1
|
Mamede L, Fall F, Schoumacher M, Ledoux A, Bugli C, De Tullio P, Quetin-Leclercq J, Govaerts B, Frédérich M. Comparison of extraction methods in vitro Plasmodium falciparum: A 1H NMR and LC-MS joined approach. Biochem Biophys Res Commun 2024; 703:149684. [PMID: 38367514 DOI: 10.1016/j.bbrc.2024.149684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Malaria is a parasitic disease that remains a global concern and the subject of many studies. Metabolomics has emerged as an approach to better comprehend complex pathogens and discover possible drug targets, thus giving new insights that can aid in the development of antimalarial therapies. However, there is no standardized method to extract metabolites from in vitro Plasmodium falciparum intraerythrocytic parasites, the stage that causes malaria. Additionally, most methods are developed with either LC-MS or NMR analysis in mind, and have rarely been evaluated with both tools. In this work, three extraction methods frequently found in the literature were reproduced and samples were analyzed through both LC-MS and 1H NMR, and evaluated in order to reveal which is the most repeatable and consistent through an array of different tools, including chemometrics, peak detection and annotation. The most reliable method in this study proved to be a double extraction with methanol and methanol/water (80:20, v/v). Metabolomic studies in the field should move towards standardization of methodologies and the use of both LC-MS and 1H NMR in order to make data more comparable between studies and facilitate the achievement of biologically interpretable information.
Collapse
Affiliation(s)
- Lúcia Mamede
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Fanta Fall
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Brussels, Belgium
| | - Matthieu Schoumacher
- Laboratory of Pharmaceutical Chemistry, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Allison Ledoux
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Céline Bugli
- Statistical Methodology and Computing Service (SMCS/LIDAM), UCLouvain, Louvain-la-Neuve, Belgium
| | - Pascal De Tullio
- Laboratory of Pharmaceutical Chemistry, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Brussels, Belgium
| | - Bernadette Govaerts
- Statistical Methodology and Computing Service (SMCS/LIDAM), UCLouvain, Louvain-la-Neuve, Belgium
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium.
| |
Collapse
|
2
|
Bailey BL, Nguyen W, Cowman AF, Sleebs BE. Chemo-proteomics in antimalarial target identification and engagement. Med Res Rev 2023; 43:2303-2351. [PMID: 37232495 PMCID: PMC10947479 DOI: 10.1002/med.21975] [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: 06/22/2022] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
Humans have lived in tenuous battle with malaria over millennia. Today, while much of the world is free of the disease, areas of South America, Asia, and Africa still wage this war with substantial impacts on their social and economic development. The threat of widespread resistance to all currently available antimalarial therapies continues to raise concern. Therefore, it is imperative that novel antimalarial chemotypes be developed to populate the pipeline going forward. Phenotypic screening has been responsible for the majority of the new chemotypes emerging in the past few decades. However, this can result in limited information on the molecular target of these compounds which may serve as an unknown variable complicating their progression into clinical development. Target identification and validation is a process that incorporates techniques from a range of different disciplines. Chemical biology and more specifically chemo-proteomics have been heavily utilized for this purpose. This review provides an in-depth summary of the application of chemo-proteomics in antimalarial development. Here we focus particularly on the methodology, practicalities, merits, and limitations of designing these experiments. Together this provides learnings on the future use of chemo-proteomics in antimalarial development.
