380 DOI: 10.21203/rs.3.rs-3888175/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Most Plasmodium vivax infections contain genetically distinct parasites, but the consequences of this polyclonality on the development of asexual parasites, their sexual differentiation, and their transmission remain unknown. We describe infections of Saimiri monkeys with two strains of P. vivax and the analyses of 117,350 parasites characterized by single cell RNA sequencing and individually genotyped. In our model, consecutive inoculations fail to establish polyclonal infections. By contrast, simultaneous inoculations of two strains lead to sustained polyclonal infections, although without detectable differences in parasite regulation or sexual commitment. Analyses of sporozoites dissected from mosquitoes fed on coinfected monkeys show that all genotypes are successfully transmitted to mosquitoes. However, after sporozoite inoculation, not all genotypes contribute to the subsequent blood infections, highlighting an important bottleneck during pre-erythrocytic development. Overall, these studies provide new insights on the mechanisms regulating the establishment of polyclonal P. vivax infections and their consequences for disease transmission.
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Affiliation(s)
- Brittany Hazzard
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Haikel N. Bogale
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tales V. Pascini
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela C. Ellis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shuchi Amin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer S. Armistead
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, USA
| | - John H. Adams
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, USA
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Lead contact
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7
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Leela N, Prommana P, Kamchonwongpaisan S, Taechalertpaisarn T, Shaw PJ. Antimalarial target vulnerability of the putative Plasmodium falciparum methionine synthase. PeerJ 2024; 12:e16595. [PMID: 38239295 PMCID: PMC10795524 DOI: 10.7717/peerj.16595] [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: 06/30/2023] [Accepted: 11/14/2023] [Indexed: 01/22/2024] Open
Abstract
Background Plasmodium falciparum possesses a cobalamin-dependent methionine synthase (MS). MS is putatively encoded by the PF3D7_1233700 gene, which is orthologous and syntenic in Plasmodium. However, its vulnerability as an antimalarial target has not been assessed. Methods We edited the PF3D7_1233700 and PF3D7_0417200 (dihydrofolate reductase-thymidylate synthase, DHFR-TS) genes and obtained transgenic P. falciparum parasites expressing epitope-tagged target proteins under the control of the glmS ribozyme. Conditional loss-of-function mutants were obtained by treating transgenic parasites with glucosamine. Results DHFR-TS, but not MS mutants showed a significant proliferation defect over 96 h, suggesting that P. falciparum MS is not a vulnerable antimalarial target.
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Affiliation(s)
- Nirut Leela
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Bangkok, Thailand
| | - Parichat Prommana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Tana Taechalertpaisarn
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Bangkok, Thailand
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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8
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Dooley NL, Chabikwa TG, Pava Z, Loughland JR, Hamelink J, Berry K, Andrew D, Soon MSF, SheelaNair A, Piera KA, William T, Barber BE, Grigg MJ, Engwerda CR, Lopez JA, Anstey NM, Boyle MJ. Single cell transcriptomics shows that malaria promotes unique regulatory responses across multiple immune cell subsets. Nat Commun 2023; 14:7387. [PMID: 37968278 PMCID: PMC10651914 DOI: 10.1038/s41467-023-43181-7] [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: 11/23/2022] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
Plasmodium falciparum malaria drives immunoregulatory responses across multiple cell subsets, which protects from immunopathogenesis, but also hampers the development of effective anti-parasitic immunity. Understanding malaria induced tolerogenic responses in specific cell subsets may inform development of strategies to boost protective immunity during drug treatment and vaccination. Here, we analyse the immune landscape with single cell RNA sequencing during P. falciparum malaria. We identify cell type specific responses in sub-clustered major immune cell types. Malaria is associated with an increase in immunosuppressive monocytes, alongside NK and γδ T cells which up-regulate tolerogenic markers. IL-10-producing Tr1 CD4 T cells and IL-10-producing regulatory B cells are also induced. Type I interferon responses are identified across all cell types, suggesting Type I interferon signalling may be linked to induction of immunoregulatory networks during malaria. These findings provide insights into cell-specific and shared immunoregulatory changes during malaria and provide a data resource for further analysis.
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Affiliation(s)
- Nicholas L Dooley
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Julianne Hamelink
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- University of Queensland, Brisbane, QLD, Australia
| | - Kiana Berry
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Queensland University of Technology, Brisbane, QLD, Australia
| | - Dean Andrew
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kim A Piera
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Timothy William
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
- Subang Jaya Medical Centre, Selangor, Malaysia
| | - Bridget E Barber
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | | | - J Alejandro Lopez
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Kota Kinabalu Sabah-Menzies School of Health Research Program, Kota Kinabalu, Sabah, Malaysia
| | - Michelle J Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Environment and Sciences, Griffith University, Brisbane, QLD, Australia.
- University of Queensland, Brisbane, QLD, Australia.
- Queensland University of Technology, Brisbane, QLD, Australia.
- Burnet Institute, Melbourne, VIC, Australia.
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9
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Subudhi AK, Green JL, Satyam R, Salunke RP, Lenz T, Shuaib M, Isaioglou I, Abel S, Gupta M, Esau L, Mourier T, Nugmanova R, Mfarrej S, Shivapurkar R, Stead Z, Rached FB, Ostwal Y, Sougrat R, Dada A, Kadamany AF, Fischle W, Merzaban J, Knuepfer E, Ferguson DJP, Gupta I, Le Roch KG, Holder AA, Pain A. DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages. Nat Microbiol 2023; 8:2154-2169. [PMID: 37884813 PMCID: PMC10627835 DOI: 10.1038/s41564-023-01497-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Malaria-associated pathogenesis such as parasite invasion, egress, host cell remodelling and antigenic variation requires concerted action by many proteins, but the molecular regulation is poorly understood. Here we have characterized an essential Plasmodium-specific Apicomplexan AP2 transcription factor in Plasmodium falciparum (PfAP2-P; pathogenesis) during the blood-stage development with two peaks of expression. An inducible knockout of gene function showed that PfAP2-P is essential for trophozoite development, and critical for var gene regulation, merozoite development and parasite egress. Chromatin immunoprecipitation sequencing data collected at timepoints matching the two peaks of pfap2-p expression demonstrate PfAP2-P binding to promoters of genes controlling trophozoite development, host cell remodelling, antigenic variation and pathogenicity. Single-cell RNA sequencing and fluorescence-activated cell sorting revealed de-repression of most var genes in Δpfap2-p parasites. Δpfap2-p parasites also overexpress early gametocyte marker genes, indicating a regulatory role in sexual stage conversion. We conclude that PfAP2-P is an essential upstream transcriptional regulator at two distinct stages of the intra-erythrocytic development cycle.
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Affiliation(s)
- Amit Kumar Subudhi
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Judith L Green
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
| | - Rohit Satyam
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Rahul P Salunke
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Muhammad Shuaib
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ioannis Isaioglou
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Luke Esau
- KAUST Core Labs, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Raushan Nugmanova
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Rupali Shivapurkar
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Zenaida Stead
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Fathia Ben Rached
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Yogesh Ostwal
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Rachid Sougrat
- KAUST Core Labs, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
- College of Medicine, Al Faisal University, Riyadh, Saudi Arabia
| | - Abdullah Fuaad Kadamany
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Jasmeen Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ellen Knuepfer
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
- Molecular and Cellular Parasitology Laboratory, Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
- School of Artificial Intelligence, Indian Institute of Technology Delhi, New Delhi, India
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK.
| | - Arnab Pain
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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10
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Kioko M, Pance A, Mwangi S, Goulding D, Kemp A, Rono M, Ochola-Oyier LI, Bull PC, Bejon P, Rayner JC, Abdi AI. Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum. Nat Commun 2023; 14:6447. [PMID: 37833314 PMCID: PMC10575976 DOI: 10.1038/s41467-023-42103-x] [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: 10/28/2022] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Plasmodium falciparum secretes extracellular vesicles (PfEVs) that contain parasite-derived RNA. However, the significance of the secreted RNA remains unexplored. Here, we compare secreted and intracellular RNA from asexual cultures of six P. falciparum lines. We find that secretion of RNA via extracellular vesicles is not only periodic throughout the asexual intraerythrocytic developmental cycle but is also highly conserved across P. falciparum isolates. We further demonstrate that the phases of RNA secreted via extracellular vesicles are discernibly shifted compared to those of the intracellular RNA within the secreting whole parasite. Finally, transcripts of genes with no known function during the asexual intraerythrocytic developmental cycle are enriched in PfEVs compared to the whole parasite. We conclude that the secretion of extracellular vesicles could be a putative posttranscriptional RNA regulation mechanism that is part of or synergise the classic RNA decay processes to maintain intracellular RNA levels in P. falciparum.
