1
|
Bento I, Parrington B, Pascual R, Goldberg AS, Wang E, Liu H, Zelle M, Takahashi JS, Elias JE, Mota MM, Rijo-Ferreira F. Circadian rhythms mediate malaria transmission potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594221. [PMID: 38798622 PMCID: PMC11118478 DOI: 10.1101/2024.05.14.594221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Malaria transmission begins when infected female Anopheles mosquitos deposit Plasmodium parasites into the mammalian host's skin during a bloodmeal. The salivary gland-resident sporozoite parasites migrate to the bloodstream, subsequently invading and replicating within hepatocytes. As Anopheles mosquitos are more active at night, with a 24-hour rhythm, we investigated whether their salivary glands are under circadian control, anticipating bloodmeals and modulating sporozoite biology for host encounters. Here we show that approximately half of the mosquito salivary gland transcriptome, particularly genes essential for efficient bloodmeals such as anti-blood clotting factors, exhibits circadian rhythmic expression. Furthermore, we demonstrate that mosquitoes prefer to feed during nighttime, with the amount of blood ingested varying cyclically throughout the day. Notably, we show a substantial subset of the sporozoite transcriptome cycling throughout the day. These include genes involved in parasite motility, potentially modulating the ability to initiate infection at different times of day. Thus, although sporozoites are typically considered quiescent, our results demonstrate their transcriptional activity, revealing robust daily rhythms of gene expression. Our findings suggest a circadian evolutionary relationship between the vector, parasite and mammalian host that together modulate malaria transmission.
Collapse
|
2
|
Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression among Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. PLoS Negl Trop Dis 2024; 18:e0011926. [PMID: 38285730 PMCID: PMC10901308 DOI: 10.1371/journal.pntd.0011926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/28/2024] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
The documentation of Plasmodium vivax malaria across Africa especially in regions where Duffy negatives are dominant suggests possibly alternative erythrocyte invasion mechanisms. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P. vivax in Africa is unclear. In this study, we examined the expression of 4,404 gene transcripts belong to 12 functional groups and 43 erythrocyte binding gene candidates in Ethiopian isolates and compared them with the Cambodian and Brazilian P. vivax transcriptomes. Overall, there were 10-26% differences in the gene expression profile amongst geographical isolates, with the Ethiopian and Cambodian P. vivax being most similar. Majority of the gene transcripts involved in protein transportation, housekeeping, and host interaction were highly transcribed in the Ethiopian isolates. Members of the reticulocyte binding protein PvRBP2a and PvRBP3 expressed six-fold higher than Duffy binding protein PvDBP1 and 60-fold higher than PvEBP/DBP2 in the Ethiopian isolates. Other genes including PvMSP3.8, PvMSP3.9, PvTRAG2, PvTRAG14, and PvTRAG22 also showed relatively high expression. Differential expression patterns were observed among geographical isolates, e.g., PvDBP1 and PvEBP/DBP2 were highly expressed in the Cambodian but not the Brazilian and Ethiopian isolates, whereas PvRBP2a and PvRBP2b showed higher expression in the Ethiopian and Cambodian than the Brazilian isolates. Compared to Pvs25, gametocyte genes including PvAP2-G, PvGAP (female gametocytes), and Pvs47 (male gametocytes) were highly expressed across geographical samples.
Collapse
Affiliation(s)
- Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Colby T. Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, United States of America
- School of Data Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Beka Abagero
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Shaoyu Li
- Mathematics and Statistics, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
- Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
3
|
Balau A, Sobral D, Abrantes P, Santos I, Mixão V, Gomes JP, Antunes S, Arez AP. Differential Gene Expression of Malaria Parasite in Response to Red Blood Cell-Specific Glycolytic Intermediate 2,3-Diphosphoglycerate (2,3-DPG). Int J Mol Sci 2023; 24:16869. [PMID: 38069204 PMCID: PMC10706422 DOI: 10.3390/ijms242316869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Innovative strategies to control malaria are urgently needed. Exploring the interplay between Plasmodium sp. parasites and host red blood cells (RBCs) offers opportunities for novel antimalarial interventions. Pyruvate kinase deficiency (PKD), characterized by heightened 2,3-diphosphoglycerate (2,3-DPG) concentration, has been associated with protection against malaria. Elevated levels of 2,3-DPG, a specific mammalian metabolite, may hinder glycolysis, prompting us to hypothesize its potential contribution to PKD-mediated protection. We investigated the impact of the extracellular supplementation of 2,3-DPG on the Plasmodium falciparum intraerythrocytic developmental cycle in vitro. The results showed an inhibition of parasite growth, resulting from significantly fewer progeny from 2,3-DPG-treated parasites. We analyzed differential gene expression and the transcriptomic profile of P. falciparum trophozoites, from in vitro cultures subjected or not subjected to the action of 2,3-DPG, using Nanopore Sequencing Technology. The presence of 2,3-DPG in the culture medium was associated with the significant differential expression of 71 genes, mostly associated with the GO terms nucleic acid binding, transcription or monoatomic anion channel. Further, several genes related to cell cycle control were downregulated in treated parasites. These findings suggest that the presence of this RBC-specific glycolytic metabolite impacts the expression of genes transcribed during the parasite trophozoite stage and the number of merozoites released from individual schizonts, which supports the potential role of 2,3-DPG in the mechanism of protection against malaria by PKD.
Collapse
Affiliation(s)
- Ana Balau
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), 1349-008 Lisbon, Portugal; (A.B.); (P.A.); (I.S.); (S.A.)
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (D.S.); (V.M.); (J.P.G.)
| | - Patrícia Abrantes
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), 1349-008 Lisbon, Portugal; (A.B.); (P.A.); (I.S.); (S.A.)
| | - Inês Santos
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), 1349-008 Lisbon, Portugal; (A.B.); (P.A.); (I.S.); (S.A.)
| | - Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (D.S.); (V.M.); (J.P.G.)
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal; (D.S.); (V.M.); (J.P.G.)
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Sandra Antunes
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), 1349-008 Lisbon, Portugal; (A.B.); (P.A.); (I.S.); (S.A.)
| | - Ana Paula Arez
- Global Health and Tropical Medicine (GHTM), Associate Laboratory in Translation and Innovation towards Global Health (LA-REAL), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), 1349-008 Lisbon, Portugal; (A.B.); (P.A.); (I.S.); (S.A.)
| |
Collapse
|
4
|
Kioko M, Pance A, Mwangi S, Goulding D, Kemp A, Rono M, Ochola-Oyier LI, Bull PC, Bejon P, Rayner JC, Abdi AI. Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum. Nat Commun 2023; 14:6447. [PMID: 37833314 PMCID: PMC10575976 DOI: 10.1038/s41467-023-42103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Plasmodium falciparum secretes extracellular vesicles (PfEVs) that contain parasite-derived RNA. However, the significance of the secreted RNA remains unexplored. Here, we compare secreted and intracellular RNA from asexual cultures of six P. falciparum lines. We find that secretion of RNA via extracellular vesicles is not only periodic throughout the asexual intraerythrocytic developmental cycle but is also highly conserved across P. falciparum isolates. We further demonstrate that the phases of RNA secreted via extracellular vesicles are discernibly shifted compared to those of the intracellular RNA within the secreting whole parasite. Finally, transcripts of genes with no known function during the asexual intraerythrocytic developmental cycle are enriched in PfEVs compared to the whole parasite. We conclude that the secretion of extracellular vesicles could be a putative posttranscriptional RNA regulation mechanism that is part of or synergise the classic RNA decay processes to maintain intracellular RNA levels in P. falciparum.
Collapse
Affiliation(s)
- Mwikali Kioko
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Open University, Milton Keynes, UK
| | - Alena Pance
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
- School of Life and Medical Science, University of Hertfordshire, Hatfield, UK
| | - Shaban Mwangi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - David Goulding
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alison Kemp
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Rono
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | | | - Pete C Bull
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Rayner
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Abdirahman I Abdi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
5
|
Lansink LIM, Skinner OP, Engel JA, Lee HJ, Soon MSF, Williams CG, SheelaNair A, Pernold CPS, Laohamonthonkul P, Akter J, Stoll T, Hill MM, Talman AM, Russell A, Lawniczak M, Jia X, Chua B, Anderson D, Creek DJ, Davenport MP, Khoury DS, Haque A. Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites. mBio 2023; 14:e0112923. [PMID: 37449844 PMCID: PMC10470790 DOI: 10.1128/mbio.01129-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Maturation rates of malaria parasites within red blood cells (RBCs) can be influenced by host nutrient status and circadian rhythm; whether host inflammatory responses can also influence maturation remains less clear. Here, we observed that systemic host inflammation induced in mice by an innate immune stimulus, lipopolysaccharide (LPS), or by ongoing acute Plasmodium infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. Importantly, plasma from LPS-conditioned or acutely infected mice directly inhibited parasite maturation during in vitro culture, which was not rescued by supplementation, suggesting the emergence of inhibitory factors in plasma. Metabolomic assessments confirmed substantial alterations to the plasma of LPS-conditioned and acutely infected mice, and identified a small number of candidate inhibitory metabolites. Finally, we confirmed rapid parasite responses to systemic host inflammation in vivo using parasite scRNA-seq, noting broad impairment in transcriptional activity and translational capacity specifically in trophozoites but not rings or schizonts. Thus, we provide evidence that systemic host inflammation rapidly triggered transcriptional alterations in circulating blood-stage Plasmodium trophozoites and predict candidate inhibitory metabolites in the plasma that may impair parasite maturation in vivo. IMPORTANCE Malaria parasites cyclically invade, multiply, and burst out of red blood cells. We found that a strong inflammatory response can cause changes to the composition of host plasma, which directly slows down parasite maturation. Thus, our work highlights a new mechanism that limits malaria parasite growth in the bloodstream.
