1
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Juribašić Kulcsár M, Gabelica V, Plavec J. Solution-State Structure of a Long-Loop G-Quadruplex Formed Within Promoters of Plasmodium falciparum B var Genes. Chemistry 2024; 30:e202401190. [PMID: 38647110 DOI: 10.1002/chem.202401190] [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: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
We report the high-resolution NMR solution-state structure of an intramolecular G-quadruplex with a diagonal loop of ten nucleotides. The G-quadruplex is formed by a 34-nt DNA sequence, d[CAG3T2A2G3TATA2CT3AG4T2AG3T2], named UpsB-Q-1. This sequence is found within promoters of the var genes of Plasmodium falciparum, which play a key role in malaria pathogenesis and evasion of the immune system. The [3+1]-hybrid G-quadruplex formed under physiologically relevant conditions exhibits a unique equilibrium between two structures, both stabilized by base stacking and non-canonical hydrogen bonding. Unique equilibrium of the two closely related 3D structures originates from a North-South repuckering of deoxyribose moiety of residue T27 in the lateral loop. Besides the 12 guanines involved in three G-quartets, most residues in loop regions are involved in interactions at both G-quartet-loop interfaces.
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Affiliation(s)
- Marina Juribašić Kulcsár
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Valérie Gabelica
- School of Pharmaceutical Sciences, University of Geneva, 1 rue Michel-Servet, CH-1211, Geneva 4, Switzerland
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000, Ljubljana, Slovenia
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2
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Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basílio Lobo G, Bao SN, Grellier P, Rayner JC. APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Sci Rep 2024; 14:11242. [PMID: 38755230 PMCID: PMC11099048 DOI: 10.1038/s41598-024-61295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
The interaction of Plasmodium falciparum-infected red blood cells (iRBCs) with the vascular endothelium plays a crucial role in malaria pathology and disease. KAHRP is an exported P. falciparum protein involved in iRBC remodelling, which is essential for the formation of protrusions or "knobs" on the iRBC surface. These knobs and the proteins that are concentrated within them allow the parasites to escape the immune response and host spleen clearance by mediating cytoadherence of the iRBC to the endothelial wall, but this also slows down blood circulation, leading in some cases to severe cerebral and placental complications. In this work, we have applied genetic and biochemical tools to identify proteins that interact with P. falciparum KAHRP using enhanced ascorbate peroxidase 2 (APEX2) proximity-dependent biotinylation and label-free shotgun proteomics. A total of 30 potential KAHRP-interacting candidates were identified, based on the assigned fragmented biotinylated ions. Several identified proteins have been previously reported to be part of the Maurer's clefts and knobs, where KAHRP resides. This study may contribute to a broader understanding of P. falciparum protein trafficking and knob architecture and shows for the first time the feasibility of using APEX2-proximity labelling in iRBCs.
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Affiliation(s)
- Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
| | - Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Zenon Zenonos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Biologics Engineering, Oncology R&D, AstraZenecaGranta Park, Cambridge, UK
| | - Christine S Hopp
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Izabela M D Bastos
- Laboratory of Host Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ariane Pandolfo Silveira
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | | | - Sônia Nair Bao
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Philippe Grellier
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
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3
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Amwoma JG, Kituyi S, Wakoli DM, Ochora DO, Chemwor G, Maisiba R, Okore W, Opot B, Juma D, Muok EM, Garges EC, Egbo TE, Nyabuga FN, Andagalu B, Akala HM. Comparative analysis of peripheral whole blood transcriptome from asymptomatic carriers reveals upregulation of subsets of surface proteins implicated in Plasmodium falciparum phenotypic plasticity. Biochem Biophys Rep 2024; 37:101596. [PMID: 38146350 PMCID: PMC10749222 DOI: 10.1016/j.bbrep.2023.101596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
The molecular mechanism underlying Plasmodium falciparum's persistence in the asymptomatic phase of infection remains largely unknown. However, large-scale shifts in the parasites' gene expression during asymptomatic infections may enhance phenotypic plasticity, maximizing their fitness and leading to the persistence of the asymptomatic infections. To uncover these mechanisms, we aimed to identify parasite genetic factors implicated in asymptomatic infections through whole transcriptome analysis. We analyzed publicly available transcriptome datasets containing asymptomatic malaria (ASM), uncomplicated malaria (SM), and malaria-naïve (NSM) samples from 35 subjects for differentially expressed genes (DEGs) and long noncoding RNAs. Our analysis identified 755 and 1773 DEGs in ASM vs SM and NSM, respectively. These DEGs revealed sets of genes coding for proteins of unknown functions (PUFs) upregulated in ASM vs SM and ASM, suggesting their role in underlying fundamental molecular mechanisms during asymptomatic infections. Upregulated genes in ASM vs SM revealed a subset of 24 clonal variant genes (CVGs) involved in host-parasite and symbiotic interactions and modulation of the symbiont of host erythrocyte aggregation pathways. Moreover, we identified 237 differentially expressed noncoding RNAs in ASM vs SM, of which 11 were found to interact with CVGs, suggesting their possible role in regulating the expression of CVGs. Our results suggest that P. falciparum utilizes phenotypic plasticity as an adaptive mechanism during asymptomatic infections by upregulating clonal variant genes, with long noncoding RNAs possibly playing a crucial role in their regulation. Thus, our study provides insights into the parasites' genetic factors that confer a fitness advantage during asymptomatic infections.
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Affiliation(s)
- Joseph G. Amwoma
- Department of Biological Sciences, University of Embu, Kenya
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Sarah Kituyi
- Department of Biological Sciences, University of Embu, Kenya
- Forgarty International Center of the National Institutes of Health, Bethesda, MD, USA
| | - Dancan M. Wakoli
- Department of Biochemistry and Molecular Biology, Egerton University, Kenya
| | - Douglas O. Ochora
- Department of Biological Sciences, School of Pure and Applied Sciences, Kisii University, Kenya
- DSI/NWU, Preclinical Drug Development Platform, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
| | - Gladys Chemwor
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Risper Maisiba
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Winnie Okore
- Department of Biomedical Sciences and Technology, Maseno University, Kenya
| | - Benjamin Opot
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Dennis Juma
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Eric M.O. Muok
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Eric C. Garges
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya
| | - Timothy E. Egbo
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya
| | | | - Ben Andagalu
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Hoseah M. Akala
- United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
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4
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Hamid A, Mäser P, Mahmoud AB. Drug Repurposing in the Chemotherapy of Infectious Diseases. Molecules 2024; 29:635. [PMID: 38338378 PMCID: PMC10856722 DOI: 10.3390/molecules29030635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Repurposing is a universal mechanism for innovation, from the evolution of feathers to the invention of Velcro tape. Repurposing is particularly attractive for drug development, given that it costs more than a billion dollars and takes longer than ten years to make a new drug from scratch. The COVID-19 pandemic has triggered a large number of drug repurposing activities. At the same time, it has highlighted potential pitfalls, in particular when concessions are made to the target product profile. Here, we discuss the pros and cons of drug repurposing for infectious diseases and analyze different ways of repurposing. We distinguish between opportunistic and rational approaches, i.e., just saving time and money by screening compounds that are already approved versus repurposing based on a particular target that is common to different pathogens. The latter can be further distinguished into divergent and convergent: points of attack that are divergent share common ancestry (e.g., prokaryotic targets in the apicoplast of malaria parasites), whereas those that are convergent arise from a shared lifestyle (e.g., the susceptibility of bacteria, parasites, and tumor cells to antifolates due to their high rate of DNA synthesis). We illustrate how such different scenarios can be capitalized on by using examples of drugs that have been repurposed to, from, or within the field of anti-infective chemotherapy.
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Affiliation(s)
- Amal Hamid
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
| | - Pascal Mäser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, 4123 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Abdelhalim Babiker Mahmoud
- Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan;
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
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5
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Natsheh IY, Alsaleh MM, Alkhawaldeh AK, Albadawi DK, Darwish MM, Shammout MJA. The dark side of drug repurposing. From clinical trial challenges to antimicrobial resistance: analysis based on three major fields. Drug Target Insights 2024; 18:8-19. [PMID: 38751378 PMCID: PMC11094707 DOI: 10.33393/dti.2024.3019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Drug repurposing is a strategic endeavor that entails the identification of novel therapeutic applications for pharmaceuticals that are already available in the market. Despite the advantageous nature of implementing this particular strategy owing to its cost-effectiveness and efficiency in reducing the time required for the drug discovery process, it is essential to bear in mind that there are various factors that must be meticulously considered and taken into account. Up to this point, there has been a noticeable absence of comprehensive analyses that shed light on the limitations of repurposing drugs. The primary aim of this review is to conduct a thorough illustration of the various challenges that arise when contemplating drug repurposing from a clinical perspective in three major fields-cardiovascular, cancer, and diabetes-and to further underscore the potential risks associated with the emergence of antimicrobial resistance (AMR) when employing repurposed antibiotics for the treatment of noninfectious and infectious diseases. The process of developing repurposed medications necessitates the application of creativity and innovation in designing the development program, as the body of evidence may differ for each specific case. In order to effectively repurpose drugs, it is crucial to consider the clinical implications and potential drawbacks that may arise during this process. By comprehensively analyzing these challenges, we can attain a deeper comprehension of the intricacies involved in drug repurposing, which will ultimately lead to the development of more efficacious and safe therapeutic approaches.