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Affiliation(s)
- Mwikali Kioko
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Open University, Milton Keynes, UK
| | - Alena Pance
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
- School of Life and Medical Science, University of Hertfordshire, Hatfield, UK
| | - Shaban Mwangi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - David Goulding
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alison Kemp
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Rono
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | | | - Pete C Bull
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Rayner
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Abdirahman I Abdi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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11
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Guttery DS, Zeeshan M, Holder AA, Tromer EC, Tewari R. Meiosis in Plasmodium: how does it work? Trends Parasitol 2023; 39:812-821. [PMID: 37541799 DOI: 10.1016/j.pt.2023.07.002] [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: 06/05/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 08/06/2023]
Abstract
Meiosis is sexual cell division, a process in eukaryotes whereby haploid gametes are produced. Compared to canonical model eukaryotes, meiosis in apicomplexan parasites appears to diverge from the process with respect to the molecular mechanisms involved; the biology of Plasmodium meiosis, and its regulation by means of post-translational modification, are largely unexplored. Here, we discuss the impact of technological advances in cell biology, evolutionary bioinformatics, and genome-wide functional studies on our understanding of meiosis in the Apicomplexa. These parasites, including Plasmodium falciparum, Toxoplasma gondii, and Eimeria spp., have significant socioeconomic impact on human and animal health. Understanding this key stage during the parasite's life cycle may well reveal attractive targets for therapeutic intervention.
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Affiliation(s)
- David S Guttery
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK; Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK.
| | - Mohammad Zeeshan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Rita Tewari
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK.
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12
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Jentho E, Sousa AGG, Ramos S, Ademolue TW, Sobral J, Costa J, Brito D, Manteiro M, Leite RB, Lilue J, Soares MP. Single-cell RNA sequencing and analysis of rodent blood stage Plasmodium. STAR Protoc 2023; 4:102491. [PMID: 37581982 PMCID: PMC10436236 DOI: 10.1016/j.xpro.2023.102491] [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: 03/30/2023] [Revised: 05/30/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Bulk RNA sequencing of Plasmodium spp., the causative parasite of malaria, fails to discriminate developmental-stage-specific gene regulation. Here, we provide a protocol that uses single-cell RNA sequencing of FACS-sorted Plasmodium-chabaudi-chabaudi-AS-infected red blood cells (iRBCs) to characterize developmental-stage-specific modulation of gene expression during malaria blood stage. We describe steps for infecting mice, monitoring disease progression, preparing iRBCs, and single-cell sequencing iRBCs. We then detail procedures for analyzing scRNA-seq data. For complete details on the use and execution of this protocol, please refer to Ramos et al.1.
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Affiliation(s)
- Elisa Jentho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal; Jena University Hospital, Department of Anesthesiology and Intensive Care Medicine, Friedrich-Schiller-University, Jena, Germany.
| | | | - Susana Ramos
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - João Sobral
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João Costa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Denise Brito
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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13
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Abstract
Plasmodium falciparum, the human malaria parasite, infects two hosts and various cell types, inducing distinct morphological and physiological changes in the parasite in response to different environmental conditions. These variations required the parasite to adapt and develop elaborate molecular mechanisms to ensure its spread and transmission. Recent findings have significantly improved our understanding of the regulation of gene expression in P. falciparum. Here, we provide an up-to-date overview of technologies used to highlight the transcriptomic adjustments occurring in the parasite throughout its life cycle. We also emphasize the complementary and complex epigenetic mechanisms regulating gene expression in malaria parasites. This review concludes with an outlook on the chromatin architecture, the remodeling systems, and how this 3D genome organization is critical in various biological processes.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
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14
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Hollin T, Le Roch KG. Sex determination and transmission: Leveraging genetic screens to reveal Plasmodium's secrets. Cell Host Microbe 2023; 31:1430-1432. [PMID: 37708851 DOI: 10.1016/j.chom.2023.08.007] [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: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Genes and regulatory mechanisms governing malaria parasite transmission and development in mosquitoes are incompletely understood. Recently, Russell and colleagues identified genes required for parasite sexual development. In this issue of Cell Host & Microbe, Ukegbu and colleagues report a genetic approach to study genes enabling parasite survival in mosquito stages.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell, and Systems Biology, University of California Riverside, Riverside, CA, USA.
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15
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Kengne-Ouafo JA, Bah SY, Kemp A, Stewart L, Amenga-Etego L, Deitsch KW, Rayner JC, Billker O, Binka FN, Sutherland CJ, Awandare GA, Urban BC, Dinko B. The global transcriptome of Plasmodium falciparum mid-stage gametocytes (stages II-IV) appears largely conserved and gametocyte-specific gene expression patterns vary in clinical isolates. Microbiol Spectr 2023; 11:e0382022. [PMID: 37698406 PMCID: PMC10581088 DOI: 10.1128/spectrum.03820-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/09/2023] [Indexed: 09/13/2023] Open
Abstract
Our overall understanding of the developmental biology of malaria parasites has been greatly enhanced by recent advances in transcriptomic analysis. However, most of these investigations rely on laboratory strains (LS) that were adapted into in vitro culture many years ago, and the transcriptomes of clinical isolates (CI) circulating in human populations have not been assessed. In this study, RNA-seq was used to compare the global transcriptome of mid-stage gametocytes derived from three short-term cultured CI, with gametocytes derived from the NF54 reference laboratory strain. The core transcriptome appeared to be consistent between CI- and LS-derived gametocyte preparations, but some important differences were also observed. A majority of gametocyte-specific genes (43/53) appear to have relatively higher expression in CI-derived gametocytes than in LS-derived gametocytes, but a K-means clustering analysis showed that genes involved in flagellum- and microtubule-based processes (movement/motility) were more abundant in both groups, albeit with some differences between them. In addition, gametocytes from one CI described as CI group II gametocytes (CI:GGII) showed gene expression variation in the form of reduced gametocyte-specific gene expression compared to the other two CI-derived gametocytes (CI gametocyte group I, CI:GGI), although the mixed developmental stages used in our study is a potential confounder, only partially mitigated by the inclusion of multiple replicates for each CI. Overall, our study suggests that there may be subtle differences in the gene expression profiles of mid-stage gametocytes from CI relative to the NF54 reference strain of Plasmodium falciparum. Thus, it is necessary to deploy gametocyte-producing clinical parasite isolates to fully understand the diversity of gene expression strategies that may occur during the sequestered development of parasite sexual stages. IMPORTANCE Maturing gametocytes of Plasmodium falciparum are known to sequester away from peripheral circulation into the bone marrow until they are mature. Blocking gametocyte sequestration can prevent malaria transmission from humans to mosquitoes, but most studies aim to understand gametocyte development utilizing long-term adapted laboratory lines instead of clinical isolates. This is a particular issue for our understanding of the sexual stages, which are known to decrease rapidly during adaptation to long-term culture, meaning that many LS are unable to produce transmissible gametocytes. Using RNA-seq, we investigated the global transcriptome of mid-stage gametocytes derived from three clinical isolates and a reference strain (NF54). This identified important differences in gene expression profiles between immature gametocytes of CI and the NF54 reference strain of P. falciparum, suggesting increased investment in gametocytogenesis in clinical isolates. Our transcriptomic data highlight the use of clinical isolates in studying the morphological, cellular features and molecular biology of gametocytes.
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Affiliation(s)
- Jonas A. Kengne-Ouafo
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Saikou Y. Bah
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Alison Kemp
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Lindsay Stewart
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lucas Amenga-Etego
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York City, New York, USA
| | - Julian C. Rayner
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Oliver Billker
- Malaria Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fred N. Binka
- Department of Epidemiology and Biostatistics, School of Public Health, University of Health and Allied Sciences, Ho, Ghana
| | - Colin J. Sutherland
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gordon A. Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Britta C. Urban
- Faculty of Biological Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Bismarck Dinko
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
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16
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Quaye IK, Aleksenko L, Paganotti GM, Peloewetse E, Haiyambo DH, Ntebela D, Oeuvray C, Greco B. Malaria Elimination in Africa: Rethinking Strategies for Plasmodium vivax and Lessons from Botswana. Trop Med Infect Dis 2023; 8:392. [PMID: 37624330 PMCID: PMC10458071 DOI: 10.3390/tropicalmed8080392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
The global malaria community has picked up the theme of malaria elimination in more than 90% of the world's population in the next decade. Recent reports of Plasmodium vivax (P. vivax) in sub-Saharan Africa, including in Duffy-negative individuals, threaten the efforts aimed at achieving elimination. This is not only in view of strategies that are tailored only to P. falciparum elimination but also due to currently revealed biological characteristics of P. vivax concerning the relapse patterns of hypnozoites and conservation of large biomasses in cryptic sites in the bone marrow and spleen. A typical scenario was observed in Botswana between 2008 and 2018, which palpably projects how P. vivax could endanger malaria elimination efforts where the two parasites co-exist. The need for the global malaria community, national malaria programs (NMPs), funding agencies and relevant stakeholders to engage in a forum to discuss and recommend clear pathways for elimination of malaria, including P. vivax, in sub-Saharan Africa is warranted.