Collapse
Affiliation(s)
- Brodie L. Bailey
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - William Nguyen
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Alan F. Cowman
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVictoriaAustralia
| |
Collapse
|
3
|
Izquierdo L. The glycobiology of plasmodium falciparum: New approaches and recent advances. Biotechnol Adv 2023; 66:108178. [PMID: 37216996 DOI: 10.1016/j.biotechadv.2023.108178] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/22/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Like any other microorganism, pathogenic protozoan parasites rely heavily on glycoconjugates and glycan binding proteins to protect themselves from the environment and to interact with their diverse hosts. A thorough comprehension of how glycobiology contributes to the survival and virulence of these organisms may reveal unknown aspects of their biology and may open much needed avenues for the design of new strategies against them. In the case of Plasmodium falciparum, which causes the vast majority of malaria cases and deaths, the restricted variety and the simplicity of its glycans seemed to confer limited significance to the role played by glycoconjugates in the parasite. Nonetheless, the last 10 to 15 years of research are revealing a clearer and more defined picture. Thus, the use of new experimental techniques and the results obtained provide new avenues for understanding the biology of the parasite, as well as opportunities for the development of much required new tools against malaria.
Collapse
Affiliation(s)
- Luis Izquierdo
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia, Spain; CIBER de Enfermedades Infecciosas, Madrid, Spain.
| |
Collapse
|
4
|
Recent metabolomic developments for antimalarial drug discovery. Parasitol Res 2022; 121:3351-3380. [PMID: 36194273 DOI: 10.1007/s00436-022-07673-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/14/2022] [Indexed: 10/10/2022]
Abstract
Malaria is a parasitic disease that remains a global health issue, responsible for a significant death and morbidity toll. Various factors have impacted the use and delayed the development of antimalarial therapies, such as the associated financial cost and parasitic resistance. In order to discover new drugs and validate parasitic targets, a powerful omics tool, metabolomics, emerged as a reliable approach. However, as a fairly recent method in malaria, new findings are timely and original practices emerge frequently. This review aims to discuss recent research towards the development of new metabolomic methods in the context of uncovering antiplasmodial mechanisms of action in vitro and to point out innovative metabolic pathways that can revitalize the antimalarial pipeline.
Collapse
|
5
|
Tornyigah B, Ndam NT. Preservation of Parasite RNA in the Field. Methods Mol Biol 2022; 2470:19-25. [PMID: 35881335 DOI: 10.1007/978-1-0716-2189-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The pathogenesis of malaria is largely attributable to the parasite's ability to modulate its cytoadhesion phenotype. This relates to the multigenic families comprising dozens to hundreds of members, whose expression, often mutually exclusive, allows the parasite to vary its adhesive properties and antigenic appearance. This phenomenon is mainly described for the variant surface antigens that the parasite expresses on the infected erythrocyte. In order to decipher these gene expression spectra and identify potential antigenic candidates and/or targets of therapeutic interest, the analysis of the transcriptomes of the parasites directly isolated from patients with well-defined clinical presentation is important. RNA stabilization is an absolute prerequisite for a precise and accurate transcriptome profiling. Immediate stabilization of RNA of biological samples is therefore necessary to prevent degradation by ribonucleases (RNase) or cellular changes. This chapter described methodology for preserving parasite RNA samples from malaria patients in the field for transcriptome studies.
Collapse
Affiliation(s)
- Bernard Tornyigah
- Université de Paris, MERIT, IRD, Paris, France
- Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | | |
Collapse
|
6
|
Briquet S, Gissot M, Silvie O. A toolbox for conditional control of gene expression in apicomplexan parasites. Mol Microbiol 2021; 117:618-631. [PMID: 34564906 PMCID: PMC9293482 DOI: 10.1111/mmi.14821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023]
Abstract
Apicomplexan parasites encompass diverse pathogens for humans and animals, including the causative agents of malaria and toxoplasmosis, Plasmodium spp. and Toxoplasma gondii. Genetic manipulation of these parasites has become central to explore parasite biology, unravel gene function and identify new targets for therapeutic strategies. Tremendous progress has been achieved over the past years with the advent of next generation sequencing and powerful genome editing methods. In particular, various methods for conditional gene expression have been developed in both Plasmodium and Toxoplasma to knockout or knockdown essential genes, or for inducible expression of master developmental regulators or mutant versions of proteins. Conditional gene expression can be achieved at three distinct levels. At the DNA level, inducible site‐specific recombinases allow conditional genome editing. At the RNA level, regulation can be achieved during transcription, using stage‐specific or regulatable promoters, or post‐transcriptionally through alteration of mRNA stability or translation. At the protein level, several systems have been developed for inducible degradation or displacement of a protein of interest. In this review, we provide an overview of current systems for conditional control of gene expression in Plasmodium and Toxoplasma parasites, highlighting the advantages and limitations of each approach.