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Affiliation(s)
- Iyad Y. Natsheh
- Department of Medical Applied Sciences, Zarqa University College, Al-Balqa Applied University, Salt - Jordan
| | - Majd M. Alsaleh
- Department of Medical Applied Sciences, Zarqa University College, Al-Balqa Applied University, Salt - Jordan
- Department of Biology, School of Science, University of Jordan, Amman - Jordan
| | - Ahmad K. Alkhawaldeh
- Department of Medical Applied Sciences, Zarqa University College, Al-Balqa Applied University, Salt - Jordan
| | - Duaa K. Albadawi
- Department of Medical Applied Sciences, Zarqa University College, Al-Balqa Applied University, Salt - Jordan
| | - Maisa’ M. Darwish
- Department of Biology, School of Science, University of Jordan, Amman - Jordan
- National Agricultural Research Center, Amman - Jordan
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6
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Silva Pereira S, Brás D, Porqueddu T, Nascimento AM, De Niz M. Investigation of Trypanosoma-induced vascular damage sheds insights into Trypanosoma vivax sequestration. Cell Surf 2023; 10:100113. [PMID: 37954640 PMCID: PMC10632540 DOI: 10.1016/j.tcsw.2023.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/22/2023] [Accepted: 10/22/2023] [Indexed: 11/14/2023] Open
Abstract
Multiple blood-borne pathogens infecting mammals establish close interactions with the host vascular endothelium as part of their life cycles. In this work, we investigate differences in the interactions of three Trypanosoma species: T. brucei, T. congolense and T. vivax with the blood vasculature. Infection with these species results in vastly different pathologies, including different effects on vascular homeostasis, such as changes in vascular permeability and microhemorrhages. While all three species are extracellular parasites, T. congolense is strictly intravascular, while T. brucei is capable of surviving both extra- and intravascularly. Our knowledge regarding T. vivax tropism and its capacity of migration across the vascular endothelium is unknown. In this work, we show for the first time that T. vivax parasites sequester to the vascular endothelium of most organs, and that, like T. congolense, T. vivax Y486 is largely incapable of extravasation. Infection with this parasite species results in a unique effect on vascular endothelium receptors including general downregulation of ICAM1 and ESAM, and upregulation of VCAM1, CD36 and E-selectin. Our findings on the differences between the two sequestering species (T. congolense and T. vivax) and the non-sequestering, but extravasating, T. brucei raise important questions on the relevance of sequestration to the parasite's survival in the mammalian host, and the evolutionary relevance of both sequestration and extravasation.
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Affiliation(s)
- Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, Lisbon, Portugal
| | - Daniela Brás
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Teresa Porqueddu
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Ana M. Nascimento
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Center for Advanced Microscopy and Nikon Imaging Center, Northwestern University, Chicago, USA
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7
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de Roos AM, He Q, Pascual M. An immune memory-structured SIS epidemiological model for hyperdiverse pathogens. Proc Natl Acad Sci U S A 2023; 120:e2218499120. [PMID: 37910552 PMCID: PMC10636369 DOI: 10.1073/pnas.2218499120] [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: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
A hyperdiverse class of pathogens of humans and wildlife, including the malaria parasite Plasmodium falciparum, relies on multigene families to encode antigenic variation. As a result, high (asymptomatic) prevalence is observed despite high immunity in local populations under high-transmission settings. The vast diversity of "strains" and genes encoding this variation challenges the application of established models for the population dynamics of such infectious diseases. Agent-based models have been formulated to address theory on strain coexistence and structure, but their complexity can limit application to gain insights into population dynamics. Motivated by P. falciparum malaria, we develop an alternative formulation in the form of a structured susceptible-infected-susceptible population model in continuous time, where individuals are classified not only by age, as is standard, but also by the diversity of parasites they have been exposed to and retain in their specific immune memory. We analyze the population dynamics and bifurcation structure of this system of partial-differential equations, showing the existence of alternative steady states and an associated tipping point with transmission intensity. We attribute the critical transition to the positive feedback between parasite genetic diversity and force of infection. Basins of attraction show that intervention must drastically reduce diversity to prevent a rebound to high infection levels. Results emphasize the importance of explicitly considering pathogen diversity and associated specific immune memory in the population dynamics of hyperdiverse epidemiological systems. This statement is discussed in a more general context for ecological competition systems with hyperdiverse trait spaces.
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Affiliation(s)
- André M. de Roos
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam1090 GE, The Netherlands
- Santa Fe Institute, Santa Fe, NM87501
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
| | - Mercedes Pascual
- Santa Fe Institute, Santa Fe, NM87501
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL60637
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8
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [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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9
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Tewey MA, Coulibaly D, Lawton JG, Stucke EM, Zhou AE, Berry AA, Bailey JA, Pike A, Dara A, Ouattara A, Lyke KE, Ifeonu O, Laurens MB, Adams M, Takala-Harrison S, Niangaly A, Kouriba B, Koné AK, Rowe JA, Doumbo OK, Patel JJ, Tan JC, Felgner PL, Plowe CV, Thera MA, Travassos MA. Natural immunity to malaria preferentially targets the endothelial protein C receptor-binding regions of PfEMP1s. mSphere 2023; 8:e0045123. [PMID: 37791774 PMCID: PMC10597466 DOI: 10.1128/msphere.00451-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Antibody responses to variant surface antigens (VSAs) produced by the malaria parasite Plasmodium falciparum may contribute to age-related natural immunity to severe malaria. One VSA family, P. falciparum erythrocyte membrane protein-1 (PfEMP1), includes a subset of proteins that binds endothelial protein C receptor (EPCR) in human hosts and potentially disrupts the regulation of inflammatory responses, which may lead to the development of severe malaria. We probed peptide microarrays containing segments spanning five PfEMP1 EPCR-binding domain variants with sera from 10 Malian adults and 10 children to determine the differences between adult and pediatric immune responses. We defined serorecognized peptides and amino acid residues as those that elicited a significantly higher antibody response than malaria-naïve controls. We aimed to identify regions consistently serorecognized among adults but not among children across PfEMP1 variants, potentially indicating regions that drive the development of immunity to severe malaria. Adult sera consistently demonstrated broader and more intense serologic responses to constitutive PfEMP1 peptides than pediatric sera, including peptides in EPCR-binding domains. Both adults and children serorecognized a significantly higher proportion of EPCR-binding peptides than peptides that do not directly participate in receptor binding, indicating a preferential development of serologic responses at functional residues. Over the course of a single malaria transmission season, pediatric serological responses increased between the start and the peak of the season, but waned as the transmission season ended. IMPORTANCE Severe malaria and death related to malaria disproportionately affect sub-Saharan children under 5 years of age, commonly manifesting as cerebral malaria and/or severe malarial anemia. In contrast, adults in malaria-endemic regions tend to experience asymptomatic or mild disease. Our findings indicate that natural immunity to malaria targets specific regions within the EPCR-binding domain, particularly peptides containing EPCR-binding residues. Epitopes containing these residues may be promising targets for vaccines or therapeutics directed against severe malaria. Our approach provides insight into the development of natural immunity to a binding target linked to severe malaria by characterizing an "adult-like" response as recognizing a proportion of epitopes within the PfEMP1 protein, particularly regions that mediate EPCR binding. This "adult-like" response likely requires multiple years of malaria exposure, as increases in pediatric serologic response over a single malaria transmission season do not appear significant.
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Affiliation(s)
- Madison A. Tewey
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Jonathan G. Lawton
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Emily M. Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Albert E. Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea A. Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jason A. Bailey
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pike
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Antoine Dara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kirsten E. Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olukemi Ifeonu
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew B. Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew Adams
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K. Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - J. Alexandra Rowe
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | | | - John C. Tan
- Roche NimbleGen, Inc., Madison, Wisconsin, USA
| | - Philip L. Felgner
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, California, USA
| | - Christopher V. Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Mark A. Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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10
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Rosa C, Singh P, Chen P, Sinha A, Claës A, Preiser PR, Dedon PC, Baumgarten S, Scherf A, Bryant JM. Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite. EMBO Rep 2023; 24:e57090. [PMID: 37592911 PMCID: PMC10561359 DOI: 10.15252/embr.202357090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
The complex life cycle of the human malaria parasite, Plasmodium falciparum, is driven by specific transcriptional programs, but it is unclear how most genes are activated or silenced at specific times. There is an association between transcription and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks key genome-organizing proteins found in metazoans, it has all core components of the cohesin complex. To investigate the role of cohesin in P. falciparum, we functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown during early stages of the intraerythrocytic developmental cycle (IDC) upregulates a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq analyses reveal that during the IDC, SMC3 enrichment at the promoter regions of these genes inversely correlates with gene expression and chromatin accessibility. These data suggest that SMC3 binding contributes to the repression of specific genes until their appropriate time of expression, revealing a new mode of stage-specific gene repression in P. falciparum.
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Affiliation(s)
- Catarina Rosa
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
- Sorbonne Université, Collège Doctoral Complexité du Vivant ED515ParisFrance
| | - Parul Singh
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Patty Chen
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Ameya Sinha
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Aurélie Claës
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Peter R Preiser
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | | | - Artur Scherf
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Jessica M Bryant
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
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11
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Barcons-Simon A, Carrington M, Siegel TN. Decoding the impact of nuclear organization on antigenic variation in parasites. Nat Microbiol 2023; 8:1408-1418. [PMID: 37524976 DOI: 10.1038/s41564-023-01424-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Antigenic variation as a strategy to evade the host adaptive immune response has evolved in divergent pathogens. Antigenic variation involves restricted, and often mutually exclusive, expression of dominant antigens and a periodic switch in antigen expression during infection. In eukaryotes, nuclear compartmentalization, including three-dimensional folding of the genome and physical separation of proteins in compartments or condensates, regulates mutually exclusive gene expression and chromosomal translocations. In this Review, we discuss the impact of nuclear organization on antigenic variation in the protozoan pathogens Trypanosoma brucei and Plasmodium falciparum. In particular, we highlight the relevance of nuclear organization in both mutually exclusive antigen expression and genome stability, which underlie antigenic variation.
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Affiliation(s)
- Anna Barcons-Simon
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.
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12
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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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13
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Schneider V, Visone J, Harris C, Florini F, Hadjimichael E, Zhang X, Gross M, Rhee K, Ben Mamoun C, Kafsack B, Deitsch K. The human malaria parasite Plasmodium falciparum can sense environmental changes and respond by antigenic switching. Proc Natl Acad Sci U S A 2023; 120:e2302152120. [PMID: 37068249 PMCID: PMC10151525 DOI: 10.1073/pnas.2302152120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
The primary antigenic and virulence determinant of the human malaria parasite Plasmodium falciparum is a variant surface protein called PfEMP1. Different forms of PfEMP1 are encoded by a multicopy gene family called var, and switching between active genes enables the parasites to evade the antibody response of their human hosts. var gene switching is key for the maintenance of chronic infections; however, what controls switching is unknown, although it has been suggested to occur at a constant frequency with little or no environmental influence. var gene transcription is controlled epigenetically through the activity of histone methyltransferases (HMTs). Studies in model systems have shown that metabolism and epigenetic control of gene expression are linked through the availability of intracellular S-adenosylmethionine (SAM), the principal methyl donor in biological methylation modifications, which can fluctuate based on nutrient availability. To determine whether environmental conditions and changes in metabolism can influence var gene expression, P. falciparum was cultured in media with altered concentrations of nutrients involved in SAM metabolism. We found that conditions that influence lipid metabolism induce var gene switching, indicating that parasites can respond to changes in their environment by altering var gene expression patterns. Genetic modifications that directly modified expression of the enzymes that control SAM levels similarly led to profound changes in var gene expression, confirming that changes in SAM availability modulate var gene switching. These observations directly challenge the paradigm that antigenic variation in P. falciparum follows an intrinsic, programed switching rate, which operates independently of any external stimuli.