Collapse
Affiliation(s)
- Lianne I. M. Lansink
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Biology, University of York, Wentworth Way, York, Yorkshire, United Kingdom
| | - Oliver P. Skinner
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica A. Engel
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Hyun Jae Lee
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Megan S. F. Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Cameron G. Williams
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Clara P. S. Pernold
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | | | - Jasmin Akter
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Thomas Stoll
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Michelle M. Hill
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Arthur M. Talman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Andrew Russell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mara Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Brendon Chua
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Dovile Anderson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Darren J. Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Miles P. Davenport
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - David S. Khoury
- The Kirby Institute, University of New South Wales, Kensington, Sydney, New South Wales, Australia
| | - Ashraful Haque
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
6
|
Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression in Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528793. [PMID: 36824754 PMCID: PMC9949051 DOI: 10.1101/2023.02.16.528793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Plasmodium vivax uses Duffy binding protein (PvDBP1) to bind to the Duffy Antigen-Chemokine Receptor (DARC) to invade human erythrocytes. Individuals who lack DARC expression (Duffy-negative) are thought to be resistance to P. vivax. In recent years, P. vivax malaria is becoming more prevalent in Africa with a portion of these cases detected in Duffy-negatives. Apart from DBP1, members of the reticulocyte binding protein (RBP) and tryptophan-rich antigen (TRAg) families may also play a role in erythrocyte invasion. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P. vivax in Africa and more specifically the expression level of several erythrocyte binding gene candidates as compared to DBP1 are largely unknown. This paper characterized the first P. vivax transcriptome in Africa and compared with those from the Southeast Asian and South American isolates. The expression of 4,404 gene transcripts belong to 12 functional groups including 43 specific erythrocyte binding gene candidates were examined. Overall, there were 10-26% differences in the gene expression profile amongst the geographical isolates, with the Ethiopian and Cambodian P. vivax being most similar. Majority of the gene transcripts involved in protein transportation, housekeeping, and host interaction were highly transcribed in the Ethiopian P. vivax. Erythrocyte binding genes including PvRBP2a and PvRBP3 expressed six-fold higher than PvDBP1and 60-fold higher than PvEBP/DBP2. Other genes including PvRBP1a, PvMSP3.8, PvMSP3.9, PvTRAG2, PvTRAG14, and PvTRAG22 also showed relatively high expression. Differential expression was observed among geographical isolates, e.g., PvDBP1 and PvEBP/DBP2 were highly expressed in the Cambodian but not the Brazilian and Ethiopian isolates, whereas PvRBP2a and PvRBP2b showed higher expression in the Ethiopian and Cambodian than the Brazilian isolates. Compared to Pvs25, the standard biomarker for detecting female gametocytes, PvAP2-G (PVP01_1440800), GAP (PVP01_1403000), and Pvs47 (PVP01_1208000) were highly expressed across geographical samples. These findings provide an important baseline for future comparisons of P. vivax transcriptomes from Duffy-negative infections and highlight potential biomarkers for improved gametocyte detection.
Collapse
Affiliation(s)
- Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Colby T. Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Beka Abagero
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Shaoyu Li
- Mathematics and Statistics, University of North Carolina, Charlotte, NC 28223, USA
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
| |
Collapse
|
7
|
Russell AJC, Sanderson T, Bushell E, Talman AM, Anar B, Girling G, Hunziker M, Kent RS, Martin JS, Metcalf T, Montandon R, Pandey V, Pardo M, Roberts AB, Sayers C, Schwach F, Choudhary JS, Rayner JC, Voet T, Modrzynska KK, Waters AP, Lawniczak MKN, Billker O. Regulators of male and female sexual development are critical for the transmission of a malaria parasite. Cell Host Microbe 2023; 31:305-319.e10. [PMID: 36634679 DOI: 10.1016/j.chom.2022.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/04/2022] [Accepted: 12/12/2022] [Indexed: 01/13/2023]
Abstract
Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of ten mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in the determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain as well as the protein interactors of a female-determining zinc-finger protein indicate that germ-granule-like ribonucleoprotein complexes complement transcriptional processes in the regulation of both male and female development of a malaria parasite.
Collapse
Affiliation(s)
| | - Theo Sanderson
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ellen Bushell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå 90187, Sweden; Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Arthur M Talman
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Burcu Anar
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Mirjam Hunziker
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå 90187, Sweden; Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | - Robyn S Kent
- Department of Microbiology and Molecular Genetics, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Julie S Martin
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Tom Metcalf
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Vikash Pandey
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå 90187, Sweden; Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | | | - A Brett Roberts
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Claire Sayers
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå 90187, Sweden; Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
| | | | | | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Thierry Voet
- Department of Human Genetics, University of Leuven, KU Leuven, B-3000 Leuven, Belgium; KU Leuven Institute for Single Cell Omics, LISCO, KU Leuven, 3000 Leuven, Belgium
| | - Katarzyna K Modrzynska
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Andrew P Waters
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow G12 8TA, UK.
| | | | - Oliver Billker
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå 90187, Sweden; Department of Molecular Biology, Umeå University, Umeå 90187, Sweden.
| |
Collapse
|
8
|
Tebben K, Yirampo S, Coulibaly D, Koné AK, Laurens MB, Stucke EM, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Malian children infected with Plasmodium ovale and Plasmodium falciparum display very similar gene expression profiles. PLoS Negl Trop Dis 2023; 17:e0010802. [PMID: 36696438 PMCID: PMC9901758 DOI: 10.1371/journal.pntd.0010802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/06/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Plasmodium parasites caused 241 million cases of malaria and over 600,000 deaths in 2020. Both P. falciparum and P. ovale are endemic to Mali and cause clinical malaria, with P. falciparum infections typically being more severe. Here, we sequenced RNA from nine pediatric blood samples collected during infections with either P. falciparum or P. ovale, and characterized the host and parasite gene expression profiles. We found that human gene expression varies more between individuals than according to the parasite species causing the infection, while parasite gene expression profiles cluster by species. Additionally, we characterized DNA polymorphisms of the parasites directly from the RNA-seq reads and found comparable levels of genetic diversity in both species, despite dramatic differences in prevalence. Our results provide unique insights into host-pathogen interactions during malaria infections and their variations according to the infecting Plasmodium species, which will be critical to develop better elimination strategies against all human Plasmodium parasites.
Collapse
Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore Maryland, United States of America
| | - Salif Yirampo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Drissa Coulibaly
- 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
| | - Matthew B. Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Emily M. Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ahmadou Dembélé
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Andrea A. Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Christopher V. Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Kirsten E. Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - 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, United States of America
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore Maryland, United States of America
| |
Collapse
|
9
|
Habtewold T, Tapanelli S, Masters EKG, Windbichler N, Christophides GK. The circadian clock modulates Anopheles gambiae infection with Plasmodium falciparum. PLoS One 2022; 17:e0278484. [PMID: 36454885 PMCID: PMC9714873 DOI: 10.1371/journal.pone.0278484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Key behaviours, physiologies and gene expressions in Anopheles mosquitoes impact the transmission of Plasmodium. Such mosquito factors are rhythmic to closely follow diel rhythms. Here, we set to explore the impact of the mosquito circadian rhythm on the tripartite interaction between the vector, the parasite and the midgut microbiota, and investigate how this may affect the parasite infection outcomes. We assess Plasmodium falciparum infection prevalence and intensity, as a proxy for gametocyte infectivity, in Anopheles gambiae mosquitoes that received a gametocyte-containing bloodfeed and measure the abundance of the midgut microbiota at different times of the mosquito rearing light-dark cycle. Gametocyte infectivity is also compared in mosquitoes reared and maintained under a reversed light-dark regime. The effect of the circadian clock on the infection outcome is also investigated through silencing of the CLOCK gene that is central in the regulation of animal circadian rhythms. The results reveal that the A. gambiae circadian cycle plays a key role in the intensity of infection of P. falciparum gametocytes. We show that parasite gametocytes are more infectious during the night-time, where standard membrane feeding assays (SMFAs) at different time points in the mosquito natural circadian rhythm demonstrate that gametocytes are more infectious when ingested at midnight than midday. When mosquitoes were cultured under a reversed light/dark regime, disrupting their natural physiological homeostasis, and infected with P. falciparum at evening hours, the infection intensity and prevalence were significantly decreased. Similar results were obtained in mosquitoes reared under the standard light/dark regime upon silencing of CLOCK, a key regulator of the circadian rhythm, highlighting the importance of the circadian rhythm for the mosquito vectorial capacity. At that time, the mosquito midgut microbiota load is significantly reduced, while the expression of lysozyme C-1 (LYSC-1) is elevated, which is involved in both the immune response and microbiota digestion. We conclude that the tripartite interactions between the mosquito vector, the malaria parasite and the mosquito gut microbiota are finely tuned to support and maintain malaria transmission. Our data add to the knowledge framework required for designing appropriate and biologically relevant SMFA protocols.
