Next-generation diagnostic biomarkers for vivax malaria
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Plasmodium Vivax
TISSUE(S): Blood Cell, Blood Plasma, Blood
DISEASE(S): Plasmodium Vivax Malaria
SUBMITTER: 
Shalini Aggarwal
LAB HEAD: Prof. Sanjeeva Srivastava
PROVIDER: PXD015165 | Pride | 2020-01-30
REPOSITORIES: Pride
Similar Datasets
Project description:Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating this parasite directly from the infected patients is the most feasible way to study its biology and any pathogenic mechanisms which may exist. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. However, the mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of natural antisense transcripts (NATs) in P. falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed strand specific microarray. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense transcript. Our data also shows condition specific expression patterns of varying S and AS transcript levels. Genes with AS transcripts enrich to various biological processes. This is the first report detailing the presence of NATs from clinical isolates of P. vivax. The data suggests differential regulation of gene expression in diverse clinical conditions and would lead to future detailed investigations of genome regulation. Plasmodium vivax isolates were collected from patients (n = 8) with differing clinical conditions.The patients exhibited symptoms categorized as un-complicated (n =1) or complicated malaria (n = 7). Criteria for determination of complicated disease were based on World Health Organization year 2010 guidelines. Microarray array based transcriptional profiling was carried out to detect prevalence of natural antisense transcripts.
2014-01-16 | E-GEOD-45165 | biostudies-arrayexpress
Project description:This project focused in the proteomic characterization of plasma-derived exosomes from Plasmodium vivax infected FRG huHep mice, a suitable in vivo model for the development of pre-erythrocytic stages of this parasite. P. vivax is responsible for the vast majority of Malaria cases outside Africa. This parasite evolved a latent liver stage form called hypnozoite that cannot be detected using the current diagnostic methods. This represent a major limitation to the Malaria elimination goal. Exosomes are extracellular vesicles involved in intercellular communication and in a large variety of physiological functions. Recently, this vesicles have been recognized for the immense potential to be used as biomarkers in the context of non-invasive diagnostic approaches from liquid biopsies. The exploration of the protein content of exosomes secreted into the bloodstream of P. vivax infected FRG huHep mice represents an interesting approach to tackle the big challenge of identifying a hypnozoite biomarker which in the future could help to identify hypnozoites carriers in Malaria vivax relapsing patients.
2018-07-16 | PXD008945 | Pride
Project description:Plasmodium vivax is the most widely distributed human malaria parasite with 7 million annual clinical cases and 2.5 billion people living under risk of infection. Presently, there is an urgent need to discover new antigens for vaccination as only two vaccine candidates, both based on the Duffy Binding protein, are currently in clinical trials. Extracellular vesicles (EVs) are small membrane-bound vesicles involved in intercellular communication and initially described in reticulocytes, the host cell of P. vivax, as a selective disposal mechanism of the transferrin receptor (CD71) in the maturation of reticulocytes to erythrocytes. We have recently reported the proteomics identification of P. vivax proteins associated to circulating EVs in P. vivax patients using size exclusion chromatography followed by mass spectrometry. Parasite proteins, however, were detected in two out of ten patients and only three of them with more than one unique peptide (UP). To increase the signal, we have implemented the Direct Immuno-affinity Capture (DIC) technique to enrich in EVs derived from CD71-expressing cells. Remarkably, we identified parasite proteins in all patients totaling 48 proteins (24 identified with ≥2 UP) and including several previously identified P. vivax vaccine candidate antigens (MSP1, MSP3, MSP7, MSP9, Serine-repeat antigen 1, and HSP70) as well as several membrane, cytosolic and exported proteins. Notably, a member of the Plasmodium helical interspersed sub-telomeric (PHIST-c) family, previously shown to be a main component of the caveola vesicle complexes, was robustly detected in five out six analyzed patients. Humoral immune response analysis by luminex confirmed its antigenicity. Collectively, we showed that enrichment of EVs by CD71-DIC from plasma, allows a robust identification of P. vivax proteins. This study represents a major advance in identifying new antigens for vaccination against this human malaria parasite.