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Affiliation(s)
- Victoria M. Schneider
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
- Laboratory of Chemical Biology and Microbial Pathogenesis, Rockefeller University, New York, NY 10065
| | - Joseph E. Visone
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Chantal T. Harris
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Francesca Florini
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Evi Hadjimichael
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Mackensie R. Gross
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Choukri Ben Mamoun
- Section of Infectious Disease, Department of Microbial Pathogenesis, Yale School of Medicine, Yale University New Haven, CT 06510
| | - Björn F. C. Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
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14
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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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15
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Abdi AI, Achcar F, Sollelis L, Silva-Filho JL, Mwikali K, Muthui M, Mwangi S, Kimingi HW, Orindi B, Andisi Kivisi C, Alkema M, Chandrasekar A, Bull PC, Bejon P, Modrzynska K, Bousema T, Marti M. Plasmodium falciparum adapts its investment into replication versus transmission according to the host environment. eLife 2023; 12:e85140. [PMID: 36916164 PMCID: PMC10059685 DOI: 10.7554/elife.85140] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/01/2023] [Indexed: 03/14/2023] Open
Abstract
The malaria parasite life cycle includes asexual replication in human blood, with a proportion of parasites differentiating to gametocytes required for transmission to mosquitoes. Commitment to differentiate into gametocytes, which is marked by activation of the parasite transcription factor ap2-g, is known to be influenced by host factors but a comprehensive model remains uncertain. Here, we analyze data from 828 children in Kilifi, Kenya with severe, uncomplicated, and asymptomatic malaria infection over 18 years of falling malaria transmission. We examine markers of host immunity and metabolism, and markers of parasite growth and transmission investment. We find that inflammatory responses associated with reduced plasma lysophosphatidylcholine levels are associated with markers of increased investment in parasite sexual reproduction (i.e. transmission investment) and reduced growth (i.e. asexual replication). This association becomes stronger with falling transmission and suggests that parasites can rapidly respond to the within-host environment, which in turn is subject to changing transmission.
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Affiliation(s)
- Abdirahman I Abdi
- KEMRI-Wellcome Trust Research ProgrammeKilifiKenya
- Pwani University Biosciences Research Centre, Pwani UniversityKilifiKenya
| | - Fiona Achcar
- Wellcome Center for Integrative Parasitology, University of GlasgowGlasgowUnited Kingdom
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of ZurichZurichSwitzerland
| | - Lauriane Sollelis
- Wellcome Center for Integrative Parasitology, University of GlasgowGlasgowUnited Kingdom
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of ZurichZurichSwitzerland
| | - João Luiz Silva-Filho
- Wellcome Center for Integrative Parasitology, University of GlasgowGlasgowUnited Kingdom
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of ZurichZurichSwitzerland
| | | | | | | | | | | | - Cheryl Andisi Kivisi
- KEMRI-Wellcome Trust Research ProgrammeKilifiKenya
- Pwani University Biosciences Research Centre, Pwani UniversityKilifiKenya
| | - Manon Alkema
- Radboud University Nijmegen Medical CentreNijmegenNetherlands
| | - Amrita Chandrasekar
- Wellcome Center for Integrative Parasitology, University of GlasgowGlasgowUnited Kingdom
| | - Peter C Bull
- KEMRI-Wellcome Trust Research ProgrammeKilifiKenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research ProgrammeKilifiKenya
| | - Katarzyna Modrzynska
- Wellcome Center for Integrative Parasitology, University of GlasgowGlasgowUnited Kingdom
| | - Teun Bousema
- Radboud University Nijmegen Medical CentreNijmegenNetherlands
| | - Matthias Marti
- Wellcome Center for Integrative Parasitology, University of GlasgowGlasgowUnited Kingdom
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of ZurichZurichSwitzerland
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16
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Abstract
The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here, by analyzing genome organization of P. falciparum, we identify high-interacting regions (HIRs) with strong chromatin interactions at telomeres and virulence genes loci. Specifically, HIRs are highly enriched with repressive histone marks (H3K36me3 and H3K9me3) and form the transcriptional repressive center. Deletion of PfSET2, which controls H3K36me3 level, results in marked reduction of both intrachromosomal and interchromosomal interactions for HIRs. Importantly, such chromatin reorganization coordinates with dynamic changes in epigenetic feature in HIRs and transcriptional activation of var genes. Additionally, different cluster of var genes based on the pattern of chromatin interactions show distinct transcriptional activation potential after deletion of PfSET2. Our results uncover a fundamental mechanism that the epigenetic factor PfSET2 controls the 3D organization of heterochromatin to regulate the transcription activities of var genes family in P. falciparum. IMPORTANCE PfSET2 has been reported to play key role in silencing var genes in Plasmodium falciparum, while the underlying molecular mechanisms remain unclear. Here, we provide evidence that PfSET2 is essential to maintain 3D genome organization of heterochromatin region to keep var genes in transcription repressive state. These findings can contribute better understanding of the regulation of high-order chromatin structure in P. falciparum.
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17
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Patterns of Heterochromatin Transitions Linked to Changes in the Expression of Plasmodium falciparum Clonally Variant Genes. Microbiol Spectr 2023; 11:e0304922. [PMID: 36515553 PMCID: PMC9927496 DOI: 10.1128/spectrum.03049-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The survival of malaria parasites in the changing human blood environment largely depends on their ability to alter gene expression by epigenetic mechanisms. The active state of Plasmodium falciparum clonally variant genes (CVGs) is associated with euchromatin characterized by the histone mark H3K9ac, whereas the silenced state is characterized by H3K9me3-based heterochromatin. Expression switches are linked to euchromatin-heterochromatin transitions, but these transitions have not been characterized for the majority of CVGs. To define the heterochromatin distribution patterns associated with the alternative transcriptional states of CVGs, we compared H3K9me3 occupancy at a genome-wide level among several parasite subclones of the same genetic background that differed in the transcriptional state of many CVGs. We found that de novo heterochromatin formation or the complete disruption of a heterochromatin domain is a relatively rare event, and for the majority of CVGs, expression switches can be explained by the expansion or retraction of heterochromatin domains. We identified different modalities of heterochromatin changes linked to transcriptional differences, but despite this complexity, heterochromatin distribution patterns generally enable the prediction of the transcriptional state of specific CVGs. We also found that in some subclones, several var genes were simultaneously in an active state. Furthermore, the heterochromatin levels in the putative regulatory region of the gdv1 antisense noncoding RNA, a regulator of sexual commitment, varied between parasite lines with different sexual conversion rates. IMPORTANCE The malaria parasite P. falciparum is responsible for more than half a million deaths every year. P. falciparum clonally variant genes (CVGs) mediate fundamental host-parasite interactions and play a key role in parasite adaptation to fluctuations in the conditions of the human host. The expression of CVGs is regulated at the epigenetic level by changes in the distribution of a type of chromatin called heterochromatin. Here, we describe at a genome-wide level the changes in the heterochromatin distribution associated with the different transcriptional states of CVGs. Our results also reveal a likely role for heterochromatin at a particular locus in determining the parasite investment in transmission to mosquitoes. Additionally, this data set will enable the prediction of the transcriptional state of CVGs from epigenomic data, which is important for the study of parasite adaptation to the conditions of the host in natural malaria infections.
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18
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Ngulube P. Humoral Immune Responses to P. falciparum Circumsporozoite Protein (Pfcsp) Induced by the RTS, S Vaccine - Current Update. Infect Drug Resist 2023; 16:2147-2157. [PMID: 37077252 PMCID: PMC10106824 DOI: 10.2147/idr.s401247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/23/2023] [Indexed: 04/21/2023] Open
Abstract
Malaria vaccines targeting the circumsporozoite protein (CSP) of the P. falciparum parasite have been overall relatively promising. RTS, S is a pre-erythrocytic recombinant protein-based malaria vaccine that targets CSP. RTS, S effectiveness shows some limited success regardless of its 58% efficacy for severe disease. P. falciparum circumsporozoite protein (Pfcsp) has stood to be the main candidate protein for most pre-erythrocytic stage vaccines. Studies on the structural and biophysical characteristics of antibodies specific to CSP (anti-CSP) are underway to achieve fine specificity with the CSP polymorphic regions. More recent studies have proposed the use of different kinds of monoclonal antibodies, the use of appropriate adjuvants, ideal vaccination dose and frequency, and improved targeting of particular epitopes for the robust production of functional antibodies and high complement-fixing activity as other potential methods for achieving long-lasting RTS, S. This review highlights recent findings regarding humoral immune responses to CSP elicited by RTS, S vaccine.
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Affiliation(s)
- Peter Ngulube
- Department of Biological Sciences, Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo, Malawi
- Correspondence: Peter Ngulube, Email
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19
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Doreswamy S, Al Sudani H. Malaria Falciparum: Relapse After a Decade. Cureus 2022; 14:e26730. [PMID: 35967182 PMCID: PMC9364061 DOI: 10.7759/cureus.26730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2022] [Indexed: 11/07/2022] Open
Abstract
Malaria is an infection caused by the Plasmodium malaria (PM) parasite. There are still cases of malaria that are reported in the United States on an annual basis. All these cases were a result of travelers who did not receive or follow their prescribed chemoprophylaxis, recommendations for avoiding mosquito bites while traveling, or relapsed dormant plasmodium. The malaria parasite can be transmitted by the bite of an infected female mosquito, through contact with infected blood products, or from mother to child during pregnancy through the placenta. It can take anywhere from 12 to 20 days for symptoms to appear, but there are cases of delayed development and/or relapse that can occur up to 13 years after the infection. We report a 31-year-old female with a history of malarial infection in Liberia, which had been treated ten years prior to her arrival in the United States. She presented to the hospital with abdominal pain, fever, and headache. She was eventually diagnosed with plasmodium malaria infection relapse and treated with a 14-day course of primaquine 300 mg daily, with the symptoms resolving a few days after. We believe her malarial infection was caused by a dormant malarial parasite that evaded the immune system and relapsed without having a risk factor for relapse or re-infection 10 years after her original infection.