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Affiliation(s)
- Isaac K. Quaye
- Pan African Vivax and Ovale Network, Faculty of Engineering Computer and Allied Sciences, Regent University College of Science and Technology, #1 Regent Ave, McCarthy Hill, Mendskrom, Dansoman, Accra P.O. Box DS1636, Ghana
| | - Larysa Aleksenko
- Department of Health Sciences, School of Public Health, College of Health, Medicine and Life Sciences, Brunel University, Kingston Lane, Uxbridge, Middlesex, London UB8 3PH, UK;
| | - Giacomo M. Paganotti
- Botswana-University of Pennsylvania Partnership, Riverwalk, Gaborone P.O. Box 45498, Botswana;
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elias Peloewetse
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone Private Bag 00704, Botswana;
| | - Daniel H. Haiyambo
- Department of Human, Biological and Translational Medical Sciences, Faculty of Health Sciences and Veterinary Medicine, University of Namibia School of Medicine, Hage Geingob Campus, Windhoek Private Bag 13301, Namibia;
| | - Davies Ntebela
- National Malaria Program, Ministry of Health, Gaborone Private Bag 0038, Botswana;
| | - Claude Oeuvray
- Global Health Institute of Merck, Terre Bonne Building Z0, Route de Crassier 1, Eysin, 1266 Geneva, Switzerland; (C.O.); (B.G.)
| | - Beatrice Greco
- Global Health Institute of Merck, Terre Bonne Building Z0, Route de Crassier 1, Eysin, 1266 Geneva, Switzerland; (C.O.); (B.G.)
| | - the PAVON Consortium
- PAVON, Regent University College of Science and Technology, #1 Regent Avenue, McCarthy Hiil, Mendskrom, Dansoman, Accra P.O. Box DS1636, Ghana
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17
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Ouologuem DT, Dara A, Kone A, Ouattara A, Djimde AA. Plasmodium falciparum Development from Gametocyte to Oocyst: Insight from Functional Studies. Microorganisms 2023; 11:1966. [PMID: 37630530 PMCID: PMC10460021 DOI: 10.3390/microorganisms11081966] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Malaria elimination may never succeed without the implementation of transmission-blocking strategies. The transmission of Plasmodium spp. parasites from the human host to the mosquito vector depends on circulating gametocytes in the peripheral blood of the vertebrate host. Once ingested by the mosquito during blood meals, these sexual forms undergo a series of radical morphological and metabolic changes to survive and progress from the gut to the salivary glands, where they will be waiting to be injected into the vertebrate host. The design of effective transmission-blocking strategies requires a thorough understanding of all the mechanisms that drive the development of gametocytes, gametes, sexual reproduction, and subsequent differentiation within the mosquito. The drastic changes in Plasmodium falciparum shape and function throughout its life cycle rely on the tight regulation of stage-specific gene expression. This review outlines the mechanisms involved in Plasmodium falciparum sexual stage development in both the human and mosquito vector, and zygote to oocyst differentiation. Functional studies unravel mechanisms employed by P. falciparum to orchestrate the expression of stage-specific functional products required to succeed in its complex life cycle, thus providing us with potential targets for developing new therapeutics. These mechanisms are based on studies conducted with various Plasmodium species, including predominantly P. falciparum and the rodent malaria parasites P. berghei. However, the great potential of epigenetics, genomics, transcriptomics, proteomics, and functional genetic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in studies using human malaria parasites and field isolates.
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Affiliation(s)
- Dinkorma T. Ouologuem
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Antoine Dara
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Aminatou Kone
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Abdoulaye A. Djimde
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
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18
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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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19
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Shivam S, Ertl R, Sexl V, El-Matbouli M, Kumar G. Differentially expressed transcripts of Tetracapsuloides bryosalmonae (Cnidaria) between carrier and dead-end hosts involved in key biological processes: novel insights from a coupled approach of FACS and RNA sequencing. Vet Res 2023; 54:51. [PMID: 37365650 PMCID: PMC10291810 DOI: 10.1186/s13567-023-01185-7] [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: 01/23/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Tetracapsuloides bryosalmonae is a malacosporean endoparasite that infects a wide range of salmonids and causes proliferative kidney disease (PKD). Brown trout serves as a carrier host whereas rainbow trout represents a dead-end host. We thus asked if the parasite adapts to the different hosts by changing molecular mechanisms. We used fluorescent activated cell sorting (FACS) to isolate parasites from the kidney of brown trout and rainbow trout following experimental infection with T. bryosalmonae. The sorted parasite cells were then subjected to RNA sequencing. By this approach, we identified 1120 parasite transcripts that were expressed differentially in parasites derived from brown trout and rainbow trout. We found elevated levels of transcripts related to cytoskeleton organisation, cell polarity, peptidyl-serine phosphorylation in parasites sorted from brown trout. In contrast, transcripts related to translation, ribonucleoprotein complex biogenesis and subunit organisation, non-membrane bounded organelle assembly, regulation of protein catabolic process and protein refolding were upregulated in rainbow trout-derived parasites. These findings show distinct molecular adaptations of parasites, which may underlie their distinct outcomes in the two hosts. Moreover, the identification of these differentially expressed transcripts may enable the identification of novel drug targets that may be exploited as treatment against T. bryosalmonae. We here also describe for the first time how FACS based isolation of T. bryosalmonae cells from infected kidney of fish fosters research and allows to define differentially expressed parasite transcripts in carrier and dead-end fish hosts.
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Affiliation(s)
- Saloni Shivam
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Karwar Regional Station of Indian Council of Agricultural Research, Central Marine Fisheries Research Institute, Karwar, Karnataka, India
| | - Reinhard Ertl
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mansour El-Matbouli
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria
- School of Biotechnology, Badr University in Cairo, Badr City, Cairo, Egypt
| | - Gokhlesh Kumar
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria.
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20
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Parres-Mercader M, Pance A, Gómez-Díaz E. Novel systems to study vector-pathogen interactions in malaria. Front Cell Infect Microbiol 2023; 13:1146030. [PMID: 37305421 PMCID: PMC10253182 DOI: 10.3389/fcimb.2023.1146030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/04/2023] [Indexed: 06/13/2023] Open
Abstract
Some parasitic diseases, such as malaria, require two hosts to complete their lifecycle: a human and an insect vector. Although most malaria research has focused on parasite development in the human host, the life cycle within the vector is critical for the propagation of the disease. The mosquito stage of the Plasmodium lifecycle represents a major demographic bottleneck, crucial for transmission blocking strategies. Furthermore, it is in the vector, where sexual recombination occurs generating "de novo" genetic diversity, which can favor the spread of drug resistance and hinder effective vaccine development. However, understanding of vector-parasite interactions is hampered by the lack of experimental systems that mimic the natural environment while allowing to control and standardize the complexity of the interactions. The breakthrough in stem cell technologies has provided new insights into human-pathogen interactions, but these advances have not been translated into insect models. Here, we review in vivo and in vitro systems that have been used so far to study malaria in the mosquito. We also highlight the relevance of single-cell technologies to progress understanding of these interactions with higher resolution and depth. Finally, we emphasize the necessity to develop robust and accessible ex vivo systems (tissues and organs) to enable investigation of the molecular mechanisms of parasite-vector interactions providing new targets for malaria control.