Collapse
Affiliation(s)
- Sylvie Briquet
- INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
| | - Mathieu Gissot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, CIIL, Univ. Lille, Lille, France
| | - Olivier Silvie
- INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
| |
Collapse
|
7
|
Shah Z, Naung MT, Moser KA, Adams M, Buchwald AG, Dwivedi A, Ouattara A, Seydel KB, Mathanga DP, Barry AE, Serre D, Laufer MK, Silva JC, Takala-Harrison S. Whole-genome analysis of Malawian Plasmodium falciparum isolates identifies possible targets of allele-specific immunity to clinical malaria. PLoS Genet 2021; 17:e1009576. [PMID: 34033654 PMCID: PMC8184011 DOI: 10.1371/journal.pgen.1009576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/07/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Individuals acquire immunity to clinical malaria after repeated Plasmodium falciparum infections. Immunity to disease is thought to reflect the acquisition of a repertoire of responses to multiple alleles in diverse parasite antigens. In previous studies, we identified polymorphic sites within individual antigens that are associated with parasite immune evasion by examining antigen allele dynamics in individuals followed longitudinally. Here we expand this approach by analyzing genome-wide polymorphisms using whole genome sequence data from 140 parasite isolates representing malaria cases from a longitudinal study in Malawi and identify 25 genes that encode possible targets of naturally acquired immunity that should be validated immunologically and further characterized for their potential as vaccine candidates.
Collapse
Affiliation(s)
- Zalak Shah
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Myo T. Naung
- Population Health and Immunity Division, Walter Eliza Hall of Medical Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Kara A. Moser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Andrea G. Buchwald
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Karl B. Seydel
- Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Don P. Mathanga
- University of Malawi College of Medicine, Malaria Alert Centre, Blantyre, Malawi
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter Eliza Hall of Medical Institute for Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
- Disease Elimination and Maternal and Child Health, Burnet Institute, Melbourne, Victoria, Australia
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Miriam K. Laufer
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joana C. Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| |
Collapse
|
8
|
Zhou M, Varol A, Efferth T. Multi-omics approaches to improve malaria therapy. Pharmacol Res 2021; 167:105570. [PMID: 33766628 DOI: 10.1016/j.phrs.2021.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023]
Abstract
Malaria contributes to the most widespread infectious diseases worldwide. Even though current drugs are commercially available, the ever-increasing drug resistance problem by malaria parasites poses new challenges in malaria therapy. Hence, searching for efficient therapeutic strategies is of high priority in malaria control. In recent years, multi-omics technologies have been extensively applied to provide a more holistic view of functional principles and dynamics of biological mechanisms. We briefly review multi-omics technologies and focus on recent malaria progress conducted with the help of various omics methods. Then, we present up-to-date advances for multi-omics approaches in malaria. Next, we describe resistance phenomena to established antimalarial drugs and underlying mechanisms. Finally, we provide insight into novel multi-omics approaches, new drugs and vaccine developments and analyze current gaps in multi-omics research. Although multi-omics approaches have been successfully used in malaria studies, they are still limited. Many gaps need to be filled to bridge the gap between basic research and treatment of malaria patients. Multi-omics approaches will foster a better understanding of the molecular mechanisms of Plasmodium that are essential for the development of novel drugs and vaccines to fight this disastrous disease.