Collapse
Affiliation(s)
- Tibebu Habtewold
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Sofia Tapanelli
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Ellen K. G. Masters
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | |
Collapse
|
10
|
Abstract
Malaria symptoms are caused by the development of the parasites within the blood of an infected host. Bulk RNA sequencing (RNA-seq) of infected blood can reveal interactions between parasites and the host immune system during an infection, but because multiple developmental stages with distinct transcriptional profiles are concurrently present in infected blood, it is necessary to correct such analyses for differences in cell composition among samples. Gene expression deconvolution is a statistical approach that has been developed for inferring the cell composition of complex tissues characterized by bulk RNA-seq using gene expression profiles from reference cell types. Here, we describe the evaluation of a species-agnostic reference data set that can be used for efficient and accurate gene expression deconvolution of bulk RNA-seq data generated from any Plasmodium species and for correct gene expression analyses for biases caused by differences in stage composition among samples. IMPORTANCE Differences in cell type proportions among samples can introduce artifacts in gene expression analyses and mask genuine differences in gene regulation. Gene expression deconvolution allows estimation of the proportion of each cell type present in one sample directly from bulk RNA sequencing data, but this approach requires a reference data set with the signature profile of each cell type. Here, we evaluate the suitability of a rodent malaria parasite gene expression data set for estimating the proportions of each parasite developmental stage present in bulk RNA sequencing data generated from blood-stage infections with the human parasites Plasmodium falciparum and Plasmodium vivax. These analyses provide a species-agnostic approach for reliably estimating stage proportions in infected human blood and correcting subsequent gene expression analyses for these variations.
Collapse
|
11
|
Foster GJ, Sievert MAC, Button-Simons K, Vendrely KM, Romero-Severson J, Ferdig MT. Cyclical regression covariates remove the major confounding effect of cyclical developmental gene expression with strain-specific drug response in the malaria parasite Plasmodium falciparum. BMC Genomics 2022; 23:180. [PMID: 35247977 PMCID: PMC8897900 DOI: 10.1186/s12864-021-08281-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 12/24/2021] [Indexed: 12/21/2022] Open
Abstract
Background The cyclical nature of gene expression in the intraerythrocytic development cycle (IDC) of the malaria parasite, Plasmodium falciparum, confounds the accurate detection of specific transcriptional differences, e.g. as provoked by the development of drug resistance. In lab-based studies, P. falciparum cultures are synchronized to remove this confounding factor, but the rapid detection of emerging resistance to artemisinin therapies requires rapid analysis of transcriptomes extracted directly from clinical samples. Here we propose the use of cyclical regression covariates (CRC) to eliminate the major confounding effect of developmentally driven transcriptional changes in clinical samples. We show that elimination of this confounding factor reduces both Type I and Type II errors and demonstrate the effectiveness of this approach using a published dataset of 1043 transcriptomes extracted directly from patient blood samples with different patient clearance times after treatment with artemisinin. Results We apply this method to two publicly available datasets and demonstrate its ability to reduce the confounding of differences in transcript levels due to misaligned intraerythrocytic development time. Adjusting the clinical 1043 transcriptomes dataset with CRC results in detection of fewer functional categories than previously reported from the same data set adjusted using other methods. We also detect mostly the same functional categories, but observe fewer genes within these categories. Finally, the CRC method identifies genes in a functional category that was absent from the results when the dataset was adjusted using other methods. Analysis of differential gene expression in the clinical data samples that vary broadly for developmental stage resulted in the detection of far fewer transcripts in fewer functional categories while, at the same time, identifying genes in two functional categories not present in the unadjusted data analysis. These differences are consistent with the expectation that CRC reduces both false positives and false negatives with the largest effect on datasets from samples with greater variance in developmental stage. Conclusions Cyclical regression covariates have immediate application to parasite transcriptome sequencing directly from clinical blood samples and to cost-constrained in vitro experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08281-y.
Collapse
|
12
|
Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
Collapse
|
13
|
Yokoly FN, Zahouli JBZ, Small G, Ouattara AF, Opoku M, de Souza DK, Koudou BG. Assessing Anopheles vector species diversity and transmission of malaria in four health districts along the borders of Côte d'Ivoire. Malar J 2021; 20:409. [PMID: 34663359 PMCID: PMC8524949 DOI: 10.1186/s12936-021-03938-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/01/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although malaria and Anopheles mosquito vectors are highly prevalent in Côte d'Ivoire, limited data are available to help understand the malaria vector density and transmission dynamics in areas bordering the country. To address this gap, the Anopheles mosquito species diversity, the members of the Anopheles gambiae complex and the transmission of malaria were assessed in four health districts along the borders of Côte d'Ivoire. METHODS From July 2016 through December 2016 and July 2017 through December 2017, adult Anopheles mosquitoes were collected in four health districts of Côte d'Ivoire (Aboisso, Bloléquin, Odienné and Ouangolodougou) using standardized window exit trap (WET) and pyrethrum knockdown spray collection (PSC) methods. The collected mosquitoes were identified morphologically at species level and the members of the An. gambiae complex were separated using short interspersed nuclear element-based polymerase chain reaction (SINE-PCR). Anopheles gambiae sensu lato (s.l.), Anopheles funestus s.l. and Anopheles nili specimens were analysed for malaria Plasmodium parasite detection using the cytochrome oxidase I gene (COX-I), and malaria prevalence among human population through local Ministry of Health (MoH) statistical yearbooks. RESULTS A total of 281 female Anopheles were collected in Aboisso, 754 in Bloléquin, 1319 in Odienné and 2443 in Ouangolodougou. Seven Anopheles species were recorded including An. gambiae s.l. (94.8-99.1%) as the main vector, followed by An. funestus s.l. (0.4-4.3%) and An. nili (0-0.7%). Among An. gambiae s.l., Anopheles coluzzii represented the predominant species in Aboisso (89.2%) and Bloléquin (92.2%), while An. gambiae sensu stricto (s.s.) was the major species in Odienné (96.0%) and Ouangolodougou (94.2%). The Plasmodium sporozoite infection rate in An. gambiae s.l. was highest in Odienné (11.0%; n = 100) followed by Bloléquin (7.8%, n = 115), Aboisso (3.1%; n = 65) and Ouangologoudou (2.5%; n = 120). In An. funestus s.l., Plasmodium falciparum sporozoite infection rate was estimated at 6.2% (n = 32) in Bloléquin, 8.7% (n = 23) in Odienné. No An. funestus s.l. specimens were found infected with P. falciparum sporozoite infection in Ouangolodougou and Aboisso. No P. falciparum sporozoite was detected in An. nili specimens in the four health districts. Among the local human populations, malaria incidence was higher in Odienné (39.7%; n = 45,376) and Bloléquin (37.6%; n = 150,205) compared to that in Ouangolodougou (18.3%; n = 131,629) and Aboisso (19.7%; n = 364,585). CONCLUSION Anopheles vector species diversity, abundance and Plasmodium sporozoite infection were high within the health districts along the borders of the country of Côte d'Ivoire, resulting in high malaria transmission among the local populations. Anopheles gambiae s.l. and An. funestus s.l. were found to be highly infected with Plasmodium in the health districts of Bloléquin and Odienné where higher malaria incidence was observed than the other districts. This study provides important information that can be used to guide Côte d'Ivoire National Malaria Control Programme for vector control decision-making, mainly in districts that are at the country borders.
Collapse
Affiliation(s)
- Firmain N Yokoly
- Unité de Formation et de Recherche Sciences de la Nature, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire. .,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire.
| | - Julien B Z Zahouli
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire.,Centre d'Entomologie Médicale et Vétérinaire, Université Alassane Ouattara, Bouaké, Côte d'Ivoire
| | - Graham Small
- Innovative Vector Control Consortium (IVCC), Pembroke Place, Liverpool, L3 5QA, UK
| | - Allassane F Ouattara
- Unité de Formation et de Recherche Sciences de la Nature, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire.,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Millicent Opoku
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana.,European & Developing Countries Clinical Trials Partnership, Cape Town, South Africa
| | - Dziedzom K de Souza
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Benjamin G Koudou
- Unité de Formation et de Recherche Sciences de la Nature, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire.,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| |
Collapse
|
14
|
Kulkeaw K. Next-Generation Human Liver Models for Antimalarial Drug Assays. Antibiotics (Basel) 2021; 10:antibiotics10060642. [PMID: 34071885 PMCID: PMC8229011 DOI: 10.3390/antibiotics10060642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/23/2022] Open
Abstract
Advances in malaria prevention and treatment have significantly reduced the related morbidity and mortality worldwide, however, malaria continues to be a major threat to global public health. Because Plasmodium parasites reside in the liver prior to the appearance of clinical manifestations caused by intraerythrocytic development, the Plasmodium liver stage represents a vulnerable therapeutic target to prevent progression. Currently, a small number of drugs targeting liver-stage parasites are available, but all cause lethal side effects in glucose-6-phosphate dehydrogenase-deficient individuals, emphasizing the necessity for new drug development. Nevertheless, a longstanding hurdle to developing new drugs is the availability of appropriate in vitro cultures, the crucial conventional platform for evaluating the efficacy and toxicity of drugs in the preclinical phase. Most current cell culture systems rely primarily on growing immortalized or cancerous cells in the form of a two-dimensional monolayer, which is not very physiologically relevant to the complex cellular architecture of the human body. Although primary human cells are more relevant to human physiology, they are mainly hindered by batch-to-batch variation, limited supplies, and ethical issues. Advances in stem cell technologies and multidimensional culture have allowed the modelling of human infectious diseases. Here, current in vitro hepatic models and toolboxes for assaying the antimalarial drug activity are summarized. Given the physiological potential of pluripotent and adult stem cells to model liver-stage malaria, the opportunities and challenges in drug development against liver-stage malaria is highlighted, paving the way to assess the efficacy of hepatic plasmodicidal activity.