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Affiliation(s)
- Marina Parres-Mercader
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN, CSIC), Granada, Spain
| | - Alena Pance
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN, CSIC), Granada, Spain
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21
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Subudhi AK, Green JL, Satyam R, Lenz T, Salunke RP, Shuaib M, Isaioglou I, Abel S, Gupta M, Esau L, Mourier T, Nugmanova R, Mfarrej S, Sivapurkar R, Stead Z, Rached FB, Otswal Y, Sougrat R, Dada A, Kadamany AF, Fischle W, Merzaban J, Knuepfer E, Ferguson DJP, Gupta I, Le Roch KG, Holder AA, Pain A. PfAP2-MRP DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541898. [PMID: 37293082 PMCID: PMC10245809 DOI: 10.1101/2023.05.23.541898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Malaria pathogenicity results from the parasite's ability to invade, multiply within and then egress from the host red blood cell (RBC). Infected RBCs are remodeled, expressing antigenic variant proteins (such as PfEMP1, coded by the var gene family) for immune evasion and survival. These processes require the concerted actions of many proteins, but the molecular regulation is poorly understood. We have characterized an essential Plasmodium specific Apicomplexan AP2 (ApiAP2) transcription factor in Plasmodium falciparum (PfAP2-MRP; Master Regulator of Pathogenesis) during the intraerythrocytic developmental cycle (IDC). An inducible gene knockout approach showed that PfAP2-MRP is essential for development during the trophozoite stage, and critical for var gene regulation, merozoite development and parasite egress. ChIP-seq experiments performed at 16 hour post invasion (h.p.i.) and 40 h.p.i. matching the two peaks of PfAP2-MRP expression, demonstrate binding of PfAP2-MRP to the promoters of genes controlling trophozoite development and host cell remodeling at 16 h.p.i. and antigenic variation and pathogenicity at 40 h.p.i. Using single-cell RNA-seq and fluorescence-activated cell sorting, we show de-repression of most var genes in Δpfap2-mrp parasites that express multiple PfEMP1 proteins on the surface of infected RBCs. In addition, the Δpfap2-mrp parasites overexpress several early gametocyte marker genes at both 16 and 40 h.p.i., indicating a regulatory role in the sexual stage conversion. Using the Chromosomes Conformation Capture experiment (Hi-C), we demonstrate that deletion of PfAP2-MRP results in significant reduction of both intra-chromosomal and inter-chromosomal interactions in heterochromatin clusters. We conclude that PfAP2-MRP is a vital upstream transcriptional regulator controlling essential processes in two distinct developmental stages during the IDC that include parasite growth, chromatin structure and var gene expression.
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Affiliation(s)
- Amit Kumar Subudhi
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Judith L Green
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Rohit Satyam
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi, Delhi 110025, India
| | - Todd Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Rahul P Salunke
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muhammad Shuaib
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ioannis Isaioglou
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Mohit Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Luke Esau
- KAUST Core Labs, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Raushan Nugmanova
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Rupali Sivapurkar
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Zenaida Stead
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Fathia Ben Rached
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yogesh Otswal
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Rachid Sougrat
- KAUST Core Labs, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ashraf Dada
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Abdullah Fuaad Kadamany
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jasmeen Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ellen Knuepfer
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford OX1 2JD, United Kingdom
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Arnab Pain
- Pathogen Genomics Group, Bioscience Program, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- International Institute for Zoonosis Control; Hokkaido University, Sapporo, Japan
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22
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Espino-Sanchez T, Wienkers H, Marvin R, Nalder SA, García-Guerrero A, VanNatta P, Jami-Alahmadi Y, Mixon Blackwell A, Whitby F, Wohlschlegel J, Kieber-Emmons M, Hill C, A. Sigala P. Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites. Proc Natl Acad Sci U S A 2023; 120:e2301047120. [PMID: 37126705 PMCID: PMC10175771 DOI: 10.1073/pnas.2301047120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.
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Affiliation(s)
| | - Henry Wienkers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Shai-anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | | | - Peter E. VanNatta
- Department of Chemistry, University of Utah, Salt Lake City, UT84112
| | | | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | | | | | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT84112
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23
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Jeninga MD, Tang J, Selvarajah SA, Maier AG, Duffy MF, Petter M. Plasmodium falciparum gametocytes display global chromatin remodelling during sexual differentiation. BMC Biol 2023; 21:65. [PMID: 37013531 PMCID: PMC10071754 DOI: 10.1186/s12915-023-01568-4] [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: 07/15/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The protozoan malaria parasite Plasmodium falciparum has a complex life cycle during which it needs to differentiate into multiple morphologically distinct life forms. A key process for transmission of the disease is the development of male and female gametocytes in the human blood, yet the mechanisms determining sexual dimorphism in these haploid, genetically identical sexual precursor cells remain largely unknown. To understand the epigenetic program underlying the differentiation of male and female gametocytes, we separated the two sexual forms by flow cytometry and performed RNAseq as well as comprehensive ChIPseq profiling of several histone variants and modifications. RESULTS We show that in female gametocytes the chromatin landscape is globally remodelled with respect to genome-wide patterns and combinatorial usage of histone variants and histone modifications. We identified sex specific differences in heterochromatin distribution, implicating exported proteins and ncRNAs in sex determination. Specifically in female gametocytes, the histone variants H2A.Z/H2B.Z were highly enriched in H3K9me3-associated heterochromatin. H3K27ac occupancy correlated with stage-specific gene expression, but in contrast to asexual parasites this was unlinked to H3K4me3 co-occupancy at promoters in female gametocytes. CONCLUSIONS Collectively, we defined novel combinatorial chromatin states differentially organising the genome in gametocytes and asexual parasites and unravelled fundamental, sex-specific differences in the epigenetic code. Our chromatin maps represent an important resource for future understanding of the mechanisms driving sexual differentiation in P. falciparum.
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Affiliation(s)
- Myriam D Jeninga
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Jingyi Tang
- Department of Medicine, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Shamista A Selvarajah
- Department of Medicine, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Alexander G Maier
- The Australian National University, Research School of Biology, 134 Linnaeus Way, Canberra, ACT, 2601, Australia
| | - Michael F Duffy
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute, 792 Elizabeth Street, Melbourne, VIC, 3000, Australia
- Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Michaela Petter
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany.
- Department of Medicine, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia.
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24
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Mohammed M, Dziedziech A, Sekar V, Ernest M, Alves E Silva TL, Balan B, Emami SN, Biryukova I, Friedländer MR, Jex A, Jacobs-Lorena M, Henriksson J, Vega-Rodriguez J, Ankarklev J. Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut. Microbiol Spectr 2023; 11:e0367122. [PMID: 36847501 PMCID: PMC10100735 DOI: 10.1128/spectrum.03671-22] [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: 09/12/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 h after blood feeding, including the zygote and ookinete stages. This study revealed the temporal gene expression of the ApiAP2 family of transcription factors and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structural protein prediction analyses, we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation, and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody- or peptide-based transmission suppression strategies. In total, this study uncovers the P. falciparum transcriptome from early to late parasite development in the mosquito midgut, inside its natural vector, which provides an important resource for future malaria transmission-blocking initiatives. IMPORTANCE The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host. However, recent incentives in the field call for novel interventions to block parasite transmission from humans to the mosquito vector. Therefore, we need to better understand the parasite biology during its development inside the mosquito, including a deeper understanding of the expression of genes controlling parasite progression during these stages. Here, we have generated single-cell transcriptome data, covering P. falciparum's development, from gamete to ookinete inside the mosquito midgut, uncovering previously untapped parasite biology, including a repertoire of novel biomarkers to be explored in future transmission-blocking efforts. We anticipate that our study provides an important resource, which can be further explored to improve our understanding of the parasite biology as well as aid in guiding future malaria intervention strategies.
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Affiliation(s)
- Mubasher Mohammed
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Alexis Dziedziech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vaishnovi Sekar
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Medard Ernest
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Thiago Luiz Alves E Silva
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - S. Noushin Emami
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R. Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Aaron Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Johan Henriksson
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Joel Vega-Rodriguez
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Johan Ankarklev
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Microbial Single Cell Genomics, Department of Cell and Molecular Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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25
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Turkiewicz A, Manko E, Oresegun DR, Nolder D, Spadar A, Sutherland CJ, Cox-Singh J, Moon RW, Lau YL, Campino S, Clark TG. Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations. Sci Rep 2023; 13:2142. [PMID: 36750737 PMCID: PMC9905552 DOI: 10.1038/s41598-023-29368-4] [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: 10/12/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
The zoonotic Plasmodium knowlesi parasite is a growing public health concern in Southeast Asia, especially in Malaysia, where elimination of P. falciparum and P. vivax malaria has been the focus of control efforts. Understanding of the genetic diversity of P. knowlesi parasites can provide insights into its evolution, population structure, diagnostics, transmission dynamics, and the emergence of drug resistance. Previous work has revealed that P. knowlesi fall into three main sub-populations distinguished by a combination of geographical location and macaque host (Macaca fascicularis and M. nemestrina). It has been shown that Malaysian Borneo groups display profound heterogeneity with long regions of high or low divergence resulting in mosaic patterns between sub-populations, with some evidence of chromosomal-segment exchanges. However, the genetic structure of non-Borneo sub-populations is less clear. By gathering one of the largest collections of P. knowlesi whole-genome sequencing data, we studied structural genomic changes across sub-populations, with the analysis revealing differences in Borneo clusters linked to mosquito-related stages of the parasite cycle, in contrast to differences in host-related stages for the Peninsular group. Our work identifies new genetic exchange events, including introgressions between Malaysian Peninsular and M. nemestrina-associated clusters on various chromosomes, including in parasite invasion genes (DBP[Formula: see text], NBPX[Formula: see text] and NBPX[Formula: see text]), and important proteins expressed in the vertebrate parasite stages. Recombination events appear to have occurred between the Peninsular and M. fascicularis-associated groups, including in the DBP[Formula: see text] and DBP[Formula: see text] invasion associated genes. Overall, our work finds that genetic exchange events have occurred among the recognised contemporary groups of P. knowlesi parasites during their evolutionary history, leading to apparent mosaicism between these sub-populations. These findings generate new hypotheses relevant to parasite evolutionary biology and P. knowlesi epidemiology, which can inform malaria control approaches to containing the impact of zoonotic malaria on human communities.