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20
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Abstract
In eukaryotic organisms, noncoding RNAs (ncRNAs) have been implicated as important regulators of multifaceted biological processes, including transcriptional, posttranscriptional, and epigenetic regulation of gene expression. In recent years, it is becoming clear that protozoan parasites encode diverse ncRNA transcripts; however, little is known about their cellular functions. Recent advances in high-throughput “omic” studies identified many novel long ncRNAs (lncRNAs) in apicomplexan parasites, some of which undergo splicing, polyadenylation, and encode small proteins. To date, only a few of them are characterized, leaving a big gap in our understanding regarding their origin, mode of action, and functions in parasite biology. In this review, we focus on lncRNAs of the human malaria parasite Plasmodium falciparum and highlight their cellular functions and possible mechanisms of action.
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Affiliation(s)
- Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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21
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Giorgalli M, Cunningham DA, Broncel M, Sait A, Harrison TE, Hosking C, Vandomme A, Amis SI, Antonello A, Sullivan L, Uwadiae F, Torella L, Higgins MK, Langhorne J. Differential Trafficking and Expression of PIR Proteins in Acute and Chronic Plasmodium Infections. Front Cell Infect Microbiol 2022; 12:877253. [PMID: 35782145 PMCID: PMC9245118 DOI: 10.3389/fcimb.2022.877253] [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: 02/16/2022] [Accepted: 05/12/2022] [Indexed: 12/02/2022] Open
Abstract
Plasmodium multigene families are thought to play important roles in the pathogenesis of malaria. Plasmodium interspersed repeat (pir) genes comprise the largest multigene family in many Plasmodium species. However, their expression pattern and localisation remain to be elucidated. Understanding protein subcellular localisation is fundamental to reveal the functional importance and cell-cell interactions of the PIR proteins. Here, we use the rodent malaria parasite, Plasmodium chabaudi chabaudi, as a model to investigate the localisation pattern of this gene family. We found that most PIR proteins are co-expressed in clusters during acute and chronic infection; members of the S7 clade are predominantly expressed during the acute-phase, whereas members of the L1 clade dominate the chronic-phase of infection. Using peptide antisera specific for S7 or L1 PIRS, we show that these PIRs have different localisations within the infected red blood cells. S7 PIRs are exported into the infected red blood cell cytoplasm where they are co-localised with parasite-induced host cell modifications termed Maurer’s clefts, whereas L1 PIRs are localised on or close to the parasitophorous vacuolar membrane. This localisation pattern changes following mosquito transmission and during progression from acute- to chronic-phase of infection. The presence of PIRs in Maurer’s clefts, as seen for Plasmodium falciparum RIFIN and STEVOR proteins, might suggest trafficking of the PIRs on the surface of the infected erythrocytes. However, neither S7 nor L1 PIR proteins detected by the peptide antisera are localised on the surface of infected red blood cells, suggesting that they are unlikely to be targets of surface variant-specific antibodies or to be directly involved in adhesion of infected red blood cells to host cells, as described for Plasmodium falciparum VAR proteins. The differences in subcellular localisation of the two major clades of Plasmodium chabaudi PIRs across the blood cycle, and the apparent lack of expression on the red cell surface strongly suggest that the function(s) of this gene family may differ from those of other multigene families of Plasmodium, such as the var genes of Plasmodium falciparum.
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Affiliation(s)
- Maria Giorgalli
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Malgorzata Broncel
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Aaron Sait
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Thomas E. Harrison
- Laboratory of Molecular Parasitology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Caroline Hosking
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Audrey Vandomme
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Sarah I. Amis
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ana Antonello
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lauren Sullivan
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Faith Uwadiae
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Laura Torella
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Matthew K. Higgins
- Laboratory of Molecular Parasitology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jean Langhorne
- Malaria Immunology Laboratory, The Francis Crick Institute, London, United Kingdom
- *Correspondence: Jean Langhorne,
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22
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Dave B, Kanyal A, Mamatharani DV, Karmodiya K. Pervasive sequence-level variation in the transcriptome of Plasmodium falciparum. NAR Genom Bioinform 2022; 4:lqac036. [PMID: 35591889 PMCID: PMC9112769 DOI: 10.1093/nargab/lqac036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 03/09/2022] [Accepted: 05/14/2022] [Indexed: 12/05/2022] Open
Abstract
Single-nucleotide variations (SNVs) in RNA, arising from co- and post-transcriptional phenomena including transcription errors and RNA-editing, are well studied in a range of organisms. In the malaria parasite Plasmodium falciparum, stage-specific and non-specific gene-expression variations accompany the parasite's array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite's transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the P. falciparum transcriptome. SNV rates for a gene were correlated to gene length (r[Formula: see text]0.65-0.7) but not to the AT-content of that gene. Global SNV rates for the P. falciparum lines we used, and for publicly available P. vivax and P. falciparum clinical isolate datasets, were of the order of 10-3 per base, ∼10× higher than rates we calculated for bacterial datasets. These variations may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution of P. falciparum and parasite biology more broadly. We anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.
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Affiliation(s)
- Bruhad Dave
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - D V Mamatharani
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
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23
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Saxena H, Gupta A. P. falciparum PfRUVBL proteins binds at TARE region and var gene promoter located in subtelomeric region. Pathog Dis 2022; 80:6595874. [PMID: 35640888 DOI: 10.1093/femspd/ftac018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/14/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
In order to survive and establish infection, Plasmodium parasite employ various strategies to evade host immune response. Var genes family, a repertoire of 60 genes, express parasite-specific protein PfEMP1, a variable surface antigen, on the membrane of infected erythrocyte, and by continuously switching the variants of PfEMP1, helps the parasite to avoid detection and destruction by host immune system during intra-erythrocytic developmental cycle. Although chromatin modifications are recognized to be a prominent phenomenon in regulation of mono-allelic expression of these var genes, however the precise histone codes and molecular players & mechanisms guiding these modifications are yet to be unravelled in depth. In this study, we have functionally characterized RUVBL proteins of P. falciparum and shown that PfMYST (an essential lysine acetyl transferase) and PfRUVBL protein complex occupy the TARE region and var gene promoter in ring stage of the parasite. Further we have demonstrated that PfMYST/PfRUVBL complex interact with core histone, H3 & H4. Overall the findings of this study adds a layer by identifying the potential role of epigenetic regulators, PfMYST & PfRUVBL in regulation of monoallelic expression of var genes in malaria parasite.
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Affiliation(s)
- Himani Saxena
- Epigenetics and Human disease laboratory, Department of Life Sciences, Shiv Nadar University, Delhi-NCR, India
| | - Ashish Gupta
- Epigenetics and Human disease laboratory, Department of Life Sciences, Shiv Nadar University, Delhi-NCR, India
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24
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Stochastic expression of invasion genes in Plasmodium falciparum schizonts. Nat Commun 2022; 13:3004. [PMID: 35637187 PMCID: PMC9151791 DOI: 10.1038/s41467-022-30605-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/22/2022] [Indexed: 12/15/2022] Open
Abstract
Genetically identical cells are known to exhibit differential phenotypes in the same environmental conditions. These phenotypic variants are linked to transcriptional stochasticity and have been shown to contribute towards adaptive flexibility of a wide range of unicellular organisms. Here, we investigate transcriptional heterogeneity and stochastic gene expression in Plasmodium falciparum by performing the quasilinear multiple annealing and looping based amplification cycles (MALBAC) based amplification and single cell RNA sequencing of blood stage schizonts. Our data reveals significant transcriptional variations in the schizont stage with a distinct group of highly variable invasion gene transcripts being identified. Moreover, the data reflects several diversification processes including putative developmental “checkpoint”; transcriptomically distinct parasite sub-populations and transcriptional switches in variable gene families (var, rifin, phist). Most of these features of transcriptional variability are preserved in isogenic parasite cell populations (albeit with a lesser amplitude) suggesting a role of epigenetic factors in cell-to-cell transcriptional variations in human malaria parasites. Lastly, we apply quantitative RT-PCR and RNA-FISH approach and confirm stochastic expression of key invasion genes, such as, msp1, msp3, msp7, eba181 and ama1 which represent prime candidates for invasion-blocking vaccines. Genetically identical cells can be phenotypically diverse to allow adaptive flexibility in a given environment. This phenotypic diversity is driven by epigenetic and transcriptional variability. Here, Tripathi et al. perform scRNA-seq of isogenic and non-isogenic Plasmodium falciparum schizont populations to explore transcriptional heterogeneity and stochastic gene expression during the course of development.
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25
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Goo YK. Vivax Malaria and the Potential Role of the Subtelomeric Multigene vir Superfamily. Microorganisms 2022; 10:microorganisms10061083. [PMID: 35744600 PMCID: PMC9228997 DOI: 10.3390/microorganisms10061083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Vivax malaria, caused by Plasmodium vivax, remains a public health concern in Central and Southeast Asia and South America, with more than two billion people at risk of infection. Compared to Plasmodium falciparum, P. vivax is considered a benign infection. However, in recent decades, incidences of severe vivax malaria have been confirmed. The P. falciparum erythrocyte membrane protein 1 family encoded by var genes is known as a mediator of severe falciparum malaria by cytoadherence property. Correspondingly, the vir multigene superfamily has been identified as the largest multigene family in P. vivax and is implicated in cytoadherence to endothelial cells and immune response activation. In this review, the functions of vir genes are reviewed in the context of their potential roles in severe vivax malaria.
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Affiliation(s)
- Youn-Kyoung Goo
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea
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26
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Yu JL, Liu QY, Yang B, Sun YF, Wang YJ, Jiang J, Wang B, Cheng Y, Wang QB. Immunogenicity Analysis of the Recombinant Plasmodium falciparum Surface-Related Antigen in Mice. Pathogens 2022; 11:550. [PMID: 35631071 PMCID: PMC9145071 DOI: 10.3390/pathogens11050550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Plasmodium falciparum, mainly distributed in tropical and subtropical regions of the world, has received widespread attention owing to its severity. As a novel protein, P. falciparum surface-related antigen (PfSRA) has the structural and functional characteristics to be considered as a malaria vaccine candidate; however, limited information is available on its immunogenicity. Here, we expressed three fragments of recombinant PfSRA in an Escherichia coli system and further analyzed its immunogenicity. The results showed that rPfSRA-immunized mice produced specific antibodies with high endpoint titers (1:10,000 to 1:5,120,000) and affinity antibodies (i.e., rPfSRA-F1a (97.70%), rPfSRA-F2a (69.62%), and rPfSRA-F3a (91.87%)). In addition, the sera of immunized mice recognized both the native PfSRA and recombinant PfSRA, the rPfSRA antibodies inhibited the invasion of P. falciparum into the erythrocytes, and they were dose-dependent in vitro. This study confirmed PfSRA could be immunogenic, especially the F1a at the conserved region N-terminal and provided further support for it as a vaccine candidate against P.falciparum.
