Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum.
Ontology highlight
ABSTRACT:
ORGANISM(S): Plasmodium falciparum
SUBMITTER: Sachel Mok
PROVIDER: E-GEOD-44129 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Structural polymorphism in the promoter of pfmrp2 confers Plasmodium falciparum tolerance to quinoline drugs.
Mok Sachel S Liong Kek-Yee KY Lim Eng-How EH Huang Ximei X Zhu Lei L Preiser Peter Rainer PR Bozdech Zbynek Z
Molecular microbiology 20140123 5
Drug resistance in Plasmodium falciparum remains a challenge for the malaria eradication programmes around the world. With the emergence of artemisinin resistance, the efficacy of the partner drugs in the artemisinin combination therapies (ACT) that include quinoline-based drugs is becoming critical. So far only few resistance markers have been identified from which only two transmembrane transporters namely PfMDR1 (an ATP-binding cassette transporter) and PfCRT (a drug-metabolite transporter) h ...[more]
Similar Datasets
Project description:Drug resistance in Plasmodium falciparum remains a challenge for the malaria eradication programs around the world. With the emergence of artemisinin resistance, the efficacy of the partner drugs in the artemisinin combination therapies (ACT) that include quinoline based drugs is becoming critical. So far only few resistance markers have been identified and verified from which only two ABC transmembrane transporters namely PfMDR1 and PfCRT have been experimentally verified. Another P. falciparum ABC transporter, the multidrug resistance-associated protein (PfMRP2) represents an additional possible factor of drug resistance in P. falciparum. In this study, we identify a parasite clone that is derived from the 3D7 P. falciparum strain and which shows increased resistance to chloroquine and mefloquine through the trophozoite and schizont stages. We demonstrate that the resistance phenotype is caused by a 4.1 kb deletion in the 5M-bM-^@M-^Y upstream region of the pfmrp2 gene that leads to an alteration in the pfmrp2 transcription that result in increased levels of PfMRP2 protein. These results also suggest the importance of putative promoter elements in regulation of gene expression during the P. falciparum intra-erythrocytic developmental cycle and the potential of such genetic polymorphisms to underlie drug resistance phenotypes. Presented here are the data from microarray-based genome-wide transcriptomic and genomic studies of the drug-sensitive and drug-resistant 3D7 clones 11C/wt and 6A/mut. 2 P. falciparum lab clones derived from 3D7 strain were harvested during the intra-erythrocytic cycle at 8hr intervals over 48 hours to obtain a total of 6 time point samples per clone. RNA from a total of 12 samples were extracted. Synthesis 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 and used in replicate microarray hybridizations against a common RNA reference pool of 3D7 strain.
2013-02-07 | E-GEOD-44127 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-06-01 | E-GEOD-72580 | biostudies-arrayexpress
Project description:The goal of our study is to characterize the global transcriptional resposne of P.falciparum to DNA damageing agents. Alongside, we stidied the epigenetic regulation of DNA damage resposne in parasite. Further, we studied the mecanism which underlined the ARMD (mutator) phenotype of P. falciparum. In order to elucidate the transcriptiona resposne to DNA damage, P. falciparum 3D7 parasites were treated with 4 perturbating agents for 6 hours. We mapped the global nucleosome occupancy for 3 most responsive histone modifications to DNA damage by chromatin immunoprecipitation coupled with DNA microarray (ChIP-on-chip). In order to identify the transcriptional similarities between artemesinin and MMS, we carried out 6 hours of artemesinin treatment in triplicates and compared with triplicate dataset of MMS.
2016-06-01 | E-GEOD-72579 | biostudies-arrayexpress
Project description:The goal of our study is to characterize the global transcriptional resposne of P.falciparum to DNA damageing agents. Alongside, we stidied the epigenetic regulation of DNA damage resposne in parasite. Further, we studied the mecanism which underlined the ARMD (mutator) phenotype of P. falciparum. In order to elucidate the transcriptiona resposne to DNA damage, P. falciparum 3D7 parasites were treated with 4 perturbating agents for 6 hours. We mapped the global nucleosome occupancy for 3 most responsive histone modifications to DNA damage by chromatin immunoprecipitation coupled with DNA microarray (ChIP-on-chip). In order to identify the transcriptional similarities between artemesinin and MMS, we carried out 6 hours of artemesinin treatment in triplicates and compared with triplicate dataset of MMS.
2016-06-01 | E-GEOD-72578 | biostudies-arrayexpress
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:Drug resistance in Plasmodium falciparum remains a challenge for the malaria eradication programs around the world. With the emergence of artemisinin resistance, the efficacy of the partner drugs in the artemisinin combination therapies (ACT) that include quinoline based drugs is becoming critical. So far only few resistance markers have been identified and verified from which only two ABC transmembrane transporters namely PfMDR1 and PfCRT have been experimentally verified. Another P. falciparum ABC transporter, the multidrug resistance-associated protein (PfMRP2) represents an additional possible factor of drug resistance in P. falciparum. In this study, we identify a parasite clone that is derived from the 3D7 P. falciparum strain and which shows increased resistance to chloroquine and mefloquine through the trophozoite and schizont stages. We demonstrate that the resistance phenotype is caused by a 4.1 kb deletion in the 5M-bM-^@M-^Y upstream region of the pfmrp2 gene that leads to an alteration in the pfmrp2 transcription that result in increased levels of PfMRP2 protein. These results also suggest the importance of putative promoter elements in regulation of gene expression during the P. falciparum intra-erythrocytic developmental cycle and the potential of such genetic polymorphisms to underlie drug resistance phenotypes. Presented here are the data from microarray-based genome-wide transcriptomic and genomic studies of the drug-sensitive and drug-resistant 3D7 clones 11C/wt and 6A/mut. 2 P. falciparum lab clones derived from 3D7 strain were harvested during the intra-erythrocytic cycle for genomic DNA. gDNA were extracted by phenol chloroform. Synthesis of labelled target DNA was carried out as previously described: Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu & J. L. DeRisi, (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1: E5, and used in comparative genomic microarray hybridizations (CGH).