Collapse
Affiliation(s)
- Kasem Kulkeaw
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| |
Collapse
|
15
|
CRISPR/Cas9-Based Knockout of GNAQ Reveals Differences in Host Cell Signaling Necessary for Egress of Apicomplexan Parasites. mSphere 2020; 5:5/6/e01001-20. [PMID: 33361125 PMCID: PMC7763550 DOI: 10.1128/msphere.01001-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The coordinated release of apicomplexan parasites from infected host cells prior to reinvasion is a critical process for parasite survival and the spread of infection. While Toxoplasma tachyzoites and Plasmodium blood stages induce a fast disruption of their surrounding membranes during their egress from host cells, Plasmodium liver stages keep the host cell membrane intact and leave their host cell in host cell-derived vesicles called merosomes. Toxoplasma gondii and members of the genus Plasmodium are obligate intracellular parasites that leave their infected host cell upon a tightly controlled process of egress. Intracellular replication of the parasites occurs within a parasitophorous vacuole, and its membrane as well as the host plasma membrane need to be disrupted during egress, leading to host cell lysis. While several parasite-derived factors governing egress have been identified, much less is known about host cell factors involved in this process. Previously, RNA interference (RNAi)-based knockdown and antibody-mediated depletion identified a host signaling cascade dependent on guanine nucleotide-binding protein subunit alpha q (GNAQ) to be required for the egress of Toxoplasma tachyzoites and Plasmodium blood stage merozoites. Here, we used CRISPR/Cas9 technology to generate HeLa cells deficient in GNAQ and tested their capacity to support the egress of T. gondii tachyzoites and Plasmodium berghei liver stage parasites. While we were able to confirm the importance of GNAQ for the egress of T. gondii, we found that the egress of P. berghei liver stages was unaffected in the absence of GNAQ. These results may reflect differences between the lytic egress process in apicomplexans and the formation of host cell-derived vesicles termed merosomes by P. berghei liver stages. IMPORTANCE The coordinated release of apicomplexan parasites from infected host cells prior to reinvasion is a critical process for parasite survival and the spread of infection. While Toxoplasma tachyzoites and Plasmodium blood stages induce a fast disruption of their surrounding membranes during their egress from host cells, Plasmodium liver stages keep the host cell membrane intact and leave their host cell in host cell-derived vesicles called merosomes. The knockout of GNAQ, a protein involved in G-protein-coupled receptor signaling, demonstrates the importance of this host factor for the lytic egress of T. gondii tachyzoites. Contrastingly, the egress of P. berghei is independent of GNAQ at the liver stage, indicating the existence of a mechanistically distinct strategy to exit the host cell.
Collapse
|
16
|
Hollin T, Le Roch KG. From Genes to Transcripts, a Tightly Regulated Journey in Plasmodium. Front Cell Infect Microbiol 2020; 10:618454. [PMID: 33425787 PMCID: PMC7793691 DOI: 10.3389/fcimb.2020.618454] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past decade, we have witnessed significant progresses in understanding gene regulation in Apicomplexa including the human malaria parasite, Plasmodium falciparum. This parasite possesses the ability to convert in multiple stages in various hosts, cell types, and environments. Recent findings indicate that P. falciparum is talented at using efficient and complementary molecular mechanisms to ensure a tight control of gene expression at each stage of its life cycle. Here, we review the current understanding on the contribution of the epigenome, atypical transcription factors, and chromatin organization to regulate stage conversion in P. falciparum. The adjustment of these regulatory mechanisms occurring during the progression of the life cycle will be extensively discussed.
Collapse
Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| |
Collapse
|
17
|
Siegel SV, Chappell L, Hostetler JB, Amaratunga C, Suon S, Böhme U, Berriman M, Fairhurst RM, Rayner JC. Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions. Sci Rep 2020; 10:16667. [PMID: 33028892 PMCID: PMC7541449 DOI: 10.1038/s41598-020-73562-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022] Open
Abstract
Plasmodium vivax gene regulation remains difficult to study due to the lack of a robust in vitro culture method, low parasite densities in peripheral circulation and asynchronous parasite development. We adapted an RNA-seq protocol “DAFT-seq” to sequence the transcriptome of four P. vivax field isolates that were cultured for a short period ex vivo before using a density gradient for schizont enrichment. Transcription was detected from 78% of the PvP01 reference genome, despite being schizont-enriched samples. This extensive data was used to define thousands of 5′ and 3′ untranslated regions, some of which overlapped with neighbouring transcripts, and to improve the gene models of 352 genes, including identifying 20 novel gene transcripts. This dataset has also significantly increased the known amount of heterogeneity between P. vivax schizont transcriptomes from individual patients. The majority of genes found to be differentially expressed between the isolates lack Plasmodium falciparum homologs and are predicted to be involved in host-parasite interactions, with an enrichment in reticulocyte binding proteins, merozoite surface proteins and exported proteins with unknown function. An improved understanding of the diversity within P. vivax transcriptomes will be essential for the prioritisation of novel vaccine targets.
Collapse
Affiliation(s)
- Sasha V Siegel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Lia Chappell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jessica B Hostetler
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.,Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chanaki Amaratunga
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bankgok, Thailand.,Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Ulrike Böhme
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK. .,Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
| |
Collapse
|
18
|
Dash M, Pande V, Sinha A. Putative circumsporozoite protein (CSP) of Plasmodium vivax is considerably distinct from the well-known CSP and plays a role in the protein ubiquitination pathway. Gene 2020; 721S:100024. [PMID: 32550551 PMCID: PMC7285988 DOI: 10.1016/j.gene.2019.100024] [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: 07/01/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 11/29/2022]
Abstract
Amidst technical challenges which limit successful culture and genetic manipulation of P. vivax parasites, we used a computational approach to identify a critical target with evolutionary significance. The putative circumsporozoite protein on chromosome 13 of P. vivax (PvpuCSP)is distinct from the well-known vaccine candidate PfCSP. The aim of this study was to understand the role of PvpuCSP and its relatedness to the well-known CSP. The study revealed PvpuCSP as a membrane bound E3 ubiquitin ligase involved in ubiquitination. It has a species-specific tetra-peptide unit which is differentially repeated in various P. vivax strains. The PvpuCSP is different from CSP in terms of stage-specific expression and function. Since E3 ubiquitin ligases are known antimalarial drug targets targeting the proteasome pathway, PvpuCSP, with evolutionary connotation and a key role in orchestrating protein degradation in P. vivax, can be explored as a potential drug target. PvpuCSP is predicted as E3 ubiquitin ligase, a part of ubiquitination pathway. Tetra-peptide tandem repeat at C terminal of PvpuCSP is exclusive to P. vivax. Moderately expressed during all parasitic stages in host and vector Partially disordered protein with both structured domains and two distinct IDRs A transmembrane protein with highly conserved functional domain across Apicomplexa
Collapse
Affiliation(s)
- Manoswini Dash
- Division of Epidemiology and Clinical Research, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Abhinav Sinha
- Division of Epidemiology and Clinical Research, ICMR-National Institute of Malaria Research, New Delhi, India
| |
Collapse
|
19
|
Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms. Nat Commun 2020; 11:2763. [PMID: 32488076 PMCID: PMC7265539 DOI: 10.1038/s41467-020-16593-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 05/04/2020] [Indexed: 01/23/2023] Open
Abstract
Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 h suggesting a circadian basis, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches utilizing rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit daily rhythms in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 6% of Plasmodium falciparum genes show 24 h rhythms in expression under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a 24 h transcriptional rhythm and disrupting it in rodent malaria parasites shortens the IDC by 2-3 h; (v) Multiple processes including DNA replication, and the ubiquitin and proteasome pathways, are affected by loss of coordination with host rhythms and by disruption of SR10. Our results reveal malaria parasites are at least partly responsible for scheduling the IDC and coordinating their development with host daily rhythms. The mechanism underlying periodicity of Plasmodium’s intra-erythrocytic developmental cycle (IDC) is unclear. Here, Subudhi et al. show that serpentine receptor 10 (SR10) plays a role in regulating the schedule of the IDC in line with the timing of host daily rhythms.
Collapse
|
20
|
Rijo-Ferreira F, Acosta-Rodriguez VA, Abel JH, Kornblum I, Bento I, Kilaru G, Klerman EB, Mota MM, Takahashi JS. The malaria parasite has an intrinsic clock. Science 2020; 368:746-753. [PMID: 32409471 PMCID: PMC7409452 DOI: 10.1126/science.aba2658] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/11/2020] [Accepted: 04/06/2020] [Indexed: 01/08/2023]
Abstract
Malarial rhythmic fevers are the consequence of the synchronous bursting of red blood cells (RBCs) on completion of the malaria parasite asexual cell cycle. Here, we hypothesized that an intrinsic clock in the parasite Plasmodium chabaudi underlies the 24-hour-based rhythms of RBC bursting in mice. We show that parasite rhythms are flexible and lengthen to match the rhythms of hosts with long circadian periods. We also show that malaria rhythms persist even when host food intake is evenly spread across 24 hours, suggesting that host feeding cues are not required for synchrony. Moreover, we find that the parasite population remains synchronous and rhythmic even in an arrhythmic clock mutant host. Thus, we propose that parasite rhythms are generated by the parasite, possibly to anticipate its circadian environment.