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Affiliation(s)
- Jia-Li Yu
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214000, China; (J.-L.Y.); (B.Y.); (Y.-F.S.)
| | - Qing-Yang Liu
- Department of Clinical Laboratory, Wuxi 9th Affiliated Hospital of Soochow University (Wuxi 9th People’s Hospital), Wuxi 214000, China;
| | - Bo Yang
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214000, China; (J.-L.Y.); (B.Y.); (Y.-F.S.)
| | - Yi-Fan Sun
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214000, China; (J.-L.Y.); (B.Y.); (Y.-F.S.)
| | - Ya-Ju Wang
- Wuxi Red Cross Blood Center, Wuxi 214000, China; (Y.-J.W.); (J.J.)
| | - Jian Jiang
- Wuxi Red Cross Blood Center, Wuxi 214000, China; (Y.-J.W.); (J.J.)
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, China;
| | - Yang Cheng
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214000, China; (J.-L.Y.); (B.Y.); (Y.-F.S.)
| | - Qiu-Bo Wang
- Department of Clinical Laboratory, Wuxi 9th Affiliated Hospital of Soochow University (Wuxi 9th People’s Hospital), Wuxi 214000, China;
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27
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Epigenetics of malaria parasite nutrient uptake, but why? Trends Parasitol 2022; 38:618-628. [PMID: 35641406 PMCID: PMC9283302 DOI: 10.1016/j.pt.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 11/23/2022]
Abstract
The conserved plasmodial surface anion channel (PSAC) mediates nutrient uptake by bloodstream malaria parasites and is an antimalarial target. This pathogen-associated channel is linked to the clag multigene family, which is variably expanded in Plasmodium spp. Member genes are under complex epigenetic regulation, with the clag3 genes of the human P. falciparum pathogen exhibiting monoallelic transcription and mutually exclusive surface exposure on infected erythrocytes. While other multigene families use monoallelic expression to evade host immunity, the reasons of epigenetic control of clag genes are unclear. I consider existing models and their implications for nutrient acquisition and immune evasion. Understanding the reasons for epigenetic regulation of PSAC-mediated nutrient uptake will help clarify host-pathogen interactions and guide development of therapies resistant to allele switching.
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28
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Turnbull LB, Button-Simons KA, Agbayani N, Ferdig MT. Sources of transcription variation in Plasmodium falciparum. J Genet Genomics 2022; 49:965-974. [PMID: 35395422 DOI: 10.1016/j.jgg.2022.03.008] [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: 11/18/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/20/2022]
Abstract
Variation in transcript abundance can contribute to both short-term environmental response and long-term evolutionary adaptation. Most studies are designed to assess differences in mean transcription levels and do not consider other potentially important and confounding sources of transcriptional variation. Detailed quantification of variation sources will improve our ability to detect and identify the mechanisms that contribute to genome-wide transcription changes that underpin adaptive responses. To quantify innate levels of expression variation, we measured mRNA levels for more than 5000 genes in the malaria parasite, Plasmodium falciparum, among clones derived from two parasite strains across biologically and experimentally replicated batches. Using a mixed effects model, we partitioned the total variation among four sources - between strain, within strain, environmental batch effects, and stochastic noise. We found 646 genes with significant variation attributable to at least one of these sources. These genes were categorized by their predominant variation source and further examined using gene ontology enrichment analysis to associate function with each source of variation. Genes with environmental batch effect and within strain transcript variation may contribute to phenotypic plasticity, while genes with between strain variation may contribute to adaptive responses and processes that lead to parasite strain-specific survival under varied conditions.
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Affiliation(s)
- Lindsey B Turnbull
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Katrina A Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nestor Agbayani
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA; Rush School of Medicine, Chicago, IL, 60612, USA
| | - Michael T Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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29
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Tintó-Font E, Cortés A. Malaria parasites do respond to heat. Trends Parasitol 2022; 38:435-449. [PMID: 35301987 DOI: 10.1016/j.pt.2022.02.009] [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: 11/05/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 01/09/2023]
Abstract
The capacity of malaria parasites to respond to changes in their environment at the transcriptional level has been the subject of debate, but recent evidence has unambiguously demonstrated that Plasmodium spp. can produce adaptive transcriptional responses when exposed to some specific types of stress. These include metabolic conditions and febrile temperature. The Plasmodium falciparum protective response to thermal stress is similar to the response in other organisms, but it is regulated by a transcription factor evolutionarily unrelated to the conserved transcription factor that drives the heat shock (HS) response in most eukaryotes. Of the many genes that change expression during HS, only a subset constitutes an authentic response that contributes to parasite survival.
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Affiliation(s)
- Elisabet Tintó-Font
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Catalonia, Spain
| | - Alfred Cortés
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Catalonia, Spain; ICREA, Barcelona 08010, Catalonia, Spain.
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30
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Chen S, Gao Y, Fan Y, Guo S, Zhou J, Liu T, Xu W. The Dynamic Change of Immune Responses Between Acute and Recurrence Stages of Rodent Malaria Infection. Front Microbiol 2022; 13:844975. [PMID: 35250958 PMCID: PMC8891988 DOI: 10.3389/fmicb.2022.844975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria infections are persistent as frequent recrudescence of the disease may occur following the acute infection stage, but the different immune responses that control the acute and recrudescence stages are still largely unknown. Using single-cell RNA sequencing (scRNA-seq), we showed that the number of Th1 and plasma cells in the spleen was significantly reduced during the recurrence stage compared to the acute stage of Plasmodium chabaudi chabaudi AS (P. chabaudi) infection. Additionally, the ability of both CD4+ T cell responses and B cells to control P. chabaudi recurrence was significantly reduced compared to their roles in the control of acute infection. In contrast, the number of innate immune cells, including red pulp macrophages (RPMs), gamma delta (γδ) T cells, and Dendritic cells (DCs) were significantly increased during the recurrence stage and showed to be critical for P. chabaudi infection recurrence control. Thus, our data strongly suggest the complementary role of innate immune responses in controlling malaria recrudescence when adaptive immune responses are suppressed. These findings shed new light on the development of immune interventions against malaria.
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Affiliation(s)
- Suilin Chen
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
| | - Yuanli Gao
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
| | - Yongling Fan
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
| | - Shuai Guo
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
| | - Jian Zhou
- Institute of Immunology, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Jian Zhou,
| | - Taiping Liu
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
- Taiping Liu,
| | - Wenyue Xu
- Department of Pathogenic Biology, Army Medical University (Third Military Medical University), Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
- Wenyue Xu,
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Srivastava A, Garg S, Karan S, Kaushik S, Ranganathan A, Pati S, Garg LC, Singh S. Plasmodium falciparum Antigen Expression in Leishmania Parasite: A Way Forward for Live Attenuated Vaccine Development. Methods Mol Biol 2022; 2410:555-566. [PMID: 34914067 DOI: 10.1007/978-1-0716-1884-4_28] [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] [Indexed: 06/14/2023]
Abstract
Live attenuated vaccines (LAVs) are among the most critical interventions in modern medicine and have already proven their potential to save millions of lives. LAVs are always explored as potential vaccine candidates since they induce an immune response, which is as good as the wild type pathogen. For parasitic diseases, the efficacy of LAVs is still under investigation and needs extensive research to mark their presence in the field. In malaria, live attenuated sporozoites have been evaluated for a vaccine against the liver stage. This vaccine approach is limited due to the highly cumbersome technique of sporozoite isolation and related relapse issues. We have developed a novel vaccine against malaria by expressing Plasmodium falciparum antigens in Leishmania donovani promastigotes. These hybrid, recombinant L. donovani parasites mimicking P. falciparum parasite antigens were analyzed for their anti-malarial efficacy in preclinical studies. We demonstrate the potential of Leishmania spp. parasites in developing an important live vector vaccine against malaria for the induction of protective immune responses. Herein, we describe a method to express malaria parasite antigens in L. donovani promastigotes and analyze its potential for a vaccine against malaria. This methodology can be extended to live, attenuated Leishmania promastigotes parasites to develop LAV against malaria.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Science, School of Natural Sciences, Shiv Nadar University, Dadri, UP, India
| | - Swati Garg
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sweta Karan
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Shikha Kaushik
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Anand Ranganathan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Soumya Pati
- Department of Life Science, School of Natural Sciences, Shiv Nadar University, Dadri, UP, India
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India.
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
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32
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Shang X, Wang C, Fan Y, Guo G, Wang F, Zhao Y, Sheng F, Tang J, He X, Yu X, Zhang M, Zhu G, Yin S, Mu J, Culleton R, Cao J, Jiang M, Zhang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3413-3431. [PMID: 35288749 PMCID: PMC8989538 DOI: 10.1093/nar/gkac176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Heterochromatin-associated gene silencing controls multiple physiological processes in malaria parasites, however, little is known concerning the regulatory network and cis-acting sequences involved in the organization of heterochromatin and how they modulate heterochromatic gene expression. Based on systematic profiling of genome-wide occupancy of eighteen Apicomplexan AP2 transcription factors by ChIP-seq analysis, we identify and characterize eight heterochromatin-associated factors (PfAP2-HFs), which exhibit preferential enrichment within heterochromatic regions but with differential coverage profiles. Although these ApiAP2s target euchromatic gene loci via specific DNA motifs, they are likely integral components of heterochromatin independent of DNA motif recognition. Systematic knockout screenings of ApiAP2 factors coupled with RNA-seq transcriptomic profiling revealed three activators and three repressors of heterochromatic gene expression including four PfAP2-HFs. Notably, expression of virulence genes is either completely silenced or significantly reduced upon the depletion of PfAP2-HC. Integrated multi-omics analyses reveal autoregulation and feed-forward loops to be common features of the ApiAP2 regulatory network, in addition to the occurrence of dynamic interplay between local chromatin structure and ApiAP2s in transcriptional control. Collectively, this study provides a valuable resource describing the genome-wide landscape of the ApiAP2 family and insights into functional divergence and cooperation within this family during the blood-stage development of malaria parasites.