2013-02-07 | E-GEOD-44128 | biostudies-arrayexpress
Project description:The purpose of this reasearch is to identify and evaluate the global gene expression of Plasmodium knowlesi blood-stage parasites and specifically compare the gene expression profiles of samples derived from ex vivo versus long-term in vitro cultures. For ex vivo samples, a rhesus monkey was infected with P. knowlesi to obtain ring iRBCs to establish a short-term culture to immediately collect ex vivo derived time points every 4 hours in the course of the parasite’s 24-hour life cycle. For in vivo samples, they were generated from the same clone in the ex vivo culture adapted to long-term in vitro culture and were collected every 4 hours in the course of the parasite's 24-hour life cycle. Two replicate experiments(Aa and Ha) were developed from in vitro cultures. Samples labeled with Cy5 were hybridized against a reference RNA pool labeled with Cy3, consisting of equal amounts of P. knowlesi RNA from each time point.
2015-06-08 | E-GEOD-62886 | biostudies-arrayexpress
Project description:Quantitative studies of the P. falciparum transcriptome have shown that the tightly controlled progression of the parasite through the intraerythrocytic developmental cycle (IDC) is accompanied by a continuous gene expression cascade where most expressed genes exhibit a single transcriptional peak. Since proteins represent the decisive business end of gene expression, understanding the correlation between mRNA and protein levels is crucial for inferring biological activity from transcriptional gene expression data. While pertinent studies on other organisms show that as little as 20-40% of protein abundance variation may be attributable to corresponding mRNA levels, the situation in Plasmodium is further complicated by the dynamic nature of the cyclic gene expression cascade where the mRNA levels of most genes change constantly during the IDC. In this study, we simultaneously determined mRNA and protein abundance profiles for P. falciparum parasites during the IDC at 2-hour resolution based on spotted oligonucleotide microarrays and 2D-protein gels in combination with DIGE fluorescent dyes. Intriguingly, most proteins are represented by more than one isoform, presumably due to post-translational modifications. Analysis of 366 protein abundance profiles and the corresponding mRNA levels shows that in 67.2% of cases the protein abundance peaks at least 8 hours after the mRNA level peak. While it may be tempting to interpret this as evidence for widespread post-transcriptional gene regulation additional analyses including computer modeling demonstrate that in >60% of these cases the observed protein profiles including the peak lag times could arise as a consequence of the corresponding mRNA levels when simple translation and degradation dynamics are assumed. We further characterize and illustrate these dynamics and show that even human host proteins within the parasite may be subject to similar dynamics as their parasite counterparts. 24 timepoint samples were harvested from a tightly synchronous 6.5 liter biofermenter culture of P. falciparum (Dd2) at 2-hour intervals during one entire intraerythrocytic developmental cycle and compared against a 3D7 RNA reference pool.
2011-06-07 | E-GEOD-24416 | biostudies-arrayexpress
Project description:In order to study the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC), we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using chromatin-immunoprecipitation coupled to microarray (ChIP-on-chip). Genome-wide distribution of 13 histone modifications for 6 h time points of the 48 h P. falciparum IDC was done using ChIP-on-chip and compared to corresponding transcriptional profiles across the genome
2013-03-02 | E-GEOD-39238 | biostudies-arrayexpress
Project description:We described the biological role of a putative zinc finger protein (Plasmodb id: PF3D7_1008600), which plays an important role during the initiation and subsequent progression of gametocytogenesis in P. falciparum. Hence we termed the protein P. falciparum Zinc Finger Protein for Gametocytogenesis (PfZnFP-G). During the asexual intraerythrocyic developmental cycle (IDC), PfZnFP-G levels peak during the schizont stage during which it is localized in the nucleus. During the IDC, PfZnFP-G appears to be stochastically expressed in ~3% parasite population. Deactivation of PfZnFP-G appears to suppress, but not fully inhibit, production of gametocytes and vice versa overproduction of PfZnFP-G stimulates gametocytogenesis. In addition, PfZnFP-G is capable of associating with DNA binding preferentially to intergenic, promoter regions of the genome, and this binding correlates positively with transcription, particularly of other gametocyte specific genes. PfZnFP-G is also expressed in the mid-to-late gametocytes where it is present in the cytoplasm. Overall, these results suggest a dual function of PfZnFP-G in gametocytogenesis including: (i) commitment as a transcription factor and (ii) gametocyte maturation as a putative RNA binding protein. Transgenic 3D7 wild type parasite lines were generated with PfZnFP-G tagged, over-expressed and knocked-out. Transcriptional profiles across the parasite life cycle were generated. Genome occupancy of PfZnFP-G were also investigated and compared to the corresponding transcriptional profiles.
2015-11-24 | E-GEOD-75295 | biostudies-arrayexpress