RNAseq of hypnozoites and schizonts in the MPCC system
Ontology highlight
ABSTRACT:
ORGANISM(S): Plasmodium vivax
PROVIDER: GSE108016 | GEO | 2018/02/23
REPOSITORIES: GEO
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Project description:Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years, and then reactivate to cause recurrent blood-stage infection. While an important target for malaria eradication, little is known about the molecular features of the replicative and non-replicative states of intracellular P. vivax parasites, or their human host-cell dependencies and the host responses to them. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites in primary human hepatocytes and conduct transcriptional profiling. By coupling enrichment strategies with bulk and single-cell analyses, we captured both parasite and host transcripts in individual hepatocytes throughout the infection course. We define host- and state-dependent transcriptional signatures and identify previously unappreciated populations of replicative and non-replicative parasites, sharing features with sexual transmissive forms. We find that infection suppresses transcription of key hepatocyte function genes, and that P. vivax elicits an innate immune response that can be manipulated to control infection. Our work provides an extendible framework and resource for understanding host-parasite interactions and reveals new insights into the biology of P. vivax dormancy and transmission.
2022-02-25 | GSE197458 | GEO
Project description:Malaria-causing Plasmodium vivax parasites can linger in the human liver for weeks to years, and then reactivate to cause recurrent blood-stage infection. While an important target for malaria eradication, little is known about the molecular features of the replicative and non-replicative states of intracellular P. vivax parasites, or their human host-cell dependencies and the host responses to them. Here, we leverage a bioengineered human microliver platform to culture patient-derived P. vivax parasites in primary human hepatocytes and conduct transcriptional profiling. By coupling enrichment strategies with bulk and single-cell analyses, we captured both parasite and host transcripts in individual hepatocytes throughout the infection course. We define host- and state-dependent transcriptional signatures and identify previously unappreciated populations of replicative and non-replicative parasites, sharing features with sexual transmissive forms. We find that infection suppresses transcription of key hepatocyte function genes, and that P. vivax elicits an innate immune response that can be manipulated to control infection. Our work provides an extendible framework and resource for understanding host-parasite interactions and reveals new insights into the biology of P. vivax dormancy and transmission.
2022-02-25 | GSE197409 | GEO
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:A major obstacle in deciphering the hepatic stage of the malaria parasite has been the challenges associated with culturing the infected hepatocytes through the entire liver stage cycle, including that of the dormant form known as hypnozoites. Primary hepatocytes lose their specialized functions in long-term in vitro culture. Hepatocyte infection represents the first step for clinically silent infection and development of malaria parasite Plasmodium in the liver. Thus this liver stage is an ideal target for development of novel antimalarial drugs and vaccine. However, drug discovery against Plasmodium liver stage is severely hampered by the poor understanding of host-cell and parasites interactions during the liver stage infection and development. In this study, we have performed tandem mass tags (TMT) labelling based quantitative proteomic analysis in simian primary hepatocytes cultured in three different systems of susceptibility to plasmodium infection. Our results represent the first documentation of potentially essential molecular markers including asialoglycoprotein receptor (ASGPR), apolipoproteins, squalene synthase and scavenger receptor B1 (SR-BI) required for productive infection and full development in relapsing Plasmodium species. The identification of these candidate proteins for constructive infection and development of Plasmodium in malaria paves the way to explore them as therapeutic targets.
2019-09-02 | PXD013310 | Pride
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:During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and organ-specific pathology including cerebral and placental malaria. Immature gametocytes – sexual stage precursor cells – likewise disappear from circulation. Recent work has demonstrated that these sexual stage parasites are located in the hematopoietic system of the bone marrow before mature gametocytes are released into the blood stream to facilitate mosquito transmission. However, as sequestration occurs only in vivo and not during in vitro culture, the mechanisms by which it is regulated and enacted (particularly by the gametocyte stage) remain poorly understood. We generated the most comprehensive P. falciparum functional gene network to date by integrating global transcriptional data from a large set of asexual and sexual in vitro samples, patient-derived in vivo samples, and a new set of in vitro samples profiling sexual commitment. We defined more than 250 functional modules (clusters) of genes that are co-expressed primarily during the intra-erythrocytic parasite cycle, including 35 during sexual commitment and gametocyte development. Comparing the in vivo and in vitro datasets allowed us, for the first time, to map the time point of asexual parasite sequestration in patients to 22 hours post invasion, confirming previous in vitro observations on the dynamics of host cell modification and cytoadherence. Moreover, we were able to define the properties of gametocyte sequestration, demonstrating the presence of two circulating gametocyte populations: gametocyte rings between 0 and ~30 hours post invasion and mature gametocytes after around 7 days post invasion.