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Affiliation(s)
| | | | | | | | - Fei Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Fei Sheng
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892-8132, USA
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Jun Cao
- Correspondence may also be addressed to Jun Cao. Tel: +05 10 6878 1007;
| | - Mei Jiang
- Correspondence may also be addressed to Mei Jiang. Tel: +86 21 6598 5138;
| | - Qingfeng Zhang
- To whom correspondence should be addressed. Tel: +86 21 6598 5138;
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Oleinikov AV. Malaria Parasite Plasmodium falciparum Proteins on the Surface of Infected Erythrocytes as Targets for Novel Drug Discovery. BIOCHEMISTRY (MOSCOW) 2022; 87:S192-S177. [PMID: 35501996 PMCID: PMC8802247 DOI: 10.1134/s0006297922140152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Specific adhesion (sequestration) of Plasmodium falciparum parasite-infected erythrocytes (IEs) in deep vascular beds can cause severe complications resulting in death. This review describes our work on the discovery, characterization, and optimization of novel inhibitors that specifically prevent adhesion of IEs to the host vasculature during severe malaria, especially its placental and cerebral forms. The main idea of using anti-adhesion drugs in severe malaria is to release sequestered parasites (or prevent additional sequestration) as quickly as possible. This may significantly improve the outcomes for patients with severe malaria by decreasing local and systemic inflammation associated with the disease and reestablishing the microvascular blood flow. To identify anti-malarial adhesion-inhibiting molecules, we have developed a high-throughput (HT) screening approach and found a number of promising leads that can be further developed into anti-adhesion drugs providing an efficient adjunct therapy against severe forms of malaria.
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Affiliation(s)
- Andrew V Oleinikov
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33428, USA.
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34
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Possemiers H, Pham TT, Coens M, Pollenus E, Knoops S, Noppen S, Vandermosten L, D’haese S, Dillemans L, Prenen F, Schols D, Franke-Fayard B, Van den Steen PE. Skeleton binding protein-1-mediated parasite sequestration inhibits spontaneous resolution of malaria-associated acute respiratory distress syndrome. PLoS Pathog 2021; 17:e1010114. [PMID: 34843584 PMCID: PMC8659713 DOI: 10.1371/journal.ppat.1010114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/09/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
Malaria is a hazardous disease caused by Plasmodium parasites and often results in lethal complications, including malaria-associated acute respiratory distress syndrome (MA-ARDS). Parasite sequestration in the microvasculature is often observed, but its role in malaria pathogenesis and complications is still incompletely understood. We used skeleton binding protein-1 (SBP-1) KO parasites to study the role of sequestration in experimental MA-ARDS. The sequestration-deficiency of these SBP-1 KO parasites was confirmed with bioluminescence imaging and by measuring parasite accumulation in the lungs with RT-qPCR. The SBP-1 KO parasites induced similar lung pathology in the early stage of experimental MA-ARDS compared to wildtype (WT) parasites. Strikingly, the lung pathology resolved subsequently in more than 60% of the SBP-1 KO infected mice, resulting in prolonged survival despite the continuous presence of the parasite. This spontaneous disease resolution was associated with decreased inflammatory cytokine expression measured by RT-qPCR and lower expression of cytotoxic markers in pathogenic CD8+ T cells in the lungs of SBP-1 KO infected mice. These data suggest that SBP-1-mediated parasite sequestration and subsequent high parasite load are not essential for the development of experimental MA-ARDS but inhibit the resolution of the disease. Malaria is still a severe global disease with more than 200 million cases and 400 000 deaths each year. Plasmodium falciparum is the species responsible for most malaria deaths globally. The propensity of these parasites to sequester in peripheral vascular beds is assumed to play an important role in disease severity and mortality. Although sequestration has been observed in lungs of malaria patients, its role in the pathogenesis of MA-ARDS, a severe lung complication in malaria, was previously unknown. Therefore, we used sequestration-deficient SBP-1 KO Plasmodium berghei NK65 parasites to study the role of sequestration in experimental MA-ARDS. We observed that MA-ARDS developed similarly in WT and SBP-1 KO infected mice, but the majority of SBP-1 KO-infected mice were able to resolve the lung pathology despite the continuous presence of the parasite. This coincided with a prolonged survival, a decrease in inflammatory cytokine expression and lower expression of cytotoxicity markers in pathogenic CD8+ T cells. These results give important new insights in the role of parasite sequestration in malaria pathology.
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Affiliation(s)
- Hendrik Possemiers
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Thao-Thy Pham
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
- Currently at Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Belgium
| | - Marion Coens
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Emilie Pollenus
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Sofie Knoops
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Sam Noppen
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Leen Vandermosten
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Sigrid D’haese
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
- Currently at Neuro-Aging & Viro-Immunotherapy (NAVI), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Luna Dillemans
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Fran Prenen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
| | | | - Philippe E. Van den Steen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical research, KU Leuven, Belgium
- * E-mail:
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Sethumadhavan DV, Govindaraju G, Jabeena CA, Rajavelu A. Plasmodium falciparum SET2 domain is allosterically regulated by its PHD-like domain to methylate at H3K36. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194744. [PMID: 34389510 DOI: 10.1016/j.bbagrm.2021.194744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
The antigenic variation is an essential mechanism employed by the malaria parasite to establish a chronic infection in humans. Three major virulent proteins EMP1, RIFINs, and STEVOR have been implicated in contributing to the antigenic variation process and are encoded by multigene families in Plasmodium spp. The key virulence factor PfEMP1 is encoded by var genes, and it exhibits a mutually exclusive transcriptional switching between var genes, ensuring an individual parasite only transcribes a single var gene at a time. Expression of var genes is tightly regulated by two histone epigenetic methylation marks H3K36me3 and H3K9me3, of which the H3K36me3 mark is highly enriched on transcription start sites (TSSs) of suppressed var genes in P. falciparum. However, the mechanisms of H3K36me3 mark propagation on all the 59 var genes of P. falciparum are not known. Here, we have identified a PHD (Plant Homeodomain-like Domain) like domain present within the PfSET2 protein that specifically binds to the H3K36me2 mark, an intermediate product of the H3K36me3 mark formation on the nucleosome. Surprisingly, we have found that PHD - H3K36me2 interaction leads to stimulation of SET2 domain activity on the nucleosome substrates. The allosteric stimulation of the PfSET2 domain by PHD-like domain present within the same protein suggests a novel mechanism of H3K36me3 mark propagation on var genes of P. falciparum. This study proposes allosteric regulation of PfSET2 protein by H3K36me2 mark as an essential mechanism of var genes suppression to ensure successful antigenic variation by the malaria parasite.
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Affiliation(s)
- Devadathan Valiyamangalath Sethumadhavan
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram-, 695014, Kerala, India; Ph.D registered with Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Gayathri Govindaraju
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram-, 695014, Kerala, India; Ph.D registered with Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - C A Jabeena
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram-, 695014, Kerala, India; Ph.D registered with Manipal Academy of Higher Education (MAHE), Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Arumugam Rajavelu
- Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud PO, Thiruvananthapuram-, 695014, Kerala, India; Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, 600 036, India.
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36
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Expression Patterns of Plasmodium falciparum Clonally Variant Genes at the Onset of a Blood Infection in Malaria-Naive Humans. mBio 2021; 12:e0163621. [PMID: 34340541 PMCID: PMC8406225 DOI: 10.1128/mbio.01636-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clonally variant genes (CVGs) play fundamental roles in the adaptation of Plasmodium falciparum to fluctuating conditions of the human host. However, their expression patterns under the natural conditions of the blood circulation have been characterized in detail for only a few specific gene families. Here, we provide a detailed characterization of the complete P. falciparum transcriptome across the full intraerythrocytic development cycle (IDC) at the onset of a blood infection in malaria-naive human volunteers. We found that the vast majority of transcriptional differences between parasites obtained from the volunteers and the parental parasite line maintained in culture occurred in CVGs. In particular, we observed a major increase in the transcript levels of most genes of the pfmc-2tm and gbp families and of specific genes of other families, such as phist, hyp10, rif, or stevor, in addition to previously reported changes in var and clag3 gene expression. Increased transcript levels of individual pfmc-2tm, rif, and stevor genes involved activation in small subsets of parasites. Large transcriptional differences correlated with changes in the distribution of heterochromatin, confirming their epigenetic nature. Furthermore, the similar expression of several CVGs between parasites collected at different time points along the blood infection suggests that the epigenetic memory for multiple CVG families is lost during transmission stages, resulting in a reset of their transcriptional state. Finally, the CVG expression patterns observed in a volunteer likely infected by a single sporozoite suggest that new epigenetic patterns are established during liver stages.
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37
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Argyropoulos DC, Ruybal‐Pesántez S, Deed SL, Oduro AR, Dadzie SK, Appawu MA, Asoala V, Pascual M, Koram KA, Day KP, Tiedje KE. The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Mol Ecol 2021; 30:3974-3992. [PMID: 34143538 PMCID: PMC8456823 DOI: 10.1111/mec.16029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 01/16/2023]
Abstract
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (He : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.
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Affiliation(s)
- Dionne C. Argyropoulos
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Shazia Ruybal‐Pesántez
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical ResearchMelbourneVic.Australia
- Present address:
Department of Medical Biology and Bio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Burnet InstituteMelbourneVic.Australia
| | - Samantha L. Deed
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Abraham R. Oduro
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Samuel K. Dadzie
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Maxwell A. Appawu
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Victor Asoala
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Mercedes Pascual
- Department of Ecology and EvolutionUniversity of ChicagoChicagoUSA
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Karen P. Day
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Kathryn E. Tiedje
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
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38
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How much epigenetics and quantitative trait loci (QTL) mapping tell us about parasitism maintenance and resistance/susceptibility to hosts. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166214. [PMID: 34271118 DOI: 10.1016/j.bbadis.2021.166214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/07/2021] [Indexed: 01/20/2023]
Abstract
Interactions between the environment, parasites, vectors, and/or intermediate hosts are complex and involve several factors that define the success or failure of an infection. Among these interactions that can affect infections by a parasite, it is possible to highlight the genetic and epigenetic mechanisms in hosts and parasites. The interaction between genetics, epigenetics, infection, and the host's internal and external environment is decisive and dictates the outcome of a parasitic infection and the resistance, susceptibility, and transmission of this parasite. Epigenetic changes become important mediators in the regulation of gene expression, allowing the evasion of the parasite to immune host barriers, its transmission to new hosts, and the end of its development cycle. Epigenetics is a new frontier in the understanding of the interaction mechanisms between parasite and host that, along with information from the gene regions associated with complex phenotypic variations, the Quantitative Trait Loci, brings new possibilities to investigate more modern and efficient approaches to the treatment, control, and eradication of parasitic diseases. In this brief review, a general overview of the use of epigenetic information and mapping of Quantitative Trait Loci was summarized, both in genes of parasites and hosts, for understanding the mechanisms of resistance and/or susceptibility in parasitic relationships; also, the main search platforms were quantitatively compared, aiming to facilitate access data produced over a period of twenty years.
