Whole genome expression profiling of artemsinin-resistant Plasmodium falciparum field isolates [in vivo]
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ABSTRACT:
ORGANISM(S): Plasmodium falciparum
PROVIDER: GSE59097 | GEO | 2014/07/15
SECONDARY ACCESSION(S): PRJNA254409
REPOSITORIES: GEO
Similar Datasets
Project description:The objective of our study is to characterize gene expression signatures associated with in vivo artemisinin-resistance phenotype in this large-scale genome-wide association study. To achieve this goal, we employed microarray technology to establish the global gene expression profiles of isolates sampled from 1043 patients, of whom after treatment with ACTs (artemisinin combination therapy) displayed differential rates of parasite clearance.
2014-07-15 | GSE59098 | GEO
Project description:The objective of our study is to characterize gene expression signatures associated with in vivo artemisinin-resistance phenotype in this large-scale genome-wide association study. To achieve this goal, we employed microarray technology to establish the global gene expression profiles of isolates sampled from 1043 patients, of whom after treatment with ACTs (artemisinin combination therapy) displayed differential rates of parasite clearance. P. falciparum isolates were sampled from the whole blood of 1043 malaria-infected patients prior to ACT treatment. Sampling was done across 14 field sites spanning across South East Asia (Pailin, Pursat, Preah Vihear, Rattanakiri in Cambodia; Mae Sot, Srisakhet, Khun Han, Ranong in Thailand; Shwe Kyin in Myanmar; Binh Phuoc in Vietnam; Attapeu in Laos), to Bangladesh and African DR Congo from 2010 to 2012. RNA were extracted and synthesis and amplification of target DNA was carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211 (PMID 22990779), to generate sufficient material for hybridizations against a common RNA reference pool of 3D7 strain using a microarray platform.
2014-07-15 | E-GEOD-59097 | biostudies-arrayexpress
Project description:The objective of this study is to characterize gene expression signatures associated with in vivo artemisinin resistance phenotype and its transcriptional response to Artemisinin Combination Therapy (ACT) treatment . To achieve this goal, we employed microarray technology to establish the global gene expression profiles of isolates sampled from 680 patients prior to ACT treatment and 659 patients after the ACT treament.
2021-11-04 | GSE149735 | GEO
Project description:The objective of this study is to characterize gene expression signatures associated with in vivo artemisinin resistance phenotype and its transcriptional response to Artemisinin Combination Therapy (ACT) treatment . RNA-seq was applied to establish the global gene expression profiles for 196 and 180 isolates sampled from patients prior to and post to ACT treatment.
2022-02-07 | GSE169520 | GEO
Project description:Comaprision of P.falciparum clinical isolates showing Uncomplicated disease with that shwoing complicated disease(Cerebral malaria) The experiment was designed to try and identify differences if any, at the genome level between P.falciparum isolates from patients with uncomplicated malaria vs. patients with complicated malaria (Cerebral malaria). The emphasis was to highlight possible amplifications/deletions in different regions of the parasite genome.
2017-01-06 | GSE77165 | GEO
Project description:Artemisinin resistance in Plasmodium falciparum malaria has emerged in western Cambodia. This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimalarial treatment throughout the world. Using DNA microarrays we identify key features of a transcriptional profile that are associated with the delayed parasite clearance phenotype. These include reduced expression of several basic metabolic and cellular pathways in the early stages, and increased expression of essentially all functionalities associated with protein metabolism in the later stages of P. falciparum intraerythrocytic development. This is consistent with the reduced ring stage susceptibility that characterizes artemisinin resistant P. falciparum. This modulation of the P. falciparum intraerythrocytic transcriptome may result from differential expression of several regulatory proteins such as transcription factors of chromatin remodeling associated factors. In addition, the artemisinin resistant phenotype is strongly associated with a specific pattern of copy number variations, some of which are linked with differential expression of several regulatory proteins such as histone 4 and zinc permease. This study reports the first global transcriptional survey of artemisinin resistant parasites and provides a set of candidate genes for further investigation. 6 P. falciparum parasites (field isolates) which are either Artemsinin resistant or sensitive from 3 study sites (Pailin in Cambodia, Xepon in Laos, Mae Sot in Thailand) were sampled and harvested for genomic DNA. gDNA from a total of 6 samples were extracted by phenol chloroform. Synthesis of labelled target DNA was carried out as previously described: Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009), and used in comparative genomic microarray hybridizations (CGH).