Collapse
Affiliation(s)
- Filipa Rijo-Ferreira
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Victoria A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John H Abel
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Izabela Kornblum
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ines Bento
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Gokhul Kilaru
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth B Klerman
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
21
|
Sà JM, Cannon MV, Caleon RL, Wellems TE, Serre D. Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression. PLoS Biol 2020; 18:e3000711. [PMID: 32365102 PMCID: PMC7224573 DOI: 10.1371/journal.pbio.3000711] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 05/14/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022] Open
Abstract
Plasmodium vivax and P. falciparum, the parasites responsible for most human malaria worldwide, exhibit striking biological differences, which have important clinical consequences. Unfortunately, P. vivax, unlike P. falciparum, cannot be cultivated continuously in vitro, which limits our understanding of its biology and, consequently, our ability to effectively control vivax malaria. Here, we describe single-cell gene expression profiles of 9,215 P. vivax parasites from bloodstream infections of Aotus and Saimiri monkeys. Our results show that transcription of most P. vivax genes occurs during short periods of the intraerythrocytic cycle and that this pattern of gene expression is conserved in other Plasmodium species. However, we also identify a strikingly high proportion of species-specific transcripts in late schizonts, possibly associated with the specificity of erythrocyte invasion. Our findings provide new and robust markers of blood-stage parasites, including some that are specific to the elusive P. vivax male gametocytes, and will be useful for analyzing gene expression data from laboratory and field samples. Analysis of individual Plasmodium vivax parasites reveals the tight control of the expression of most genes during the intra-erythrocytic cycle and the differentiation of male and female gametocytes, and highlights differences between the development of P. vivax and P. falciparum.
Collapse
Affiliation(s)
- Juliana M. Sà
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Matthew V. Cannon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ramoncito L. Caleon
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
22
|
Moreno-Pérez DA, Patarroyo MA. Inferring Plasmodium vivax protein biology by using omics data. J Proteomics 2020; 218:103719. [PMID: 32092400 DOI: 10.1016/j.jprot.2020.103719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 11/18/2022]
Abstract
Deciphering Plasmodium vivax biology has long been a challenge for groups working on this parasite, mainly due to the complications involved in propagating it in vitro. However, adapting P. vivax strains in non-human primates and the arrival of high-performance analysis methods has led to increased knowledge regarding parasite protein composition and the ability of some molecules to trigger an immune response or participate in protein-protein interactions. This review describes the state of the art concerning proteomics-, immunomics- and interatomics-related P. vivax omic studies, discussing their potential use in developing disease control methods.
Collapse
Affiliation(s)
- D A Moreno-Pérez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24#63C-69, Bogotá, Colombia; Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Calle 222 No. 55-37, Bogotá, Colombia
| | - M A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24#63C-69, Bogotá, Colombia.
| |
Collapse
|
23
|
Ruiz JL, Gómez-Díaz E. The second life of Plasmodium in the mosquito host: gene regulation on the move. Brief Funct Genomics 2020; 18:313-357. [PMID: 31058281 DOI: 10.1093/bfgp/elz007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Malaria parasites face dynamically changing environments and strong selective constraints within human and mosquito hosts. To survive such hostile and shifting conditions, Plasmodium switches transcriptional programs during development and has evolved mechanisms to adjust its phenotype through heterogeneous patterns of gene expression. In vitro studies on culture-adapted isolates have served to set the link between chromatin structure and functional gene expression. Yet, experimental evidence is limited to certain stages of the parasite in the vertebrate, i.e. blood, while the precise mechanisms underlying the dynamic regulatory landscapes during development and in the adaptation to within-host conditions remain poorly understood. In this review, we discuss available data on transcriptional and epigenetic regulation in Plasmodium mosquito stages in the context of sporogonic development and phenotypic variation, including both bet-hedging and environmentally triggered direct transcriptional responses. With this, we advocate the mosquito offers an in vivo biological model to investigate the regulatory networks, transcription factors and chromatin-modifying enzymes and their modes of interaction with regulatory sequences, which might be responsible for the plasticity of the Plasmodium genome that dictates stage- and cell type-specific blueprints of gene expression.
Collapse
Affiliation(s)
- José L Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| |
Collapse
|
24
|
Galinski MR. Functional genomics of simian malaria parasites and host-parasite interactions. Brief Funct Genomics 2020; 18:270-280. [PMID: 31241151 PMCID: PMC6859816 DOI: 10.1093/bfgp/elz013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/21/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
Two simian malaria parasite species, Plasmodium knowlesi and Plasmodium cynomolgi, cause zoonotic infections in Southeast Asia, and they have therefore gained recognition among scientists and public health officials. Notwithstanding, these species and others including Plasmodium coatneyi have served for decades as sources of knowledge on the biology, genetics and evolution of Plasmodium, and the diverse ramifications and outcomes of malaria in their monkey hosts. Experimental analysis of these species can help to fill gaps in knowledge beyond what may be possible studying the human malaria parasites or rodent parasite species. The genome sequences for these simian malaria parasite species were reported during the last decade, and functional genomics research has since been pursued. Here research on the functional genomics analysis involving these species is summarized and their importance is stressed, particularly for understanding host–parasite interactions, and potentially testing novel interventions. Importantly, while Plasmodium falciparum and Plasmodium vivax can be studied in small New World monkeys, the simian malaria parasites can be studied more effectively in the larger Old World monkey macaque hosts, which are more closely related to humans. In addition to ex vivo analyses, experimental scenarios can include passage through Anopheline mosquito hosts and longitudinal infections in monkeys to study acute and chronic infections, as well as relapses, all in the context of the in vivo host environment. Such experiments provide opportunities for understanding functional genomic elements that govern host–parasite interactions, immunity and pathogenesis in-depth, addressing hypotheses not possible from in vitro cultures or cross-sectional clinical studies with humans.
Collapse
Affiliation(s)
- Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
25
|
Plasmodium vivax transcriptional profiling of low input cryopreserved isolates through the intraerythrocytic development cycle. PLoS Negl Trop Dis 2020; 14:e0008104. [PMID: 32119669 PMCID: PMC7067476 DOI: 10.1371/journal.pntd.0008104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 03/12/2020] [Accepted: 01/30/2020] [Indexed: 11/19/2022] Open
Abstract
Approximately one-third of the global population is at risk of Plasmodium vivax infection, and an estimated 7.51 million cases were reported in 2017. Although, P. vivax research is currently limited by the lack of a robust continuous in vitro culture system for this parasite, recent work optimizing short-term ex vivo culture of P. vivax from cryopreserved isolates has facilitated quantitative assays on synchronous parasites. Pairing this improved culture system with low-input Smart-seq2 RNAseq library preparation, we sought to determine whether transcriptional profiling of P. vivax would provide insight into the differential survival of parasites in different culture media. To this end we probed the transcriptional signature of three different ex vivo P. vivax samples in four different culture media using only 1000 cells for each time point taken during the course of the intraerythrocytic development cycle (IDC). Using this strategy, we achieved similar quality transcriptional data to previously reported P. vivax transcriptomes. We found little effect with varying culture media on parasite transcriptional signatures, identified many novel gametocyte-specific genes from transcriptomes of FACS-isolated gametocytes, and determined invasion ligand expression in schizonts in biological isolates and across the IDC. In total, these data demonstrate the feasibility and utility of P. vivax RNAseq-based transcriptomic studies using minimal biomass input to maximize experimental capacity. Plasmodium vivax is the most prevalent malaria-causing parasite species outside of Sub-Saharan Africa and has many unique and poorly understood biological characteristics that make it particularly challenging to study and combat. Transcriptomic profiling of P. vivax under various conditions has the potential to unlock new experimental abilities and aid in elucidating biology and the development of clinical interventions. However, a lack of a robust in vitro culture system for this parasite has restricted transcriptomic studies to researchers with timely access to fresh human isolates from clinics, which often are in resource-poor settings, as well as nearby, well-equipped laboratories for sample processing. This study aimed to gain insight into the differential survival of P. vivax in various culture media from the parasites transcriptional signature in each media. By implementing low-input RNA library preparation strategies, this study obtains robust transcriptomic data at various parasite development stages and in different culture conditions from just 1000 FACS-purified, P. vivax-infected erythrocytes from viable cryopreserved patient isolates. With these data, we find culture media has little effect on transcriptional profile, we characterize invasion ligand expression across intraerythrocytic development and between clinical isolates, and we define the transcriptome of sexual, transmissible stages of the P. vivax parasite. These results highlight the establishment and utility of a powerful platform for studying the transcriptomic biology of this particularly challenging parasite.