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39
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Luzak V, López-Escobar L, Siegel TN, Figueiredo LM. Cell-to-Cell Heterogeneity in Trypanosomes. Annu Rev Microbiol 2021; 75:107-128. [PMID: 34228491 DOI: 10.1146/annurev-micro-040821-012953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent developments in single-cell and single-molecule techniques have revealed surprising levels of heterogeneity among isogenic cells. These advances have transformed the study of cell-to-cell heterogeneity into a major area of biomedical research, revealing that it can confer essential advantages, such as priming populations of unicellular organisms for future environmental stresses. Protozoan parasites, such as trypanosomes, face multiple and often hostile environments, and to survive, they undergo multiple changes, including changes in morphology, gene expression, and metabolism. But why does only a subset of proliferative cells differentiate to the next life cycle stage? Why do only some bloodstream parasites undergo antigenic switching while others stably express one variant surface glycoprotein? And why do some parasites invade an organ while others remain in the bloodstream? Building on extensive research performed in bacteria, here we suggest that biological noise can contribute to the fitness of eukaryotic pathogens and discuss the importance of cell-to-cell heterogeneity in trypanosome infections. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Vanessa Luzak
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany.,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany
| | - Lara López-Escobar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany.,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany
| | - Luisa M Figueiredo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
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40
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Role of chromatin modulation in the establishment of protozoan parasite infection for developing targeted chemotherapeutics. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00356-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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41
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Cheeseman K, Jannot G, Lourenço N, Villares M, Berthelet J, Calegari-Silva T, Hamroune J, Letourneur F, Rodrigues-Lima F, Weitzman JB. Dynamic methylation of histone H3K18 in differentiating Theileria parasites. Nat Commun 2021; 12:3221. [PMID: 34050145 PMCID: PMC8163883 DOI: 10.1038/s41467-021-23477-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 04/14/2021] [Indexed: 12/31/2022] Open
Abstract
Lysine methylation on histone tails impacts genome regulation and cell fate determination in many developmental processes. Apicomplexa intracellular parasites cause major diseases and they have developed complex life cycles with fine-tuned differentiation events. Yet, apicomplexa genomes have few transcription factors and little is known about their epigenetic control systems. Tick-borne Theileria apicomplexa species have relatively small, compact genomes and a remarkable ability to transform leucocytes in their bovine hosts. Here we report enriched H3 lysine 18 monomethylation (H3K18me1) on the gene bodies of repressed genes in Theileria macroschizonts. Differentiation to merozoites (merogony) leads to decreased H3K18me1 in parasite nuclei. Pharmacological manipulation of H3K18 acetylation or methylation impacted parasite differentiation and expression of stage-specific genes. Finally, we identify a parasite SET-domain methyltransferase (TaSETup1) that can methylate H3K18 and represses gene expression. Thus, H3K18me1 emerges as an important epigenetic mark which controls gene expression and stage differentiation in Theileria parasites.
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Affiliation(s)
- Kevin Cheeseman
- Université de Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | - Guillaume Jannot
- Université de Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | - Nelly Lourenço
- Université de Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | - Marie Villares
- Université de Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | - Jérémy Berthelet
- Université de Paris, Epigenetics and Cell Fate, CNRS, Paris, France.,Université de Paris, Functional and Adaptive Biology, CNRS, Paris, France
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42
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Carrington E, Cooijmans RHM, Keller D, Toenhake CG, Bártfai R, Voss TS. The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasite Plasmodium falciparum. iScience 2021; 24:102444. [PMID: 33997710 PMCID: PMC8105651 DOI: 10.1016/j.isci.2021.102444] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/10/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
Malaria parasites undergo a complex life cycle in the human host and the mosquito vector. The ApiAP2 family of DNA-binding proteins plays a dominant role in parasite development and life cycle progression. Most ApiAP2 factors studied to date act as transcription factors regulating stage-specific gene expression. Here, we characterized an ApiAP2 factor in Plasmodium falciparum that we termed PfAP2-HC. We demonstrate that PfAP2-HC specifically binds to heterochromatin throughout the genome. Intriguingly, PfAP2-HC does not bind DNA in vivo and recruitment of PfAP2-HC to heterochromatin is independent of its DNA-binding domain but strictly dependent on heterochromatin protein 1. Furthermore, our results suggest that PfAP2-HC functions neither in the regulation of gene expression nor in heterochromatin formation or maintenance. In summary, our findings reveal PfAP2-HC as a core component of heterochromatin in malaria parasites and identify unexpected properties and substantial functional divergence among the members of the ApiAP2 family of regulatory proteins. The ApiAP2 factor AP2-HC is a core component of heterochromatin in malaria parasites Binding of AP2-HC to heterochromatin strictly depends on heterochromatin protein 1 The AP2 DNA-binding domain of AP2-HC is dispensable for heterochromatin association
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Affiliation(s)
- Eilidh Carrington
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | | | - Dominique Keller
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | | | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Till Steffen Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
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43
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Guha R, Mathioudaki A, Doumbo S, Doumtabe D, Skinner J, Arora G, Siddiqui S, Li S, Kayentao K, Ongoiba A, Zaugg J, Traore B, Crompton PD. Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype. PLoS Pathog 2021; 17:e1009430. [PMID: 33822828 PMCID: PMC8023468 DOI: 10.1371/journal.ppat.1009430] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/27/2021] [Indexed: 12/24/2022] Open
Abstract
In malaria-naïve children and adults, Plasmodium falciparum-infected red blood cells (Pf-iRBCs) trigger fever and other symptoms of systemic inflammation. However, in endemic areas where individuals experience repeated Pf infections over many years, the risk of Pf-iRBC-triggered inflammatory symptoms decreases with cumulative Pf exposure. The molecular mechanisms underlying these clinical observations remain unclear. Age-stratified analyses of uninfected, asymptomatic Malian individuals before the malaria season revealed that monocytes of adults produced lower levels of inflammatory cytokines (IL-1β, IL-6 and TNF) in response to Pf-iRBC stimulation compared to monocytes of Malian children and malaria-naïve U.S. adults. Moreover, monocytes of Malian children produced lower levels of IL-1β and IL-6 following Pf-iRBC stimulation compared to 4-6-month-old infants. Accordingly, monocytes of Malian adults produced more IL-10 and expressed higher levels of the regulatory molecules CD163, CD206, Arginase-1 and TGM2. These observations were recapitulated in an in vitro system of monocyte to macrophage differentiation wherein macrophages re-exposed to Pf-iRBCs exhibited attenuated inflammatory cytokine responses and a corresponding decrease in the epigenetic marker of active gene transcription, H3K4me3, at inflammatory cytokine gene loci. Together these data indicate that Pf induces epigenetic reprogramming of monocytes/macrophages toward a regulatory phenotype that attenuates inflammatory responses during subsequent Pf exposure. Trial Registration: ClinicalTrials.gov NCT01322581.
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Affiliation(s)
- Rajan Guha
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail: (RG); (PDC)
| | - Anna Mathioudaki
- Structural and Computational Biology Unit, The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Gunjan Arora
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Shafiuddin Siddiqui
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kassoum Kayentao
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Judith Zaugg
- Structural and Computational Biology Unit, The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Boubacar Traore
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail: (RG); (PDC)
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44
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Connacher J, Josling GA, Orchard LM, Reader J, Llinás M, Birkholtz LM. H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum. Epigenetics Chromatin 2021; 14:19. [PMID: 33794978 PMCID: PMC8017609 DOI: 10.1186/s13072-021-00393-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background The Plasmodium sexual gametocyte stages are the only transmissible form of the malaria parasite and are thus responsible for the continued transmission of the disease. Gametocytes undergo extensive functional and morphological changes from commitment to maturity, directed by an equally extensive control program. However, the processes that drive the differentiation and development of the gametocyte post-commitment, remain largely unexplored. A previous study reported enrichment of H3K36 di- and tri-methylated (H3K36me2&3) histones in early-stage gametocytes. Using chromatin immunoprecipitation followed by high-throughput sequencing, we identify a stage-specific association between these repressive histone modifications and transcriptional reprogramming that define a stage II gametocyte transition point. Results Here, we show that H3K36me2 and H3K36me3 from stage II gametocytes are associated with repression of genes involved in asexual proliferation and sexual commitment, indicating that H3K36me2&3-mediated repression of such genes is essential to the transition from early gametocyte differentiation to intermediate development. Importantly, we show that the gene encoding the transcription factor AP2-G as commitment master regulator is enriched with H3K36me2&3 and actively repressed in stage II gametocytes, providing the first evidence of ap2-g gene repression in post-commitment gametocytes. Lastly, we associate the enhanced potency of the pan-selective Jumonji inhibitor JIB-04 in gametocytes with the inhibition of histone demethylation including H3K36me2&3 and a disruption of normal transcriptional programs. Conclusions Taken together, our results provide the first description of an association between global gene expression reprogramming and histone post-translational modifications during P. falciparum early sexual development. The stage II gametocyte-specific abundance of H3K36me2&3 manifests predominantly as an independent regulatory mechanism targeted towards genes that are repressed post-commitment. H3K36me2&3-associated repression of genes is therefore involved in key transcriptional shifts that accompany the transition from early gametocyte differentiation to intermediate development. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00393-9.