Collapse
Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ayşegül Varol
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
| |
Collapse
|
9
|
Gunnarsson S, Prabakaran S. In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework. Malar J 2021; 20:71. [PMID: 33546698 PMCID: PMC7866754 DOI: 10.1186/s12936-021-03598-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Plasmodium falciparum causes the deadliest form of malaria, which remains one of the most prevalent infectious diseases. Unfortunately, the only licensed vaccine showed limited protection and resistance to anti-malarial drug is increasing, which can be largely attributed to the biological complexity of the parasite’s life cycle. The progression from one developmental stage to another in P. falciparum involves drastic changes in gene expressions, where its infectivity to human hosts varies greatly depending on the stage. Approaches to identify candidate genes that are responsible for the development of infectivity to human hosts typically involve differential gene expression analysis between stages. However, the detection may be limited to annotated proteins and open reading frames (ORFs) predicted using restrictive criteria. Methods The above problem is particularly relevant for P. falciparum; whose genome annotation is relatively incomplete given its clinical significance. In this work, systems proteogenomics approach was used to address this challenge, as it allows computational detection of unannotated, novel Open Reading Frames (nORFs), which are neglected by conventional analyses. Two pairs of transcriptome/proteome were obtained from a previous study where one was collected in the mosquito-infectious oocyst sporozoite stage, and the other in the salivary gland sporozoite stage with human infectivity. They were then re-analysed using the proteogenomics framework to identify nORFs in each stage. Results Translational products of nORFs that map to antisense, intergenic, intronic, 3′ UTR and 5′ UTR regions, as well as alternative reading frames of canonical proteins were detected. Some of these nORFs also showed differential expression between the two life cycle stages studied. Their regulatory roles were explored through further bioinformatics analyses including the expression regulation on the parent reference genes, in silico structure prediction, and gene ontology term enrichment analysis. Conclusion The identification of nORFs in P. falciparum sporozoites highlights the biological complexity of the parasite. Although the analyses are solely computational, these results provide a starting point for further experimental validation of the existence and functional roles of these nORFs,
Collapse
Affiliation(s)
- Sophie Gunnarsson
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
| |
Collapse
|
10
|
Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease. Sci Rep 2021; 11:2149. [PMID: 33495500 PMCID: PMC7835236 DOI: 10.1038/s41598-020-77881-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/12/2020] [Indexed: 01/24/2023] Open
Abstract
The myxozoan parasite, Tetracapsuloidesbryosalmonae has a two-host life cycle alternating between freshwater bryozoans and salmonid fish. Infected fish can develop Proliferative Kidney Disease, characterised by a gross lymphoid-driven kidney pathology in wild and farmed salmonids. To facilitate an in-depth understanding of T.bryosalmonae-host interactions, we have used a two-host parasite transcriptome sequencing approach in generating two parasite transcriptome assemblies; the first derived from parasite spore sacs isolated from infected bryozoans and the second from infected fish kidney tissues. This approach was adopted to minimize host contamination in the absence of a complete T.bryosalmonae genome. Parasite contigs common to both infected hosts (the intersect transcriptome; 7362 contigs) were typically AT-rich (60–75% AT). 5432 contigs within the intersect were annotated. 1930 unannotated contigs encoded for unknown transcripts. We have focused on transcripts encoding proteins involved in; nutrient acquisition, host–parasite interactions, development, cell-to-cell communication and proteins of unknown function, establishing their potential importance in each host by RT-qPCR. Host-specific expression profiles were evident, particularly in transcripts encoding proteases and proteins involved in lipid metabolism, cell adhesion, and development. We confirm for the first time the presence of homeobox proteins and a frizzled homologue in myxozoan parasites. The novel insights into myxozoan biology that this study reveals will help to focus research in developing future disease control strategies.