Collapse
|
26
|
Bettencourt P. Current Challenges in the Identification of Pre-Erythrocytic Malaria Vaccine Candidate Antigens. Front Immunol 2020; 11:190. [PMID: 32153565 PMCID: PMC7046804 DOI: 10.3389/fimmu.2020.00190] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/24/2020] [Indexed: 12/27/2022] Open
Abstract
Plasmodium spp.-infected mosquitos inject sporozoites into the skin of a mammalian host during a blood meal. These enter the host's circulatory system and establish an infection in the liver. After a silent metamorphosis, merozoites invade the blood leading to the symptomatic and transmissible stages of malaria. The silent pre-erythrocytic malaria stage represents a bottleneck in the disease which is ideal to block progression to clinical malaria, through chemotherapeutic and immunoprophylactic interventions. RTS,S/AS01, the only malaria vaccine close to licensure, although with poor efficacy, blocks the sporozoite invasion mainly through the action of antibodies against the CSP protein, a major component of the pellicle of the sporozoite. Strikingly, sterile protection against malaria can be obtained through immunization with radiation-attenuated sporozoites, genetically attenuated sporozoites or through chemoprophylaxis with infectious sporozoites in animals and humans, but the deployability of sporozoite-based live vaccines pose tremendous challenges. The protection induced by sporozoites occurs in the pre-erythrocytic stages and is mediated mainly by antibodies against the sporozoite and CD8+ T cells against peptides presented by MHC class I molecules in infected hepatocytes. Thus, the identification of malaria antigens expressed in the sporozoite and liver-stage may provide new vaccine candidates to be included, alone or in combination, as recombinant protein-based, virus-like particles or sub-unit virally-vectored vaccines. Here I review the efforts being made to identify Plasmodium falciparum antigens expressed during liver-stage with focus on the development of parasite, hepatocyte, mouse models, and resulting rate of infection in order to identify new vaccine candidates and to improve the efficacy of the current vaccines. Finally, I propose new approaches for the identification of liver-stage antigens based on immunopeptidomics.
Collapse
|
27
|
Brashear AM, Roobsoong W, Siddiqui FA, Nguitragool W, Sattabongkot J, López-Uribe MM, Miao J, Cui L. A glance of the blood stage transcriptome of a Southeast Asian Plasmodium ovale isolate. PLoS Negl Trop Dis 2019; 13:e0007850. [PMID: 31730621 PMCID: PMC6881071 DOI: 10.1371/journal.pntd.0007850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/27/2019] [Accepted: 10/16/2019] [Indexed: 11/24/2022] Open
Abstract
Plasmodium ovale accounts for a disproportionate number of travel-related malaria cases. This parasite is understudied since there is a reliance on clinical samples. We collected a P. ovale curtisi parasite isolate from a clinical case in western Thailand and performed RNA-seq analysis on the blood stage transcriptomes. Using both de novo assembly and alignment-based methods, we detected the transcripts for 6628 out of 7280 annotated genes. For those lacking evidence of expression, the vast majority belonged to the PIR and STP1 gene families. We identified new splicing patterns for over 2500 genes, and mapped at least one untranslated region for over half of all annotated genes. Our analysis also detected a notable presence of anti-sense transcripts for over 10% of P. ovale curtisi genes. This transcriptomic analysis provides new insights into the blood-stage biology of this neglected parasite. Ovale malaria can be caused by one of two Plasmodium parasites, P. ovale curtisi and P. ovale wallikeri. P. ovale parasites are especially adept at evading prophylactic antimalarial drugs and traveling internationally, which makes them interesting from a global health perspective. Due to the lack of a continuous culture system for these parasites, research on P. ovale parasites has lagged behind and relies on clinical samples. Recent genome sequencing of a few P. ovale clinical isolates provides the blueprint of the parasite genome and in silico prediction of parasite genes. However, confirmation of the annotated genes and proof of their expression are needed. Here we obtained a P. ovale curtisi clinical isolate from western Thailand and performed RNA-seq analysis on the blood-stage parasites. High-quality RNA-seq data has enabled us to identify transcripts for 6628 of the 7280 annotated genes. Consistent with the blood stage development, housekeeping genes such as those involved in translation and metabolism are highly expressed. Prediction of the UTRs as well as detection of anti-sense transcripts and potential splicing patterns suggests the presence of complex gene regulation mechanisms for this parasite. This transcriptome dataset will serve as a useful resource for future studies of P. ovale.
Collapse
Affiliation(s)
- Awtum M Brashear
- Department of Entomology, Pennsylvania State University, Department of Entomology, University Park, Pennsylvania, United States of America.,Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Faiza A Siddiqui
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Margarita M López-Uribe
- Department of Entomology, Pennsylvania State University, Department of Entomology, University Park, Pennsylvania, United States of America
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, Department of Entomology, University Park, Pennsylvania, United States of America.,Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| |
Collapse
|
28
|
Chan LJ, Dietrich MH, Nguitragool W, Tham WH. Plasmodium vivax Reticulocyte Binding Proteins for invasion into reticulocytes. Cell Microbiol 2019; 22:e13110. [PMID: 31469946 PMCID: PMC7003471 DOI: 10.1111/cmi.13110] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/25/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
Abstract
Plasmodium vivax is responsible for most of the malaria infections outside Africa and is currently the predominant malaria parasite in countries under elimination programs. P. vivax preferentially enters young red cells called reticulocytes. Advances in understanding the molecular and cellular mechanisms of entry are hampered by the inability to grow large numbers of P. vivax parasites in a long‐term in vitro culture. Recent progress in understanding the biology of the P. vivax Reticulocyte Binding Protein (PvRBPs) family of invasion ligands has led to the identification of a new invasion pathway into reticulocytes, an understanding of their structural architecture and PvRBPs as targets of the protective immune response to P. vivax infection. This review summarises current knowledge on the role of reticulocytes in P. vivax infection, the function of the PvRBP family of proteins in generating an immune response in human populations, and the characterization of anti‐PvRBP antibodies in blocking parasite invasion.
Collapse
Affiliation(s)
- Li-Jin Chan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie H Dietrich
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
29
|
Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN. The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle. Science 2019; 365:eaaw2619. [PMID: 31439762 PMCID: PMC7056351 DOI: 10.1126/science.aaw2619] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/12/2019] [Indexed: 12/25/2022]
Abstract
Malaria parasites adopt a remarkable variety of morphological life stages as they transition through multiple mammalian host and mosquito vector environments. We profiled the single-cell transcriptomes of thousands of individual parasites, deriving the first high-resolution transcriptional atlas of the entire Plasmodium berghei life cycle. We then used our atlas to precisely define developmental stages of single cells from three different human malaria parasite species, including parasites isolated directly from infected individuals. The Malaria Cell Atlas provides both a comprehensive view of gene usage in a eukaryotic parasite and an open-access reference dataset for the study of malaria parasites.
Collapse
Affiliation(s)
- Virginia M Howick
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Andrew J C Russell
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tallulah Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Haynes Heaton
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Kedar Natarajan
- Danish Institute of Advanced Study (D-IAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hellen Butungi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Wits Research Institute for Malaria, MRC Collaborating Centre for Multi-disciplinary Research on Malaria, School of Pathology, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | - Tom Metcalf
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lisa H Verzier
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jeremy K Herren
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Wits Research Institute for Malaria, MRC Collaborating Centre for Multi-disciplinary Research on Malaria, School of Pathology, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Oliver Billker
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Arthur M Talman
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
| |
Collapse
|
30
|
Ngotho P, Soares AB, Hentzschel F, Achcar F, Bertuccini L, Marti M. Revisiting gametocyte biology in malaria parasites. FEMS Microbiol Rev 2019; 43:401-414. [PMID: 31220244 PMCID: PMC6606849 DOI: 10.1093/femsre/fuz010] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/05/2019] [Indexed: 12/21/2022] Open
Abstract
Gametocytes are the only form of the malaria parasite that is transmissible to the mosquito vector. They are present at low levels in blood circulation and significant knowledge gaps exist in their biology. Recent reductions in the global malaria burden have brought the possibility of elimination and eradication, with renewed focus on malaria transmission biology as a basis for interventions. This review discusses recent insights into gametocyte biology in the major human malaria parasite, Plasmodium falciparum and related species.
Collapse
Affiliation(s)
- Priscilla Ngotho
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Alexandra Blancke Soares
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Franziska Hentzschel
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK
| | - Lucia Bertuccini
- Core Facilities, Microscopy Area, Instituto Superiore di Sanita, Via Regina Elena 299, 00161 Rome, Italy
| | - Matthias Marti
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Road, Glasgow G12 8TA, UK.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston 02115, MA, USA
| |
Collapse
|
31
|
Knuepfer E, Wright KE, Kumar Prajapati S, Rawlinson TA, Mohring F, Koch M, Lyth OR, Howell SA, Villasis E, Snijders AP, Moon RW, Draper SJ, Rosanas-Urgell A, Higgins MK, Baum J, Holder AA. Divergent roles for the RH5 complex components, CyRPA and RIPR in human-infective malaria parasites. PLoS Pathog 2019; 15:e1007809. [PMID: 31185066 PMCID: PMC6588255 DOI: 10.1371/journal.ppat.1007809] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 06/21/2019] [Accepted: 05/01/2019] [Indexed: 12/26/2022] Open
Abstract
Malaria is caused by Plasmodium parasites, which invade and replicate in erythrocytes. For Plasmodium falciparum, the major cause of severe malaria in humans, a heterotrimeric complex comprised of the secreted parasite proteins, PfCyRPA, PfRIPR and PfRH5 is essential for erythrocyte invasion, mediated by the interaction between PfRH5 and erythrocyte receptor basigin (BSG). However, whilst CyRPA and RIPR are present in most Plasmodium species, RH5 is found only in the small Laverania subgenus. Existence of a complex analogous to PfRH5-PfCyRPA-PfRIPR targeting BSG, and involvement of CyRPA and RIPR in invasion, however, has not been addressed in non-Laverania parasites. Here, we establish that unlike P. falciparum, P. knowlesi and P. vivax do not universally require BSG as a host cell invasion receptor. Although we show that both PkCyRPA and PkRIPR are essential for successful invasion of erythrocytes by P. knowlesi parasites in vitro, neither protein forms a complex with each other or with an RH5-like molecule. Instead, PkRIPR is part of a different trimeric protein complex whereas PkCyRPA appears to function without other parasite binding partners. It therefore appears that in the absence of RH5, outside of the Laverania subgenus, RIPR and CyRPA have different, independent functions crucial for parasite survival. Malaria is one of the most devastating infectious diseases, causing significant human suffering and death. It is caused by parasites of the genus Plasmodium proliferating in the bloodstream. Understanding the mechanism of erythrocyte invasion is key for developing novel intervention strategies. P. falciparum, the cause of the most severe form of malaria, requires the interaction of a trimeric protein complex RH5-CyRPA-RIPR with the host receptor BSG for successful invasion. We show here that the BSG receptor is not essential for invasion by two other major causes of human malaria, P. vivax and P. knowlesi. Furthermore, we analyzed the role of CyRPA and RIPR in the absence of an RH5-like molecule in P. knowlesi and show that these molecules do not associate to form a protein complex unlike in the presence of RH5 in P. falciparum. PkRIPR is part of a different protein complex. Despite this difference CyRPA and RIPR still have essential functions during host cell invasion in other important human malaria-causing parasites.