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Affiliation(s)
- Jessica Connacher
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Gabrielle A Josling
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lindsey M Orchard
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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45
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McDaniels JM, Huckaby AC, Carter SA, Lingeman S, Francis A, Congdon M, Santos W, Rathod PK, Guler JL. Extrachromosomal DNA amplicons in antimalarial-resistant Plasmodium falciparum. Mol Microbiol 2021; 115:574-590. [PMID: 33053232 PMCID: PMC8246734 DOI: 10.1111/mmi.14624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022]
Abstract
Extrachromosomal (ec) DNAs are genetic elements that exist separately from the genome. Since ecDNA can carry beneficial genes, they are a powerful adaptive mechanism in cancers and many pathogens. For the first time, we report ecDNA contributing to antimalarial resistance in Plasmodium falciparum, the most virulent human malaria parasite. Using pulse field gel electrophoresis combined with PCR-based copy number analysis, we detected two ecDNA elements that differ in migration and structure. Entrapment in the electrophoresis well and low susceptibility to exonucleases revealed that the biologically relevant ecDNA element is large and complex in structure. Using deep sequencing, we show that ecDNA originates from the chromosome and expansion of an ecDNA-specific sequence may improve its segregation or expression. We speculate that ecDNA is maintained using established mechanisms due to shared characteristics with the mitochondrial genome. Implications of ecDNA discovery in this organism are wide-reaching due to the potential for new strategies to target resistance development.
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Affiliation(s)
| | - Adam C. Huckaby
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | | | | | - Audrey Francis
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | | | | | | | - Jennifer L. Guler
- Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
- Division of Infectious Diseases and International HealthDepartment of MedicineUniversity of VirginiaCharlottesvilleVAUSA
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46
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Witmer K, Dahalan FA, Metcalf T, Talman AM, Howick VM, Lawniczak MKN. Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage. Front Cell Infect Microbiol 2021; 11:604129. [PMID: 33732658 PMCID: PMC7958875 DOI: 10.3389/fcimb.2021.604129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/15/2021] [Indexed: 12/31/2022] Open
Abstract
The crossing of the mosquito midgut epithelium by the malaria parasite motile ookinete form represents the most extreme population bottleneck in the parasite life cycle and is a prime target for transmission blocking strategies. However, we have little understanding of the clonal variation that exists in a population of ookinetes in the vector, partially because the parasites are difficult to access and are found in low numbers. Within a vector, variation may result as a response to specific environmental cues or may exist independent of those cues as a potential bet-hedging strategy. Here we use single-cell RNA-seq to profile transcriptional variation in Plasmodium berghei ookinetes across different vector species, and between and within individual midguts. We then compare our results to low-input transcriptomes from individual Anopheles coluzzii midguts infected with the human malaria parasite Plasmodium falciparum. Although the vast majority of transcriptional changes in ookinetes are driven by development, we have identified candidate genes that may be responding to environmental cues or are clonally variant within a population. Our results illustrate the value of single-cell and low-input technologies in understanding clonal variation of parasite populations.
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Affiliation(s)
- Kathrin Witmer
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Farah Aida Dahalan
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tom Metcalf
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Arthur M. Talman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Virginia M. Howick
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Wellcome Centre for Integrative Parasitology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mara K. N. Lawniczak
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
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47
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Bui HTN, Passecker A, Brancucci NMB, Voss TS. Investigation of Heterochromatin Protein 1 Function in the Malaria Parasite Plasmodium falciparum Using a Conditional Domain Deletion and Swapping Approach. mSphere 2021; 6:e01220-20. [PMID: 33536327 PMCID: PMC7860992 DOI: 10.1128/msphere.01220-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum encodes a single ortholog of heterochromatin protein 1 (PfHP1) that plays a crucial role in the epigenetic regulation of various survival-related processes. PfHP1 is essential for parasite proliferation and the heritable silencing of genes linked to antigenic variation, host cell invasion, and sexual conversion. Here, we employed CRISPR/Cas9-mediated genome editing combined with the DiCre/loxP system to investigate how the PfHP1 chromodomain (CD), hinge domain, and chromoshadow domain (CSD) contribute to overall PfHP1 function. We show that the 76 C-terminal residues are responsible for targeting PfHP1 to the nucleus. Furthermore, we reveal that each of the three functional domains of PfHP1 are required for heterochromatin formation, gene silencing, and mitotic parasite proliferation. Finally, we discovered that the hinge domain and CSD of HP1 are functionally conserved between P. falciparum and P. berghei, a related malaria parasite infecting rodents. In summary, our study provides new insights into PfHP1 function and offers a tool for further studies on epigenetic regulation and life cycle decision in malaria parasites.IMPORTANCE Malaria is caused by unicellular Plasmodium species parasites that repeatedly invade and replicate inside red blood cells. Some blood-stage parasites exit the cell cycle and differentiate into gametocytes that are essential for malaria transmission via the mosquito vector. Epigenetic control mechanisms allow the parasites to alter the expression of surface antigens and to balance the switch between parasite multiplication and gametocyte production. These processes are crucial to establish chronic infection and optimize parasite transmission. Here, we performed a mutational analysis of heterochromatin protein 1 (HP1) in P. falciparum We demonstrate that all three domains of this protein are indispensable for the proper function of HP1 in parasite multiplication, heterochromatin formation, and gene silencing. Moreover, expression of chimeric proteins revealed the functional conservation of HP1 proteins between different Plasmodium species. These results provide new insight into the function and evolution of HP1 as an essential epigenetic regulator of parasite survival.
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Affiliation(s)
- Hai T N Bui
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Armin Passecker
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicolas M B Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Till S Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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48
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Reed J, Kirkman LA, Kafsack BF, Mason CE, Deitsch KW. Telomere length dynamics in response to DNA damage in malaria parasites. iScience 2021; 24:102082. [PMID: 33644714 PMCID: PMC7887396 DOI: 10.1016/j.isci.2021.102082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Accepted: 01/14/2021] [Indexed: 10/26/2022] Open
Abstract
Malaria remains a major cause of morbidity and mortality in the developing world. Recent work has implicated chromosome end stability and the repair of DNA breaks through telomere healing as potent drivers of variant antigen diversification, thus associating basic mechanisms for maintaining genome integrity with aspects of host-parasite interactions. Here we applied long-read sequencing technology to precisely examine the dynamics of telomere addition and chromosome end stabilization in response to double-strand breaks within subtelomeric regions. We observed that the process of telomere healing induces the initial synthesis of telomere repeats well in excess of the minimal number required for end stability. However, once stabilized, these newly created telomeres appear to function normally, eventually returning to a length nearing that of intact chromosome ends. These results parallel recent observations in humans, suggesting an evolutionarily conserved mechanism for chromosome end repair.
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Affiliation(s)
- Jake Reed
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Laura A Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.,Department of Internal Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, USA
| | - Björn F Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.,Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY, USA.,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA.,Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA.,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medical College, New York, NY, USA
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
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49
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Gurung P, Gomes AR, Martins RM, Juranek SA, Alberti P, Mbang-Benet DE, Urbach S, Gazanion E, Guitard V, Paeschke K, Lopez-Rubio JJ. PfGBP2 is a novel G-quadruplex binding protein in Plasmodium falciparum. Cell Microbiol 2021; 23:e13303. [PMID: 33340385 DOI: 10.1111/cmi.13303] [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: 07/10/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
Guanine-quadruplexes (G4s) are non-canonical DNA structures that can regulate key biological processes such as transcription, replication and telomere maintenance in several organisms including eukaryotes, prokaryotes and viruses. Recent reports have identified the presence of G4s within the AT-rich genome of Plasmodium falciparum, the protozoan parasite causing malaria. In Plasmodium, potential G4-forming sequences (G4FS) are enriched in the telomeric and sub-telomeric regions of the genome where they are associated with telomere maintenance and recombination events within virulence genes. However, there is a little understanding about the biological role of G4s and G4-binding proteins. Here, we provide the first snapshot of G4-interactome in P. falciparum using DNA pull-down assay followed by LC-MS/MS. Interestingly, we identified ~24 potential G4-binding proteins (G4-BP) that bind to a stable G4FS (AP2_G4). Furthermore, we characterised the role of G-strand binding protein 2 (PfGBP2), a putative telomere-binding protein in P. falciparum. We validated the interaction of PfGBP2 with G4 in vitro as well as in vivo. PfGBP2 is expressed throughout the intra-erythrocytic developmental cycle and is essential for the parasites in the presence of G4-stabilising ligand, pyridostatin. Gene knockout studies showed the role of PfGBP2 in the expression of var genes. Taken together, this study suggests that PfGBP2 is a bona fide G4-binding protein, which is likely to be involved in the regulation of G4-related functions in these malarial parasites. In addition, this study sheds light on this understudied G4 biology in P. falciparum.
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Affiliation(s)
- Pratima Gurung
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Ana Rita Gomes
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Rafael M Martins
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Patrizia Alberti
- Laboratory Genome Structure and Instability, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U 1154, Paris, France
| | - Diane-Ethna Mbang-Benet
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Serge Urbach
- BioCampus Montpellier, CNRS UMR 5203, IGF, Montpellier, France
| | - Elodie Gazanion
- Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Vincent Guitard
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jose-Juan Lopez-Rubio
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
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50
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Chen H, Raffaele S, Dong S. Silent control: microbial plant pathogens evade host immunity without coding sequence changes. FEMS Microbiol Rev 2021; 45:6095737. [PMID: 33440001 DOI: 10.1093/femsre/fuab002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Both animals and plants have evolved a robust immune system to surveil and defeat invading pathogenic microbes. Evasion of host immune surveillance is the key for pathogens to initiate successful infection. To evade the host immunity, plant pathogens evolved a variety of strategies such as masking themselves from host immune recognitions, blocking immune signaling transductions, reprogramming immune responses and adapting to immune microenvironmental changes. Gain of new virulence genes, sequence and structural variations enables plant pathogens to evade host immunity through changes in the genetic code. However, recent discoveries demonstrated that variations at the transcriptional, post-transcriptional, post-translational and glycome level enable pathogens to cope with the host immune system without coding sequence changes. The biochemical modification of pathogen associated molecular patterns and silencing of effector genes emerged as potent ways for pathogens to hide from host recognition. Altered processing in mRNA activities provide pathogens with resilience to microenvironment changes. Importantly, these hiding variants are directly or indirectly modulated by catalytic enzymes or enzymatic complexes and cannot be revealed by classical genomics alone. Unveiling these novel host evasion mechanisms in plant pathogens enables us to better understand the nature of plant disease and pinpoints strategies for rational diseases management in global food protection.
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Affiliation(s)
- Han Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, 24 Chemin de Borde Rouge - Auzeville, CS52627, F31326 Castanet Tolosan Cedex, France
| | - Suomeng Dong
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
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