2015-01-13 | GSE64887 | GEO
Project description:During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and organ-specific pathology including cerebral and placental malaria. Immature gametocytes M-bM-^@M-^S sexual stage precursor cells M-bM-^@M-^S likewise disappear from circulation. Recent work has demonstrated that these sexual stage parasites are located in the hematopoietic system of the bone marrow before mature gametocytes are released into the blood stream to facilitate mosquito transmission. However, as sequestration occurs only in vivo and not during in vitro culture, the mechanisms by which it is regulated and enacted (particularly by the gametocyte stage) remain poorly understood. We generated the most comprehensive P. falciparum functional gene network to date by integrating global transcriptional data from a large set of asexual and sexual in vitro samples, patient-derived in vivo samples, and a new set of in vitro samples profiling sexual commitment. We defined more than 250 functional modules (clusters) of genes that are co-expressed primarily during the intra-erythrocytic parasite cycle, including 35 during sexual commitment and gametocyte development. Comparing the in vivo and in vitro datasets allowed us, for the first time, to map the time point of asexual parasite sequestration in patients to 22 hours post invasion, confirming previous in vitro observations on the dynamics of host cell modification and cytoadherence. Moreover, we were able to define the properties of gametocyte sequestration, demonstrating the presence of two circulating gametocyte populations: gametocyte rings between 0 and ~30 hours post invasion and mature gametocytes after around 7 days post invasion. We used 164/TdTom, a transgenic parasite line expressing a red fluorescent protein reporter under a gametocyte-specific promoter to generate schizont samples. Schizonts were subsequently isolated from both the fluorescent and non-fluorescent population by FACS and prepared for microarray analysis. Two biological replicates were produced for both the fluorescent and the non-fluorescent samples.
2015-01-13 | E-GEOD-64887 | biostudies-arrayexpress
Project description:The apicomplexan parasites Plasmodium spp. are the causative agents of malaria, a disease that poses a significant global health burden. Plasmodium spp. initiate infection of the human host by transforming and replicating within hepatocytes. Yet, despite the liver stage being a critical step during infection, most transcriptomic studies have focused on more technically accessible stages of the Plasmodium life cycle, limiting our ability to target these parasites to prevent disease. We have conducted an extensive RNA-seq analysis of the Plasmodium berghei liver stage at high-resolution, covering early (2—18 hpi) and mid-stages (24—48 hpi) of the liver stage of infection. Our data revealed hundreds of genes are differentially expressed as early as 2 hours post-infection, and that multiple genes shown to be important for later infection may be upregulated as early as 12 hpi. Using hierarchical clustering along with co-expression analysis, we identified clusters functionally enriched for important liver-stage processes such as interactions with the host cell and redox homeostasis. Furthermore, some of these clusters were highly correlated to the expression of ApiAP2 transcription factors, while showing enrichment of mostly uncharacterized DNA binding motifs hinting at alternative uncharacterized targets during this stage. Our work represents a window into the previously undescribed transcriptome of the early LS upon host cell infection and offers a comprehensive view of the Plasmodium liver stage. Using the tractable organism P. berghei, our dataset provides a blueprint for future studies in the human-infective parasites, P. falciparum and P. vivax.
2020-02-22 | GSE145731 | GEO
Project description:Co-infection with soil transmitted helminths (STH) and Plasmodium spp. parasites is a common occurrence in tropical developing countries, but the consequences of this interaction remain poorly understood. Here, we performed a multi-omic analysis on the peripheral blood and fecal samples of 130 individuals in Tierralta, Córdoba, Colombia who were infected with P. vivax alone (n = 33), co-infected with P. vivax and STH (n = 27), infected with STH alone (n = 39) or were infected with neither P. vivax nor STH (n = 31). In addition to Complete Blood Count (CBC) with differential, transcriptional profiling of peripheral blood samples was performed by RNA-Seq, fecal microbial communities were determined by 16S ribosomal RNA gene sequencing and circulating cytokine levels were measured by bead-based immunoassays. Differences in blood cell counts were driven primarily by P. vivax infection, including an increased percentage of neutrophils that was associated with a transcriptional signature of neutrophil activation in the blood. P. vivax infection was also associated with increased levels of IL-6, IL-8 and IL-10 and these cytokine levels were not affected by STH co-infection. Surprisingly, P. vivax infection was more strongly associated with changes in the microbiome than STH infection. Children infected with P. vivax exhibited elevated Bacteroides and reduced Prevotella and Clostridiaceae, but these differences were not observed in individuals co-infected with STH. We also observed that P. vivax parasitemia is higher in STH-infected population. When we used machine learning to identify the most important predictors of P. vivax parasite burden from all measured variables, bacterial taxa were the strongest predictors of parasitemia levels in P. vivax infected individuals. In contrast, circulating TGF- β was identified as the strongest predictor of T. trichiura egg burden. This study provides unexpected evidence that the gut microbiota may have a stronger link with P. vivax than with STH infection.
2020-09-29 | GSE144792 | GEO
Project description:Dormancy enables pathogens to survive unfavorable conditions and maximize their chance for transmission. Relapsing malaria parasites, such as Plasmodium vivax, ovale and cynomolgi employ this strategy. After inoculation by the bite of an infected mosquito, the so-called hypnozoites stay quiescent inside liver cells before reactivating, proliferating and establishing blood stage infection. Despite recent advances in molecular characterization of hypnozoites the mechanisms leading to hypnozoite formation and reactivation remain a mystery. Here we integrate various omics approaches to explore the involvement of gene regulatory mechanisms in these processes. By profiling the genome-wide distribution of repressive and activating epigenetic marks we identify a small set of genes that gets epigenetically silenced during liver stage development, a process that is conserved amongst relapsing parasites. Furthermore, by combining single-cell transcriptomics, chromatin accessibility profiling and fluorescent in situ RNA hybridization we show that these genes are expressed in hypnozoites and their silencing coincides with parasite development. Intriguingly, genes with clear hypnozoite-specific expression are almost exclusively encoding for proteins with RNA-binding domains. Overall, these findings support a model in which repressive RNA-binding proteins keep hypnozoites in a developmentally competent, but dormant state and heterochromatin-mediated silencing of these genes enables hypnozoite reactivation. Further testing of this hypothesis could provide decisive clues for targeted reactivation and killing of these vicious pathogens.
2024-01-24 | GSE180257 | GEO