Collapse
Affiliation(s)
- Ellen Knuepfer
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail: (EK); (KEW); (JB); (AAH)
| | - Katherine E. Wright
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (EK); (KEW); (JB); (AAH)
| | | | | | - Franziska Mohring
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Marion Koch
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Oliver R. Lyth
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Steven A. Howell
- Proteomics Science and Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Elizabeth Villasis
- Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ambrosius P. Snijders
- Proteomics Science and Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Robert W. Moon
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Simon J. Draper
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Matthew K. Higgins
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (EK); (KEW); (JB); (AAH)
| | - Anthony A. Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail: (EK); (KEW); (JB); (AAH)
| |
Collapse
|
32
|
Ramaprasad A, Subudhi AK, Culleton R, Pain A. A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites. Malar J 2019; 18:26. [PMID: 30683099 PMCID: PMC6347755 DOI: 10.1186/s12936-019-2659-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The transcriptional regulation that occurs in malaria parasites during the erythrocytic stages of infection can be studied in vivo with rodent malaria parasites propagated in mice. Time-series transcriptome profiling commonly involves the euthanasia of groups of mice at specific time points followed by the extraction of parasite RNA from whole blood samples. Current methodologies for parasite RNA extraction involve several steps and when multiple time points are profiled, these protocols are laborious, time-consuming, and require the euthanization of large cohorts of mice. RESULTS A simplified protocol has been designed for parasite RNA extraction from blood volumes as low as 20 μL (microsamples), serially bled from mice via tail snips and directly lysed with TRIzol reagent. Gene expression data derived from microsampling using RNA-seq were closely matched to those derived from larger volumes of leucocyte-depleted and saponin-treated blood obtained from euthanized mice with high reproducibility between biological replicates. Transcriptome profiling of microsamples taken at different time points during the intra-erythrocytic developmental cycle of the rodent malaria parasite Plasmodium vinckei revealed the transcriptional cascade commonly observed in malaria parasites. CONCLUSIONS Microsampling is a quick, robust and cost-efficient approach to sample collection for in vivo time-series transcriptomic studies in rodent malaria parasites.
Collapse
Affiliation(s)
- Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia. .,Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Amit Kumar Subudhi
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Richard Culleton
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
| |
Collapse
|
33
|
Kim A, Popovici J, Menard D, Serre D. Plasmodium vivax transcriptomes reveal stage-specific chloroquine response and differential regulation of male and female gametocytes. Nat Commun 2019; 10:371. [PMID: 30670687 PMCID: PMC6342968 DOI: 10.1038/s41467-019-08312-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/26/2018] [Indexed: 12/12/2022] Open
Abstract
Studies of Plasmodium vivax gene expression are complicated by the lack of in vitro culture system and the difficulties associated with studying clinical infections that often contain multiple clones and a mixture of parasite stages. Here, we characterize the transcriptomes of P. vivax parasites from 26 malaria patients. We show that most parasite mRNAs derive from trophozoites and that the asynchronicity of P. vivax infections is therefore unlikely to confound gene expression studies. Analyses of gametocyte genes reveal two distinct clusters of co-regulated genes, suggesting that male and female gametocytes are independently regulated. Finally, we analyze gene expression changes induced by chloroquine and show that this antimalarial drug efficiently eliminates most P. vivax parasite stages but, in contrast to P. falciparum, does not affect trophozoites.
Collapse
Affiliation(s)
- Adam Kim
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA
| | - Jean Popovici
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12 201, Cambodia
| | - Didier Menard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12 201, Cambodia
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724, Paris, France
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD, 21201, USA.
| |
Collapse
|
34
|
Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
Collapse
Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| |
Collapse
|
35
|
Strzelecka PM, Ranzoni AM, Cvejic A. Dissecting human disease with single-cell omics: application in model systems and in the clinic. Dis Model Mech 2018; 11:dmm036525. [PMID: 30401698 PMCID: PMC6262815 DOI: 10.1242/dmm.036525] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Probing cellular population diversity at single-cell resolution became possible only in recent years. The popularity of single-cell 'omic' approaches, which allow researchers to dissect sample heterogeneity and cell-to-cell variation, continues to grow. With continuous technological improvements, single-cell omics are becoming increasingly prevalent and contribute to the discovery of new and rare cell types, and to the deciphering of disease pathogenesis and outcome. Animal models of human diseases have significantly facilitated our understanding of the mechanisms driving pathologies and resulted in the development of more efficient therapies. The application of single-cell omics to animal models improves the precision of the obtained insights, and brings single-cell technology closer to the clinical field. This Review focuses on the use of single-cell omics in cellular and animal models of diseases, as well as in samples from human patients. It also highlights the potential of these approaches to further improve the diagnosis and treatment of various pathologies, and includes a discussion of the advantages and remaining challenges in implementing these technologies into clinical practice.
Collapse
Affiliation(s)
- Paulina M Strzelecka
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Anna M Ranzoni
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge CB2 1QR, UK
| |
Collapse
|
36
|
Lee HJ, Georgiadou A, Otto TD, Levin M, Coin LJ, Conway DJ, Cunnington AJ. Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. Microbiol Mol Biol Rev 2018; 82:e00071-17. [PMID: 29695497 PMCID: PMC5968457 DOI: 10.1128/mmbr.00071-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptomics, the analysis of genome-wide RNA expression, is a common approach to investigate host and pathogen processes in infectious diseases. Technical and bioinformatic advances have permitted increasingly thorough analyses of the association of RNA expression with fundamental biology, immunity, pathogenesis, diagnosis, and prognosis. Transcriptomic approaches can now be used to realize a previously unattainable goal, the simultaneous study of RNA expression in host and pathogen, in order to better understand their interactions. This exciting prospect is not without challenges, especially as focus moves from interactions in vitro under tightly controlled conditions to tissue- and systems-level interactions in animal models and natural and experimental infections in humans. Here we review the contribution of transcriptomic studies to the understanding of malaria, a parasitic disease which has exerted a major influence on human evolution and continues to cause a huge global burden of disease. We consider malaria a paradigm for the transcriptomic assessment of systemic host-pathogen interactions in humans, because much of the direct host-pathogen interaction occurs within the blood, a readily sampled compartment of the body. We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases. We propose that the potential of transcriptomic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in study design rather than as a consequence of technological constraints. Further advances will require the integration of transcriptomic data with analytical approaches from other scientific disciplines, including epidemiology and mathematical modeling.
Collapse
Affiliation(s)
- Hyun Jae Lee
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Thomas D Otto
- Centre of Immunobiology, University of Glasgow, Glasgow, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | |
Collapse
|
37
|
Smith ML, Styczynski MP. Systems Biology-Based Investigation of Host-Plasmodium Interactions. Trends Parasitol 2018; 34:617-632. [PMID: 29779985 DOI: 10.1016/j.pt.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/20/2022]
Abstract
Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology.
Collapse
Affiliation(s)
- Maren L Smith
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA.
| |
Collapse
|
38
|
Reid AJ, Talman AM, Bennett HM, Gomes AR, Sanders MJ, Illingworth CJR, Billker O, Berriman M, Lawniczak MK. Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites. eLife 2018; 7:33105. [PMID: 29580379 PMCID: PMC5871331 DOI: 10.7554/elife.33105] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/04/2018] [Indexed: 12/18/2022] Open
Abstract
Single-cell RNA-sequencing is revolutionising our understanding of seemingly homogeneous cell populations but has not yet been widely applied to single-celled organisms. Transcriptional variation in unicellular malaria parasites from the Plasmodium genus is associated with critical phenotypes including red blood cell invasion and immune evasion, yet transcriptional variation at an individual parasite level has not been examined in depth. Here, we describe the adaptation of a single-cell RNA-sequencing (scRNA-seq) protocol to deconvolute transcriptional variation for more than 500 individual parasites of both rodent and human malaria comprising asexual and sexual life-cycle stages. We uncover previously hidden discrete transcriptional signatures during the pathogenic part of the life cycle, suggesting that expression over development is not as continuous as commonly thought. In transmission stages, we find novel, sex-specific roles for differential expression of contingency gene families that are usually associated with immune evasion and pathogenesis.