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Affiliation(s)
- Anna Turkiewicz
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emilia Manko
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Damiola R Oresegun
- Division of Infection, School of Medicine, University of St Andrews, St Andrews, UK
| | - Debbie Nolder
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Janet Cox-Singh
- Division of Infection, School of Medicine, University of St Andrews, St Andrews, UK
| | - Robert W Moon
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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26
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Espino-Sanchez TJ, Wienkers H, Marvin RG, Nalder SA, García-Guerrero AE, VanNatta PE, Jami-Alahmadi Y, Blackwell AM, Whitby FG, Wohlschlegel JA, Kieber-Emmons MT, Hill CP, Sigala PA. Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525242. [PMID: 36747727 PMCID: PMC9900762 DOI: 10.1101/2023.01.23.525242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs ( c and c -2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c -2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c 1 for inducible knockdown. Translational repression of cyt c and cyt c 1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c -2 knockdown or knock-out had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c -2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c -2 has an unusually open active site in which heme is stably coordinated by only a single axial amino-acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution. SIGNIFICANCE STATEMENT Mitochondria are critical organelles in eukaryotic cells that drive oxidative metabolism. The mitochondrion of Plasmodium malaria parasites is a major drug target that has many differences from human cells and remains poorly studied. One key difference from humans is that malaria parasites express two cytochrome c proteins that differ significantly from each other and play untested and uncertain roles in the mitochondrial electron transport chain (ETC). Our study revealed that one cyt c is essential for ETC function and parasite viability while the second, more divergent protein has unusual structural and biochemical properties and is not required for growth of blood-stage parasites. This work elucidates key biochemical properties and evolutionary differences in the mitochondrial ETC of malaria parasites.
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Affiliation(s)
- Tanya J. Espino-Sanchez
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Henry Wienkers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Rebecca G. Marvin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Shai-anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Aldo E. García-Guerrero
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Peter E. VanNatta
- Department of Chemistry, University of Utah, Salt Lake City, UT, United States
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, CA, United States
| | - Amanda Mixon Blackwell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Frank G. Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, CA, United States
| | | | - Christopher P. Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States,Corresponding author: Paul Sigala
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27
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Zanghi G, Patel H, Camargo N, Smith JL, Bae Y, Flannery EL, Chuenchob V, Fishbaugher ME, Mikolajczak SA, Roobsoong W, Sattabongkot J, Hayes K, Vaughan AM, Kappe SHI. Global gene expression of human malaria parasite liver stages throughout intrahepatocytic development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522945. [PMID: 36711670 PMCID: PMC9881933 DOI: 10.1101/2023.01.05.522945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Plasmodium falciparum (Pf) is causing the greatest malaria burden, yet the liver stages (LS) of this most important parasite species have remained poorly studied. Here, we used a human liver-chimeric mouse model in combination with a novel fluorescent PfNF54 parasite line (PfNF54cspGFP) to isolate PfLS-infected hepatocytes and generate transcriptomes that cover the major LS developmental phases in human hepatocytes. RNA-seq analysis of early Pf LS trophozoites two days after infection, revealed a central role of translational regulation in the transformation of the extracellular invasive sporozoite into intracellular LS. The developmental time course gene expression analysis indicated that fatty acid biosynthesis, isoprenoid biosynthesis and iron metabolism are sustaining LS development along with amino acid metabolism and biosynthesis. Countering oxidative stress appears to play an important role during intrahepatic LS development. Furthermore, we observed expression of the variant PfEMP1 antigen-encoding var genes, and we confirmed expression of PfEMP1 protein during LS development. Transcriptome comparison of the late Pf liver stage schizonts with P. vivax (Pv) late liver stages revealed highly conserved gene expression profiles among orthologous genes. A notable difference however was the expression of genes regulating sexual stage commitment. While Pv schizonts expressed markers of sexual commitment, the Pf LS parasites were not sexually committed and showed expression of gametocytogenesis repression factors. Our results provide the first comprehensive gene expression profile of the human malaria parasite Pf LS isolated during in vivo intrahepatocytic development. This data will inform biological studies and the search for effective intervention strategies that can prevent infection.
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Affiliation(s)
- Gigliola Zanghi
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Hardik Patel
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Nelly Camargo
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Jenny L. Smith
- Research Scientific Computing, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Yeji Bae
- Research Scientific Computing, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Erika L. Flannery
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Novartis Institute for Tropical Diseases, Emeryville, CA, United State
| | - Vorada Chuenchob
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Novartis Institute for Tropical Diseases, Emeryville, CA, United State
| | - Matthew E. Fishbaugher
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Novartis Institute for Tropical Diseases, Emeryville, CA, United State
| | - Sebastian A Mikolajczak
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Novartis Institute for Tropical Diseases, Emeryville, CA, United State
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Kiera Hayes
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
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28
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Chandley P, Ranjan R, Kumar S, Rohatgi S. Host-parasite interactions during Plasmodium infection: Implications for immunotherapies. Front Immunol 2023; 13:1091961. [PMID: 36685595 PMCID: PMC9845897 DOI: 10.3389/fimmu.2022.1091961] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Malaria is a global infectious disease that remains a leading cause of morbidity and mortality in the developing world. Multiple environmental and host and parasite factors govern the clinical outcomes of malaria. The host immune response against the Plasmodium parasite is heterogenous and stage-specific both in the human host and mosquito vector. The Plasmodium parasite virulence is predominantly associated with its ability to evade the host's immune response. Despite the availability of drug-based therapies, Plasmodium parasites can acquire drug resistance due to high antigenic variations and allelic polymorphisms. The lack of licensed vaccines against Plasmodium infection necessitates the development of effective, safe and successful therapeutics. To design an effective vaccine, it is important to study the immune evasion strategies and stage-specific Plasmodium proteins, which are targets of the host immune response. This review provides an overview of the host immune defense mechanisms and parasite immune evasion strategies during Plasmodium infection. Furthermore, we also summarize and discuss the current progress in various anti-malarial vaccine approaches, along with antibody-based therapy involving monoclonal antibodies, and research advancements in host-directed therapy, which can together open new avenues for developing novel immunotherapies against malaria infection and transmission.
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Affiliation(s)
- Pankaj Chandley
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, India
| | - Ravikant Ranjan
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, India
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Soma Rohatgi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, India,*Correspondence: Soma Rohatgi,
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29
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Hussain T, Linera-Gonzalez J, Beck JM, Fierro MA, Mair GR, Smith RC, Beck JR. The PTEX Pore Component EXP2 Is Important for Intrahepatic Development during the Plasmodium Liver Stage. mBio 2022; 13:e0309622. [PMID: 36445080 PMCID: PMC9765067 DOI: 10.1128/mbio.03096-22] [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: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
During vertebrate infection, obligate intracellular malaria parasites develop within a parasitophorous vacuole, which constitutes the interface between the parasite and its hepatocyte or erythrocyte host cells. To traverse this barrier, Plasmodium spp. utilize a dual-function pore formed by EXP2 for nutrient transport and, in the context of the PTEX translocon, effector protein export across the vacuole membrane. While critical to blood-stage survival, less is known about EXP2/PTEX function in the liver stage, although major differences in the export mechanism are suggested by absence of the PTEX unfoldase HSP101 in the intrahepatic vacuole. Here, we employed the glucosamine-activated glmS ribozyme to study the role of EXP2 during Plasmodium berghei liver-stage development in hepatoma cells. Insertion of the glmS sequence into the exp2 3' untranslated region (UTR) enabled glucosamine-dependent depletion of EXP2 after hepatocyte invasion, allowing separation of EXP2 function during intrahepatic development from a recently reported role in hepatocyte invasion. Postinvasion EXP2 knockdown reduced parasite size and largely abolished expression of the mid- to late-liver-stage marker LISP2. As an orthogonal approach to monitor development, EXP2-glmS parasites and controls were engineered to express nanoluciferase. Activation of glmS after invasion substantially decreased luminescence in hepatoma monolayers and in culture supernatants at later time points corresponding to merosome detachment, which marks the culmination of liver-stage development. Collectively, our findings extend the utility of the glmS ribozyme to study protein function in the liver stage and reveal that EXP2 is important for intrahepatic parasite development, indicating that PTEX components also function at the hepatocyte-parasite interface. IMPORTANCE After the mosquito bite that initiates a Plasmodium infection, parasites first travel to the liver and develop in hepatocytes. This liver stage is asymptomatic but necessary for the parasite to transition to the merozoite form, which infects red blood cells and causes malaria. To take over their host cells, avoid immune defenses, and fuel their growth, these obligately intracellular parasites must import nutrients and export effector proteins across a vacuole membrane in which they reside. In the blood stage, these processes depend on a translocon called PTEX, but it is unclear if PTEX also functions during the liver stage. Here, we adapted the glmS ribozyme to control expression of EXP2, the membrane pore component of PTEX, during the liver stage of the rodent malaria parasite Plasmodium berghei. Our results show that EXP2 is important for intracellular development in the hepatocyte, revealing that PTEX components are also functionally important during liver-stage infection.