2022-02-22 | PXD029439 | Pride
Project description:Background: Malaria is a public health problem in parts of Thailand, where Plasmodium falciparum and Plasmodium vivax are the main causes of infection. In the northwestern border province of Tak parasite prevalence is now estimated to be less than 1% by microscopy. Nonetheless, microscopy is insensitive at low-level parasitaemia. The objective of this study was to assess the current epidemiology of falciparum and vivax malaria in Tak using molecular methods to detect exposure to and infection with parasites; in particular, the prevalence of asymptomatic infections and infections with submicroscopic parasite levels. Methods: Three-hundred microlitres of whole blood from finger-prick were collected into capillary tubes from residents of a sentinel village and from patients at a malaria clinic. Pelleted cellular fractions were screened by quantitative PCR to determine parasite prevalence, while plasma was probed on a protein microarray displaying hundreds of P. falciparum and P. vivax proteins to obtain antibody response profiles in those individuals. Results: Of 219 samples from the village, qPCR detected 25 (11.4%) Plasmodium sp. infections, of which 92% were asymptomatic and 100% were submicroscopic. Of 61 samples from the clinic patients, 27 (44.3%) were positive by qPCR, of which 25.9% had submicroscopic parasite levels. Cryptic mixed infections, misdiagnosed as single-species infections by microscopy, were found in 7 (25.9%) malaria patients. All sample donors, parasitaemic and non-parasitaemic alike, had serological evidence of parasite exposure, with 100% seropositivity to at least 54 antigens. Antigens significantly associated with asymptomatic infections were P. falciparum MSP2, DnaJ protein, putative E1E2 ATPase, and three others.
2014-06-22 | GSE55265 | GEO
Project description:Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating this parasite directly from the infected patients is the most feasible way to study its biology and any pathogenic mechanisms which may exist. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. However, the mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of natural antisense transcripts (NATs) in P. falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed strand specific microarray. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense transcript. Our data also shows condition specific expression patterns of varying S and AS transcript levels. Genes with AS transcripts enrich to various biological processes. This is the first report detailing the presence of NATs from clinical isolates of P. vivax. The data suggests differential regulation of gene expression in diverse clinical conditions and would lead to future detailed investigations of genome regulation.
2014-01-16 | GSE45165 | GEO
Project description:Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole genome sequencing (30X coverage). This analysis revealed over 18,261 single nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Sal1 strain obtained in 1970. This full-genome sequence of a P. vivax isolate, the second overall and first of an uncultured patient isolate, shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous to synonymous SNPs encode two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in P. falciparum. This analysis provides a new data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies. Genome DNA from Peruvian P. vivax Isolate IQ07 vs. Reference Sal1
2010-10-02 | E-GEOD-23982 | biostudies-arrayexpress
Project description:Malaria parasites transmitted by mosquito bite are remarkably efficient in establishing human infections. The infection process requires ~30 minutes and is highly complex as quiescent sporozoites injected with mosquito saliva must be rapidly activated in the skin, migrate through the body, and infect the liver. This process is poorly understood for Plasmodium vivax due to low infectivity in the in vitro models. To study this skin-to-liver stage of malaria, we developed quantitative bioassays coupled with transcriptomics to evaluate parasite changes linked with mammalian microenvironmental factors. Our in vitro phenotype and RNA-seq analyses revealedkey microenvironmental relationships with distinct biological functions. M ost notable, preservation of sporozoite quiescence by exposure to insect-like factors coupled with strategic activation limits untimely activation of invasion-associated genes to dramatically increase hepatocyte invasion rates. We also report the first transcriptomic analysis of the P. vivax sporozoite interaction in salivary glands identifying 118 infection-related differentially-regulated Anopheles dirus genes. These results provide important new insights in malaria parasite biology and identify priority targets for antimalarial therapeutic interventions to block P. vivax infection.
2018-08-16 | GSE117538 | GEO
Project description:High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n=14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n=85) present in the arrays showed perfect correlation (r2=0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r≥0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates.