Collapse
Affiliation(s)
- Adam J Reid
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Arthur M Talman
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Hayley M Bennett
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Ana R Gomes
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Mandy J Sanders
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Oliver Billker
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Matthew Berriman
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Mara Kn Lawniczak
- Malaria Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| |
Collapse
|
39
|
Bourgard C, Albrecht L, Kayano ACAV, Sunnerhagen P, Costa FTM. Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics. Front Cell Infect Microbiol 2018; 8:34. [PMID: 29473024 PMCID: PMC5809496 DOI: 10.3389/fcimb.2018.00034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research.
Collapse
Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil.,Laboratory of Regulation of Gene Expression, Instituto Carlos Chagas, Curitiba, Brazil
| | - Ana C A V Kayano
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| |
Collapse
|
40
|
Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput Biol 2018; 14:e1005895. [PMID: 29300748 PMCID: PMC5771636 DOI: 10.1371/journal.pcbi.1005895] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/17/2018] [Accepted: 11/24/2017] [Indexed: 12/17/2022] Open
Abstract
Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1), choline, and pantothenate (vitamin B5) metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models. Malaria kills nearly one-half million people a year and over 1 billion people are at risk of becoming infected by the parasite. Plasmodial infections are difficult to treat for a myriad of reasons, but the ability of the organism to remain latent in hosts and the complex life cycles greatly contributed to the difficulty in treat malaria. Genome-scale metabolic models (GeMMs) enable hierarchical integration of disparate data types into a framework amenable to computational simulations enabling deeper mechanistic insights from high-throughput data measurements. In this study, GeMMs of multiple Plasmodium species are used to study metabolic similarities and differences across the Plasmodium genus. In silico gene-knock out simulations across species and stages uncovered functional metabolic differences between human- and rodent-infecting species as well as across the parasite’s life-cycle stages. These findings may help identify drug regimens that are more effective in targeting human-infecting species across multiple stages of the organism.
Collapse
Affiliation(s)
- Alyaa M. Abdel-Haleem
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Centre (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE) division, Thuwal, Saudi Arabia
| | - Hooman Hefzi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, CA, United States of America
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Centre (CBRC), Thuwal, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Centre (CBRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Centre (CBRC), Thuwal, Saudi Arabia
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
| | - Nathan E. Lewis
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, La Jolla, CA, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America
| | - Neema Jamshidi
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States of America
- Department of Radiological Sciences, University of California, Los Angeles, CA, United States of America
- * E-mail: ,
| |
Collapse
|
41
|
Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development. mBio 2017; 8:mBio.01986-17. [PMID: 29233900 PMCID: PMC5727417 DOI: 10.1128/mbio.01986-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Malaria parasites have a complex life cycle with multiple developmental stages in mosquito and vertebrate hosts, and different developmental stages express unique sets of genes. Unexpectedly, many transcription factors (TFs) commonly found in eukaryotic organisms are absent in malaria parasites; instead, a family of genes encoding proteins similar to the plant Apetala2 (ApiAP2) transcription factors is expanded in the parasites. Several malaria ApiAP2 genes have been shown to play a critical role in parasite development; however, the functions of the majority of the ApiAP2 genes remain to be elucidated. In particular, no study on the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family has been reported so far. This study systematically investigated the functional roles of PyApiAP2 genes in parasite development. Twenty-four of the 26 PyApiAP2 genes were selected for disruption, and 12 were successfully knocked out using the clustered regularly interspaced short palindromic repeat–CRISPR-associated protein 9 (CRISPR-Cas9) method. The effects of gene knockout (KO) on parasite development in mouse and mosquito stages were evaluated. Ten of 12 successfully disrupted genes, including two genes that have not been functionally characterized in any Plasmodium species previously, were shown to be critical for P. yoelii development of sexual and mosquito stages. Additionally, seven of the genes were labeled for protein expression analysis, revealing important information supporting their functions. This study represents the first systematic functional characterization of the P. yoelii ApiAP2 gene family and discovers important insights on the roles of the ApiAP2 genes in parasite development. Malaria is a parasitic disease that infects hundreds of millions of people, leading to an estimated 0.35 million deaths in 2015. A better understanding of the mechanism of gene expression regulation during parasite development may provide important clues for disease control and prevention. In this study, systematic gene disruption experiments were performed to study the functional roles of members of the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family in parasite development. Genes that are critical for the development of male and female gametocytes, oocysts, and sporozoites were characterized. The protein expression profiles for seven of the PyApiAP2 gene products were also analyzed, revealing important information on their functions. This study provides expression and functional information for many PyApiAP2 genes, which can be explored for disease management.
Collapse
|
42
|
Yeoh LM, Goodman CD, Mollard V, McFadden GI, Ralph SA. Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. BMC Genomics 2017; 18:734. [PMID: 28923023 PMCID: PMC5604118 DOI: 10.1186/s12864-017-4100-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into sexual forms, termed gametocytes, which are ingested by a mosquito vector. Sexual differentiation produces either female or male gametocytes, and involves significant morphological and biochemical changes. These transformations prepare gametocytes for the rapid progression to gamete formation and fertilisation, which occur within 20 min of ingestion. Here we present the transcriptomes of asexual, female, and male gametocytes in P. berghei, and a comprehensive statistically-based differential-expression analysis of the transcriptional changes that underpin this sexual differentiation. RESULTS RNA-seq analysis revealed numerous differences in the transcriptomes of female and male gametocytes compared to asexual stages. Overall, there is net downregulation of transcripts in gametocytes compared to asexual stages, with this trend more marked in female gametocytes. Our analysis identified transcriptional changes in previously-characterised gametocyte-specific pathways, which validated our approach. We also detected many previously-unreported female- and male-specific pathways and genes. Transcriptional biases in stage and gender were then used to investigate sex-specificity and sexual dimorphism of Plasmodium in an evolutionary context. Sex-related gene expression is well conserved between Plasmodium species, but relatively poorly conserved in related organisms outside this genus. This pattern of conservation is most evident in genes necessary for both male and female gametocyte formation. However, this trend is less pronounced for male-specific genes, which are more highly conserved outside the genus than genes specific to female development. CONCLUSIONS We characterised the transcriptional changes that are integral to the development of the female and male sexual forms of Plasmodium. These differential-expression patterns provide a vital insight into understanding the gender-specific characteristics of this essential stage that is the primary target for treatments that block parasite transmission. Our results also offer insight into the evolution of sex genes through Alveolata, and suggest that many Plasmodium sex genes evolved within the genus. We further hypothesise that male gametocytes co-opted pre-existing cellular machinery in their evolutionary history, whereas female gametocytes evolved more through the development of novel, parasite-specific pathways.
Collapse
Affiliation(s)
- Lee M Yeoh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | | | - Vanessa Mollard
- School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | - Geoffrey I McFadden
- School of BioSciences, The University of Melbourne, Parkville, 3010, Australia.
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia.
| |
Collapse
|
43
|
Abstract
Malaria is caused in humans by five species of single-celled eukaryotic Plasmodium parasites (mainly Plasmodium falciparum and Plasmodium vivax) that are transmitted by the bite of Anopheles spp. mosquitoes. Malaria remains one of the most serious infectious diseases; it threatens nearly half of the world's population and led to hundreds of thousands of deaths in 2015, predominantly among children in Africa. Malaria is managed through a combination of vector control approaches (such as insecticide spraying and the use of insecticide-treated bed nets) and drugs for both treatment and prevention. The widespread use of artemisinin-based combination therapies has contributed to substantial declines in the number of malaria-related deaths; however, the emergence of drug resistance threatens to reverse this progress. Advances in our understanding of the underlying molecular basis of pathogenesis have fuelled the development of new diagnostics, drugs and insecticides. Several new combination therapies are in clinical development that have efficacy against drug-resistant parasites and the potential to be used in single-dose regimens to improve compliance. This ambitious programme to eliminate malaria also includes new approaches that could yield malaria vaccines or novel vector control strategies. However, despite these achievements, a well-coordinated global effort on multiple fronts is needed if malaria elimination is to be achieved.
Collapse
Affiliation(s)
- Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
| | | | | | | | - Wesley C Van Voorhis
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Seattle, Washington, USA
| | | |
Collapse
|
44
|
Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia. Proc Natl Acad Sci U S A 2016; 113:E8096-E8105. [PMID: 27911780 DOI: 10.1073/pnas.1608828113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cambodia, in which both Plasmodium vivax and Plasmodium falciparum are endemic, has been the focus of numerous malaria-control interventions, resulting in a marked decline in overall malaria incidence. Despite this decline, the number of P vivax cases has actually increased. To understand better the factors underlying this resilience, we compared the genetic responses of the two species to recent selective pressures. We sequenced and studied the genomes of 70 P vivax and 80 P falciparum isolates collected between 2009 and 2013. We found that although P falciparum has undergone population fracturing, the coendemic P vivax population has grown undisrupted, resulting in a larger effective population size, no discernable population structure, and frequent multiclonal infections. Signatures of selection suggest recent, species-specific evolutionary differences. Particularly, in contrast to P falciparum, P vivax transcription factors, chromatin modifiers, and histone deacetylases have undergone strong directional selection, including a particularly strong selective sweep at an AP2 transcription factor. Together, our findings point to different population-level adaptive mechanisms used by P vivax and P falciparum parasites. Although population substructuring in P falciparum has resulted in clonal outgrowths of resistant parasites, P vivax may use a nuanced transcriptional regulatory approach to population maintenance, enabling it to preserve a larger, more diverse population better suited to facing selective threats. We conclude that transcriptional control may underlie P vivax's resilience to malaria control measures. Novel strategies to target such processes are likely required to eradicate P vivax and achieve malaria elimination.
Collapse
|