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Affiliation(s)
- Tahir Hussain
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | | | - John M. Beck
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Manuel A. Fierro
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Gunnar R. Mair
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
| | - Ryan C. Smith
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Josh R. Beck
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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30
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Hazzard B, Sá JM, Ellis AC, Pascini TV, Amin S, Wellems TE, Serre D. Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts. PLoS Negl Trop Dis 2022; 16:e0010991. [PMID: 36525464 PMCID: PMC9803293 DOI: 10.1371/journal.pntd.0010991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/30/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Plasmodium vivax infections often consist of heterogenous populations of parasites at different developmental stages and with distinct transcriptional profiles, which complicates gene expression analyses. The advent of single cell RNA sequencing (scRNA-seq) enabled disentangling this complexity and has provided robust and stage-specific characterization of Plasmodium gene expression. However, scRNA-seq information is typically derived from the end of each mRNA molecule (usually the 3'-end) and therefore fails to capture the diversity in transcript isoforms documented in bulk RNA-seq data. Here, we describe the sequencing of scRNA-seq libraries using Pacific Biosciences (PacBio) chemistry to characterize full-length Plasmodium vivax transcripts from single cell parasites. Our results show that many P. vivax genes are transcribed into multiple isoforms, primarily through variations in untranslated region (UTR) length or splicing, and that the expression of many isoforms is developmentally regulated. Our findings demonstrate that long read sequencing can be used to characterize mRNA molecules at the single cell level and provides an additional resource to better understand the regulation of gene expression throughout the Plasmodium life cycle.
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Affiliation(s)
- Brittany Hazzard
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Angela C. Ellis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tales V. Pascini
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shuchi Amin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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31
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Real E, Nardella F, Scherf A, Mancio-Silva L. Repurposing of Plasmodium falciparum var genes beyond the blood stage. Curr Opin Microbiol 2022; 70:102207. [PMID: 36183663 DOI: 10.1016/j.mib.2022.102207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/03/2022] [Indexed: 01/25/2023]
Abstract
A commonly observed survival strategy in protozoan parasites is the sequential expression of clonally variant-surface antigens to avoid elimination by the host's immune response. In malaria-causing P. falciparum, the immunovariant erythrocyte-membrane protein-1 (PfEMP1) adhesin family, encoded by var genes, is responsible for both antigenic variation and cytoadherence of infected erythrocytes to the microvasculature. Until recently, the biological function of these variant genes was believed to be restricted to intraerythrocytic developmental stages. With the advent of new technologies, var gene expression has been confirmed in transmission and pre-erythrocytic stages. Here, we discuss how repurposing of var gene expression beyond chronic blood-stage infection may be critical for successful transmission.
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Affiliation(s)
- Eliana Real
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France
| | - Flore Nardella
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France
| | - Artur Scherf
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France.
| | - Liliana Mancio-Silva
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 25 Rue du Dr Roux, F-75015 Paris, France.
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32
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Afriat A, Zuzarte-Luís V, Bahar Halpern K, Buchauer L, Marques S, Chora ÂF, Lahree A, Amit I, Mota MM, Itzkovitz S. A spatiotemporally resolved single-cell atlas of the Plasmodium liver stage. Nature 2022; 611:563-569. [PMID: 36352220 DOI: 10.1038/s41586-022-05406-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/03/2022] [Indexed: 11/10/2022]
Abstract
Malaria infection involves an obligatory, yet clinically silent liver stage1,2. Hepatocytes operate in repeating units termed lobules, exhibiting heterogeneous gene expression patterns along the lobule axis3, but the effects of hepatocyte zonation on parasite development at the molecular level remain unknown. Here we combine single-cell RNA sequencing4 and single-molecule transcript imaging5 to characterize the host and parasite temporal expression programmes in a zonally controlled manner for the rodent malaria parasite Plasmodium berghei ANKA. We identify differences in parasite gene expression in distinct zones, including potentially co-adaptive programmes related to iron and fatty acid metabolism. We find that parasites develop more rapidly in the pericentral lobule zones and identify a subpopulation of periportally biased hepatocytes that harbour abortive infections, reduced levels of Plasmodium transcripts and parasitophorous vacuole breakdown. These 'abortive hepatocytes', which appear predominantly with high parasite inoculum, upregulate immune recruitment and key signalling programmes. Our study provides a resource for understanding the liver stage of Plasmodium infection at high spatial resolution and highlights the heterogeneous behaviour of both the parasite and the host hepatocyte.
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Affiliation(s)
- Amichay Afriat
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Vanessa Zuzarte-Luís
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lisa Buchauer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sofia Marques
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Ângelo Ferreira Chora
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Aparajita Lahree
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Maria M Mota
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal.
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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33
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Nair S, Li X, Nkhoma SC, Anderson T. Fitness Costs of pfhrp2 and pfhrp3 Deletions Underlying Diagnostic Evasion in Malaria Parasites. J Infect Dis 2022; 226:1637-1645. [PMID: 35709327 PMCID: PMC10205895 DOI: 10.1093/infdis/jiac240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Rapid diagnostic tests based on detection of histidine-rich proteins (HRPs) are widely used for malaria diagnosis, but parasites carrying pfhrp deletions can evade detection and are increasing in frequency in some countries. Models aim to predict conditions under which pfhrp2 and/or pfhrp3 deletions will increase, but a key parameter-the fitness cost of deletions-is unknown. METHODS We removed pfhrp2 and/or pfhrp3 from a Malawian parasite clone using gene editing approaches) and measured fitness costs by conducting pairwise competition experiments. RESULTS We observed significant fitness costs of 0.087 ± 0.008 (1 standard error) per asexual cycle for pfhrp2 deletion and 0.113 ± 0.008 for the pfhrp2/3 double deletion, relative to the unedited progenitor parasite. Selection against deletions is strong and comparable to that resulting from drug resistance mutations. CONCLUSIONS Prior modeling suggested that diagnostic selection may drive increased frequency of pfhrp deletions only when fitness costs are mild. Our experiments show that costs of pfhrp deletions are higher than these thresholds, but modeling and empirical results can be reconciled if the duration of infection is short. These results may inform future modeling to understand why pfhrp2/3 deletions are increasing in some locations (Ethiopia and Eritrea) but not in others (Mekong region).
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Affiliation(s)
- Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Standwell C Nkhoma
- BEI Resources, American Type Culture Collection, Manassas, Virginia, USA
| | - Tim Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
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34
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Rezvani Y, Keroack CD, Elsworth B, Arriojas A, Gubbels MJ, Duraisingh MT, Zarringhalam K. Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles. PLoS Biol 2022; 20:e3001816. [PMID: 36137068 PMCID: PMC9531838 DOI: 10.1371/journal.pbio.3001816] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/04/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Babesia is a genus of apicomplexan parasites that infect red blood cells in vertebrate hosts. Pathology occurs during rapid replication cycles in the asexual blood stage of infection. Current knowledge of Babesia replication cycle progression and regulation is limited and relies mostly on comparative studies with related parasites. Due to limitations in synchronizing Babesia parasites, fine-scale time-course transcriptomic resources are not readily available. Single-cell transcriptomics provides a powerful unbiased alternative for profiling asynchronous cell populations. Here, we applied single-cell RNA sequencing to 3 Babesia species (B. divergens, B. bovis, and B. bigemina). We used analytical approaches and algorithms to map the replication cycle and construct pseudo-synchronized time-course gene expression profiles. We identify clusters of co-expressed genes showing "just-in-time" expression profiles, with gradually cascading peaks throughout asexual development. Moreover, clustering analysis of reconstructed gene curves reveals coordinated timing of peak expression in epigenetic markers and transcription factors. Using a regularized Gaussian graphical model, we reconstructed co-expression networks and identified conserved and species-specific nodes. Motif analysis of a co-expression interactome of AP2 transcription factors identified specific motifs previously reported to play a role in DNA replication in Plasmodium species. Finally, we present an interactive web application to visualize and interactively explore the datasets.