Collapse
|
11
|
Oberstaller J, Otto TD, Rayner JC, Adams JH. Essential Genes of the Parasitic Apicomplexa. Trends Parasitol 2021; 37:304-316. [PMID: 33419671 DOI: 10.1016/j.pt.2020.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
Genome-scale mutagenesis screens for genes essential for apicomplexan parasite survival have been completed in three species: Plasmodium falciparum, the major human malaria parasite, Plasmodium berghei, a model rodent malaria parasite, and the more distantly related Toxoplasma gondii, the causative agent of toxoplasmosis. These three species share 2606 single-copy orthologs, 1500 of which have essentiality data in all three screens. In this review, we explore the overlap between these datasets to define the core essential genes of the phylum Apicomplexa. We further discuss the implications of these groundbreaking studies for understanding apicomplexan parasite biology, and we identify promising areas of focus for developing new pan-apicomplexan parasite interventions.
Collapse
Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Centre of Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge, Cambridgeshire, CB2 0XY, UK
| | - John H Adams
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
| |
Collapse
|
12
|
Kucharski M, Tripathi J, Nayak S, Zhu L, Wirjanata G, van der Pluijm RW, Dhorda M, Dondorp A, Bozdech Z. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 2020; 19:363. [PMID: 33036628 PMCID: PMC7547485 DOI: 10.1186/s12936-020-03436-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies. Results The utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10 ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest 2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available to date was generated, and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates. Conclusions Overall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.
Collapse
Affiliation(s)
- Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Jaishree Tripathi
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Sourav Nayak
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Rob W van der Pluijm
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mehul Dhorda
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,WorldWide Antimalarial Resistance Network-Asia Regional Centre, Bangkok, Thailand
| | - Arjen Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| |
Collapse
|
13
|
Baig AM, Khaleeq A, Nazim F. Targeting CNS Related Protist Pathogens: Calcium Ion Dependency in the Brain-Eating Amoebae. ACS Chem Neurosci 2020; 11:2385-2387. [PMID: 31840980 DOI: 10.1021/acschemneuro.9b00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Of the free-living amoebae (FLA) Naegleria fowleri, Balamuthia mandrillaris, and Acanthamoeba spp. are known to cause encephalitis. Coined with the term "brain-eating amoebae" (BEA), infection of the central nervous system with FLA has a high mortality rate. A combination of diagnostic delay, lack of new drug development, and incomplete understanding of the dependencies of FLA have resulted in the failure of introducing safer and effective drugs. We inferred that being a shape-changing entity the FLA should have a dependency on calcium (Ca2+) ions that could be targeted to cripple the pathogenicity of the FLA. We used genomic, transcriptomic, and proteomic information available on FLA in online databases to evidence the presence of various Ca2+ion influx regulating channels, reviewing adapter proteins at first and then targeting human-like voltage-gated Ca2+ channels with nifedipine and verapamil that are used clinically for noninfectious diseases to see their effect in trophozoites of Acanthamoeba spp. in particular.
Collapse
Affiliation(s)
- Abdul Mannan Baig
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Areeba Khaleeq
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | - Fizza Nazim
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| |
Collapse
|
14
|
Carolino K, Winzeler EA. The antimalarial resistome - finding new drug targets and their modes of action. Curr Opin Microbiol 2020; 57:49-55. [PMID: 32682267 PMCID: PMC7763834 DOI: 10.1016/j.mib.2020.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022]
Abstract
To this day, malaria remains a global burden, affecting millions of people, especially those in sub-Saharan Africa and Asia. The rise of drug resistance to current antimalarial treatments, including artemisinin-based combination therapies, has made discovering new small molecule compounds with novel modes of action an urgent matter. The concerted effort to construct enormous compound libraries and develop high-throughput phenotypic screening assays to find compounds effective at specifically clearing malaria-causing Plasmodium parasites at any stage of the life cycle has provided many antimalarial prospects, but does not indicate their target or mode of action. Here, we review recent advances in antimalarial drug discovery efforts, focusing on the following 'omics' approaches in mode of action studies: IVIEWGA, CETSA, metabolomic profiling.
Collapse
Affiliation(s)
- Krypton Carolino
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.
| |
Collapse
|