2010-12-07 | E-GEOD-25879 | biostudies-arrayexpress
Project description:Artemisinin resistance in Plasmodium falciparum malaria has emerged in western Cambodia. This is a major threat to global plans to control and eliminate malaria as the artemisinins are a key component of antimalarial treatment throughout the world. Using DNA microarrays we identify key features of a transcriptional profile that are associated with the delayed parasite clearance phenotype. These include reduced expression of several basic metabolic and cellular pathways in the early stages, and increased expression of essentially all functionalities associated with protein metabolism in the later stages of P. falciparum intraerythrocytic development. This is consistent with the reduced ring stage susceptibility that characterizes artemisinin resistant P. falciparum. This modulation of the P. falciparum intraerythrocytic transcriptome may result from differential expression of several regulatory proteins such as transcription factors of chromatin remodeling associated factors. In addition, the artemisinin resistant phenotype is strongly associated with a specific pattern of copy number variations, some of which are linked with differential expression of several regulatory proteins such as histone 4 and zinc permease. This study reports the first global transcriptional survey of artemisinin resistant parasites and provides a set of candidate genes for further investigation. 11 P. falciparum parasites (field isolates) which are either Artemsinin resistant or sensitive from 3 study sites (Pailin in Cambodia, Xepon in Laos, Mae Sot in Thailand) were sampled, grown ex-vivo over 48 hours and harvested at regular intervals. RNA from a total of 91 samples were extracted. Synthesis of target DNA was carried out as previously described: Mackinnon, M.J. et al. Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 5, e1000644 (2009), and used in microarray hybridizations.
2010-12-07 | E-GEOD-25878 | biostudies-arrayexpress
Project description:The objective of this study is to characterize the gene expression signatures associated with in vivo artemisinin resistance phenotype and its transcriptional response to Artemisinin Combination Therapy (ACT) or Triple artemisinin combination therapy (TACT). Using stranded RNA-seq protocol expression profiles of Plasmodb annotated transcripts along with anti-sense, alternatively spliced and non-coding isoforms expressed in clinical isolates were generated for 310 pre-treated, 300 post-treated and 24 timepoints from the intra-erythrocyte development cycle.
2024-09-30 | GSE242548 | GEO
Project description:A testing association of parasite genotypes with clinical resistance phenotype. Submission of genotypes from all microarray genotyped samples Comparison of DNA from clinical isolates and generated by next-generation sequencing with prolonged clearance half-life
2014-05-28 | E-GEOD-56390 | biostudies-arrayexpress
Project description:Mechanisms regulating gene expression in malaria parasites are not well understood. Little is known about how this parasite regulates its gene expression during transition from one developmental stage to another and in response to various environmental conditions. Parasites in a diseased host face environments which differ from the static, well adapted in vitro conditions in culture. Parasites thus need to adapt quickly and effectively to these conditions by establishing transcriptional states which is best suited for better survival. With the discovery of natural antisense transcripts (NATs) in this parasite and considering the various proposed mechanisms by which NATs might regulate gene expression, it has been speculated that these might be playing a critical role in gene regulation. We report here the diversity of NATs that exist in this parasite, using isolates taken directly from patients with differing clinical symptoms caused by malaria infection. A total of 797 NATs targeted against annotated loci have been detected using a custom designed strand specific microarray. Out of these, 545 are unique to this study. The majority of NATs were positively correlated with the expression pattern of the sense transcript. Many were found to be differentially regulated in response to disease conditions. Antisense transcripts mapped to a wide variety of biochemical/ metabolic pathways, especially pathways pertaining to the central carbon metabolism and stress related pathways. Our data strongly suggests that a large group of NATs detected here are unannotated transcription units antisense to annotated gene models. The results reveal a previously unknown set of NATs that prevails in this parasite, their differential regulation in disease conditions and mapping to functionally well annotated genes. The results detailed here call for studies to deduce the possible mechanism of action, which would help in understanding the in vivo pathological adaptations of these parasites.
2014-04-30 | GSE44921 | GEO