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Affiliation(s)
- Yasaman Rezvani
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Department of Physics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
- * E-mail: (MTD); (KZ)
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- * E-mail: (MTD); (KZ)
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35
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Ruberto AA, Maher SP, Vantaux A, Joyner CJ, Bourke C, Balan B, Jex A, Mueller I, Witkowski B, Kyle DE. Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets. Front Cell Infect Microbiol 2022; 12:986314. [PMID: 36093191 PMCID: PMC9453201 DOI: 10.3389/fcimb.2022.986314] [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: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 12/12/2022] Open
Abstract
The resilience of Plasmodium vivax, the most widely-distributed malaria-causing parasite in humans, is attributed to its ability to produce dormant liver forms known as hypnozoites, which can activate weeks, months, or even years after an initial mosquito bite. The factors underlying hypnozoite formation and activation are poorly understood, as is the parasite's influence on the host hepatocyte. Here, we shed light on transcriptome-wide signatures of both the parasite and the infected host cell by sequencing over 1,000 P. vivax-infected hepatocytes at single-cell resolution. We distinguish between replicating schizonts and hypnozoites at the transcriptional level, identifying key differences in transcripts encoding for RNA-binding proteins associated with cell fate. In infected hepatocytes, we show that genes associated with energy metabolism and antioxidant stress response are upregulated, and those involved in the host immune response downregulated, suggesting both schizonts and hypnozoites alter the host intracellular environment. The transcriptional markers in schizonts, hypnozoites, and infected hepatocytes revealed here pinpoint potential factors underlying dormancy and can inform therapeutic targets against P. vivax liver-stage infection.
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Affiliation(s)
- Anthony A. Ruberto
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Steven P. Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Chester J. Joyner
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Caitlin Bourke
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Balu Balan
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Aaron Jex
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Ivo Mueller
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Dennis E. Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
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36
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Ruberto AA, Bourke C, Vantaux A, Maher SP, Jex A, Witkowski B, Snounou G, Mueller I. Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures. PLoS Negl Trop Dis 2022; 16:e0010633. [PMID: 35926062 PMCID: PMC9380936 DOI: 10.1371/journal.pntd.0010633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 08/16/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Background Plasmodium vivax sporozoites reside in the salivary glands of a mosquito before infecting a human host and causing malaria. Previous transcriptome-wide studies in populations of these parasite forms were limited in their ability to elucidate cell-to-cell variation, thereby masking cellular states potentially important in understanding malaria transmission outcomes. Methodology/Principal findings In this study, we performed transcription profiling on 9,947 P. vivax sporozoites to assess the extent to which they differ at single-cell resolution. We show that sporozoites residing in the mosquito’s salivary glands exist in distinct developmental states, as defined by their transcriptomic signatures. Additionally, relative to P. falciparum, P. vivax displays overlapping and unique gene usage patterns, highlighting conserved and species-specific gene programs. Notably, distinguishing P. vivax from P. falciparum were a subset of P. vivax sporozoites expressing genes associated with translational regulation and repression. Finally, our comparison of single-cell transcriptomic data from P. vivax sporozoite and erythrocytic forms reveals gene usage patterns unique to sporozoites. Conclusions/Significance In defining the transcriptomic signatures of individual P. vivax sporozoites, our work provides new insights into the factors driving their developmental trajectory and lays the groundwork for a more comprehensive P. vivax cell atlas. Plasmodium vivax is the second most common cause of malaria worldwide. It is particularly challenging for malaria elimination as it forms both active blood-stage infections, as well as asymptomatic liver-stage infections that can persist for extended periods of time. The activation of persister forms in the liver (hypnozoites) are responsible for relapsing infections occurring weeks or months following primary infection via a mosquito bite. How P. vivax persists in the liver remains a major gap in understanding of this organism. It has been hypothesized that there is pre-programming of the infectious sporozoite while it is in the salivary-glands that determines if the cell’s fate once in the liver is to progress towards immediate liver stage development or persist for long-periods as a hypnozoite. The aim of this study was to see if such differences were distinguishable at the transcript level in salivary-gland sporozoites. While we found significant variation amongst sporozoites, we did not find clear evidence that they are transcriptionally pre-programmed as has been suggested. Nevertheless, we highlight several intriguing patterns that appear to be P. vivax specific relative to non-relapsing species that cause malaria prompting further investigation.
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Affiliation(s)
- Anthony A. Ruberto
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Caitlin Bourke
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Kingdom of Cambodia
| | - Steven P. Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Aaron Jex
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Kingdom of Cambodia
| | - Georges Snounou
- Commissariat à l’Énergie Atomique et aux Énergies Alternatives-Université Paris Sud 11-INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA-HB), Infectious Disease Models and Innovative Therapies (IDMIT) Department, Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), Fontenay-aux-Roses, France
| | - Ivo Mueller
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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Cárdenas P, Corredor V, Santos-Vega M. Genomic epidemiological models describe pathogen evolution across fitness valleys. SCIENCE ADVANCES 2022; 8:eabo0173. [PMID: 35857510 PMCID: PMC9278859 DOI: 10.1126/sciadv.abo0173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Genomics is fundamentally changing epidemiological research. However, systematically exploring hypotheses in pathogen evolution requires new modeling tools. Models intertwining pathogen epidemiology and genomic evolution can help understand processes such as the emergence of novel pathogen genotypes with higher transmissibility or resistance to treatment. In this work, we present Opqua, a flexible simulation framework that explicitly links epidemiology to sequence evolution and selection. We use Opqua to study determinants of evolution across fitness valleys. We confirm that competition can limit evolution in high-transmission environments and find that low transmission, host mobility, and complex pathogen life cycles facilitate reaching new adaptive peaks through population bottlenecks and decoupling of selective pressures. The results show the potential of genomic epidemiological modeling as a tool in infectious disease research.
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Affiliation(s)
- Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Mauricio Santos-Vega
- Grupo Biología Matemática y Computacional, Departamento Ingeniería Biomédica, Universidad de los Andes, Bogotá, D.C., Colombia
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38
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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39
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Single-cell views of the Plasmodium life cycle. Trends Parasitol 2022; 38:748-757. [DOI: 10.1016/j.pt.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
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40
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Mancio-Silva L, Gural N, Real E, Wadsworth MH, Butty VL, March S, Nerurkar N, Hughes TK, Roobsoong W, Fleming HE, Whittaker CA, Levine SS, Sattabongkot J, Shalek AK, Bhatia SN. A single-cell liver atlas of Plasmodium vivax infection. Cell Host Microbe 2022; 30:1048-1060.e5. [PMID: 35443155 DOI: 10.1016/j.chom.2022.03.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022]
Abstract
Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years and reactivate to cause recurrent blood-stage infection. Although they are an important target for malaria eradication, little is known about the molecular features of replicative and non-replicative intracellular liver-stage parasites and their host cell dependence. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites for transcriptional profiling. Coupling enrichment strategies with bulk and single-cell analyses, we capture both parasite and host transcripts in individual hepatocytes throughout the course of infection. We define host- and state-dependent transcriptional signatures and identify unappreciated populations of replicative and non-replicative parasites that share features with sexual transmissive forms. We find that infection suppresses the transcription of key hepatocyte function genes and elicits an anti-parasite innate immune response. Our work provides a foundation for understanding host-parasite interactions and reveals insights into the biology of P. vivax dormancy and transmission.
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Affiliation(s)
- Liliana Mancio-Silva
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France.
| | - Nil Gural
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Eliana Real
- Institut Pasteur, Université Paris Cité, Inserm U1201, CNRS EMR9195, Unité de Biologie des Interactions Hôte-Parasite, 75015 Paris, France
| | - Marc H Wadsworth
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Vincent L Butty
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Sandra March
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Niketa Nerurkar
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Travis K Hughes
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Heather E Fleming
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Charlie A Whittaker
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Stuart S Levine
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; BioMicro Center, MIT, Cambridge, MA 02139, USA
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine Mahidol University, Bangkok 10400, Thailand
| | - Alex K Shalek
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Department of Chemistry, MIT, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; The Wyss Institute for Biologically Inspired Engineering Harvard University Boston, MA 02215, USA.