2016-10-18 | GSE55644 | GEO
Project description:Plasmodium vivax is a protozoan parasite responsible for the great majority of Malaria cases outside Sub-Saharan Africa. This parasite is characterized by the presence of latent liver stage forms called hypnozoites which cause relapsing blood infections estimated to contribute up to 79% of vivax malaria cases in endemic regions. P. vivax hypnozoites are considered a major bottleneck for the malaria elimination goal not only due to symptomatic recurrent blood infections experienced by individuals carrying this parasite form but also for continue silent parasite transmission among the population. Importantly, diagnose of hypnozoites cannot be achieved with the current diagnostic tools. Extracellular vesicles (EVs) are nanovesicles secreted by all cell types involved in intercellular communication. EVs are characterized by the presence of molecules from the cell of origin being thus considered as a fingerprint of cell physiological status. Due to this property and to the great EVs stability in biofluids, they are emerging as promising biomarkers for non-invasive diagnosis of a large range of diseases. We have previously reported that plasma-derived EVs from P. vivax infected liver chimeric mice (FRG huHep), a model of liver stage infection of this parasite, contain P. vivax proteins. In this project, we have performed a proteomic characterization of EVs derived from liver chimeric FRG huHEP mice. Pharmacological treatment of FRG huHep mice with a schizontycidal experimental drug (MMV48) was performed to generate infections enriched with latent hypnozoites, an unexplored approach to study EVs specific from this liver stage. The identification of parasite proteins associated to EVs in this model represents a significant advance in the road to identify P. vivax hypnozoite biomarkers that can be implemented for the future diagnose of hypnozoites carriers in endemic regions. Biological samples used • P. vivax FRG huHep mice in vivo model: Female FRG KO mice engrafted with human hepatocytes (FRG KO huHep) were infected with P. vivax as previously described[8]. Mice were divided in 5 experimental groups. Group 1 (3 mice) was uninfected, Group 2 (6 mice) was inoculated with P. vivax sporozoites by the bite of 20 mosquitos and euthanized after 8 days post-inoculation; Group 3 (6 mice) was infected by intravenous injection of P. vivax sporozoites (0.8 million) and euthanized after 8 days post-infection; Group 4 (6 mice) was infected by intravenous injection of P. vivax sporozoites (1 million sporozoites) and euthanized after 21 days post-infection; Group 5 (3 mice) was infected by intravenous injection (1 million sporozoites) and treated with Tafenoquine (10 mg/kg) at 14 dpi and euthanized at 21 days post-infection. MMV048 mice treatment (30 mg/kg) was performed as follows: 3 mice of Group 2 and 3 received intravenous injections of the drug at 4 days post-infection. 3 mice of Group 4 received intravenous injections of the drug at 17 days post-infection. 3 DMSO-treated animals were used as controls in groups 2, 3 and 4. After euthanasia, whole blood was extracted by cardiac venipuncture for plasma collection as previously described. Plasma-derived EVs were purified as follows: Plasma were thawed on ice, centrifuged at 2000 x g for 10 min and supernatant collected. EVs were purified by SEC using commercial Sepharose (iZON) following manufacturer instructions. SEC fractions were characterized for the presence of EV markers CD9 and plasma-derived EVs marker CD5L in a BBA and by NTA. Protein concentration was determined by BCA (Thermo Scientific).
2022-08-26 | PXD035719 | Pride
Project description:Malaria is the most important vector-borne disease in Southeast Asia. In Thailand, malaria incidence has been in decline, with the annual parasite incidence dropping to 0.56 in 2007. The Myanmar-Thai border province of Tak is considered meso-endemic for malaria, and both Plasmodium vivax (Pv) and P. falciparum (Pf) are equally present. As part of the International Centers for Excellence in Malaria Research (ICEMR) - Southeast Asia project, malaria surveillance is conducted in Tak on both the healthy population and hospital patients, and parasite prevalence is reportedly <1%. However, little is known about the immuno-epidemiology associated with Pf and Pv infections in the region regarding the breadth and targets of the antibody response to the malaria parasites. Our hypothesis is that the serological profiles of the population will reflect the low parasite prevalence in Tak, showing little antibody reactivity to Pv and Pf. To examine this question, we developed a protein microarray displaying the top 500 most immunogenic antigens of these two Plasmodium species. We collected whole blood samples from healthy residents of Mae Salid Noi village during a Mass Blood Survey for malaria in the region. Whole blood was sent to UCI for qPCR and serology analysis. Blood plasma was probed on the protein microarray; genomic DNA was extracted from RBC pellets and screened by qPCR for infection confirmation and species identification. One-hundred percent (n=381) of serum samples were reactive to both Pv and Pf antigens, including all qPCR-negative samples.
2016-02-01 | GSE75593 | GEO