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Howick VM, Peacock L, Kay C, Collett C, Gibson W, Lawniczak MKN. Single-cell transcriptomics reveals expression profiles of Trypanosoma brucei sexual stages. PLoS Pathog 2022; 18:e1010346. [PMID: 35255094 PMCID: PMC8939820 DOI: 10.1371/journal.ppat.1010346] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/22/2022] [Accepted: 02/06/2022] [Indexed: 01/26/2023] Open
Abstract
Early diverging lineages such as trypanosomes can provide clues to the evolution of sexual reproduction in eukaryotes. In Trypanosoma brucei, the pathogen that causes Human African Trypanosomiasis, sexual reproduction occurs in the salivary glands of the insect host, but analysis of the molecular signatures that define these sexual forms is complicated because they mingle with more numerous, mitotically-dividing developmental stages. We used single-cell RNA-sequencing (scRNAseq) to profile 388 individual trypanosomes from midgut, proventriculus, and salivary glands of infected tsetse flies allowing us to identify tissue-specific cell types. Further investigation of salivary gland parasite transcriptomes revealed fine-scale changes in gene expression over a developmental progression from putative sexual forms through metacyclics expressing variant surface glycoprotein genes. The cluster of cells potentially containing sexual forms was characterized by high level transcription of the gamete fusion protein HAP2, together with an array of surface proteins and several genes of unknown function. We linked these expression patterns to distinct morphological forms using immunofluorescence assays and reporter gene expression to demonstrate that the kinetoplastid-conserved gene Tb927.10.12080 is exclusively expressed at high levels by meiotic intermediates and gametes. Further experiments are required to establish whether this protein, currently of unknown function, plays a role in gamete formation and/or fusion.
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Affiliation(s)
- Virginia M. Howick
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Lori Peacock
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Chris Kay
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Clare Collett
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Mara K. N. Lawniczak
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
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42
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Shaw WR, Marcenac P, Catteruccia F. Plasmodium development in Anopheles: a tale of shared resources. Trends Parasitol 2022; 38:124-135. [PMID: 34548252 PMCID: PMC8758519 DOI: 10.1016/j.pt.2021.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
Interactions between the Anopheles mosquito vector and Plasmodium parasites shape how malaria is transmitted in endemic regions. The long association of these two organisms has led to evolutionary processes that minimize fitness costs of infection and benefit both players through shared nutrient resources, parasite immune suppression, and mosquito tolerance to infection. In this review we explore recent data describing how Plasmodium falciparum, the deadliest malaria parasite, associates with one of its most important natural mosquito hosts, Anopheles gambiae, and we discuss the implications of these findings for parasite transmission and vector control strategies currently in development.
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Affiliation(s)
- W Robert Shaw
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Perrine Marcenac
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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43
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Parreira KS, Scarpelli P, Rezende Lima W, Garcia RS. Contribution of Transcriptome to Elucidate the Biology of Plasmodium spp. Curr Top Med Chem 2022; 22:169-187. [PMID: 35021974 DOI: 10.2174/1568026622666220111140803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/22/2022]
Abstract
In the present review, we discuss some of the new technologies that have been applied to elucidate how Plasmodium spp escape from the immune system and subvert the host physiology to orchestrate the regulation of its biological pathways. Our manuscript describes how techniques such as microarray approaches, RNA-Seq and single-cell RNA sequencing have contributed to the discovery of transcripts and changed the concept of gene expression regulation in closely related malaria parasite species. Moreover, the text highlights the contributions of high-throughput RNA sequencing for the current knowledge of malaria parasite biology, physiology, vaccine target and the revelation of new players in parasite signaling.
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Affiliation(s)
| | - Pedro Scarpelli
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo, Brazil
| | - Wânia Rezende Lima
- Departamento de Medicina, Instituto de Biotecnologia-Universidade Federal de Catalão
| | - R S Garcia
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo, Brazil
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44
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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45
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A transcriptional switch controls sex determination in Plasmodium falciparum. Nature 2022; 612:528-533. [PMID: 36477538 PMCID: PMC9750867 DOI: 10.1038/s41586-022-05509-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Sexual reproduction and meiotic sex are deeply rooted in the eukaryotic tree of life, but mechanisms determining sex or mating types are extremely varied and are only well characterized in a few model organisms1. In malaria parasites, sexual reproduction coincides with transmission to the vector host. Sex determination is non-genetic, with each haploid parasite capable of producing either a male or a female gametocyte in the human host2. The hierarchy of events and molecular mechanisms that trigger sex determination and maintenance of sexual identity are yet to be elucidated. Here we show that the male development 1 (md1) gene is both necessary and sufficient for male fate determination in the human malaria parasite Plasmodium falciparum. We show that Md1 has a dual function stemming from two separate domains: in sex determination through its N terminus and in male development from its conserved C-terminal LOTUS/OST-HTH domain. We further identify a bistable switch at the md1 locus, which is coupled with sex determination and ensures that the male-determining gene is not expressed in the female lineage. We describe one of only a few known non-genetic mechanisms of sex determination in a eukaryote and highlight Md1 as a potential target for interventions that block malaria transmission.
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46
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Alacid E, Richards TA. A cell-cell atlas approach for understanding symbiotic interactions between microbes. Curr Opin Microbiol 2021; 64:47-59. [PMID: 34655935 DOI: 10.1016/j.mib.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023]
Abstract
Natural environments are composed of a huge diversity of microorganisms interacting with each other to form complex functional networks. Our understanding of the operative nature of host-symbiont associations is limited because propagating such associations in a laboratory is challenging. The advent of single-cell technologies applied to, for example, animal cells and apicomplexan parasites has revolutionized our understanding of development and disease. Such cell atlas approaches generate maps of cell-specific processes and variations within cellular populations. These methods can now be combined with cellular-imaging so that interaction stage versus transcriptome state can be quantized for microbe-microbe interactions. We predict that the combination of these methods applied to the study of symbioses will transform our understanding of many ecological interactions, including those sampled directly from natural environments.
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Affiliation(s)
- Elisabet Alacid
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
| | - Thomas A Richards
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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47
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Dia A, Jett C, Trevino SG, Chu CS, Sriprawat K, Anderson TJC, Nosten F, Cheeseman IH. Single-genome sequencing reveals within-host evolution of human malaria parasites. Cell Host Microbe 2021; 29:1496-1506.e3. [PMID: 34492224 DOI: 10.1016/j.chom.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/17/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023]
Abstract
Population genomics of bulk malaria infections is unable to examine intrahost evolution; therefore, most work has focused on the role of recombination in generating genetic variation. We used single-cell sequencing protocol for low-parasitaemia infections to generate 406 near-complete single Plasmodium vivax genomes from 11 patients sampled during sequential febrile episodes. Parasite genomes contain hundreds of de novo mutations, showing strong signatures of selection, which are enriched in the ApiAP2 family of transcription factors, known targets of adaptation. Comparing 315 P. falciparum single-cell genomes from 15 patients with our P. vivax data, we find broad complementary patterns of de novo mutation at the gene and pathway level, revealing the importance of within-host evolution during malaria infections.
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Affiliation(s)
- Aliou Dia
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Catherine Jett
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Simon G Trevino
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Cindy S Chu
- Disease Intervention and Prevention, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Timothy J C Anderson
- Disease Prevention and Intervention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - François Nosten
- Disease Intervention and Prevention, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Ian H Cheeseman
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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48
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Briggs EM, Warren FSL, Matthews KR, McCulloch R, Otto TD. Application of single-cell transcriptomics to kinetoplastid research. Parasitology 2021; 148:1223-1236. [PMID: 33678213 PMCID: PMC8311972 DOI: 10.1017/s003118202100041x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
Kinetoplastid parasites are responsible for both human and animal diseases across the globe where they have a great impact on health and economic well-being. Many species and life cycle stages are difficult to study due to limitations in isolation and culture, as well as to their existence as heterogeneous populations in hosts and vectors. Single-cell transcriptomics (scRNA-seq) has the capacity to overcome many of these difficulties, and can be leveraged to disentangle heterogeneous populations, highlight genes crucial for propagation through the life cycle, and enable detailed analysis of host–parasite interactions. Here, we provide a review of studies that have applied scRNA-seq to protozoan parasites so far. In addition, we provide an overview of sample preparation and technology choice considerations when planning scRNA-seq experiments, as well as challenges faced when analysing the large amounts of data generated. Finally, we highlight areas of kinetoplastid research that could benefit from scRNA-seq technologies.
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Affiliation(s)
- Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Felix S. L. Warren
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Keith R. Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Richard McCulloch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Thomas D. Otto
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
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Nötzel C, Kafsack BFC. There and back again: malaria parasite single-cell transcriptomics comes full circle. Trends Parasitol 2021; 37:850-852. [PMID: 34391665 DOI: 10.1016/j.pt.2021.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022]
Abstract
The Malaria Cell Atlas (MCA) is an ambitious, ongoing project to profile the intensity and heterogeneity of gene expression throughout the entire malaria parasite life cycle with single-cell resolution. Real et al. now complete the cycle by adding the transmission stages of the most virulent malaria parasite, Plasmodium falciparum, to this easy-to-use resource.
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Affiliation(s)
- Christopher Nötzel
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA; Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Björn F C Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
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