Comparative characterization of microRNA profiles of different genotypes of Toxoplasma gondii
Ontology highlight
ABSTRACT:
ORGANISM(S): Toxoplasma gondii
SUBMITTER: Min-jun Xu
PROVIDER: E-GEOD-45007 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Comparative characterization of microRNA profiles of different genotypes of Toxoplasma gondii.
Xu M J MJ Zhou D H DH Huang S Y SY Zhao F R FR Nisbet A J AJ Lin R Q RQ Song H Q HQ Zhu X Q XQ
Parasitology 20130529 9
The present study compared the miRNA expression profiles of five Toxoplasma gondii strains, namely RH (Type I, ToxoDB10), TgXD (Type I, ToxoDB10), PRU (Type II, ToxoDB1), QHO (Type II, ToxoDB1) and TgC7 (ToxoDB9), by Solexa deep sequencing, bioinformatics analysis and real-time quantitative PCR. A total of 7, 15, 10, 12 and 10 miRNAs were found from RH, TgXD, PRU, QHO and TgC7 strains, respectively. Thirteen miRNAs were shared by three genotypes, with only one miRNA shared by all of the 5 strain ...[more]
Similar Datasets
Project description:Transcriptome analysis of peritoneal lavage of mice infected with T. gondii Toxoplasma gondii is the causative agent of toxoplasmosis in human and animals. In mouse model, T. gondii strains can be divided into three groups, including the virulent, intermediately virulent and non-virulent. The clonal Type I, II and III T. gondii strains belong to these three groups respectively. To better understand the basis of virulence phenotypes, we investigated mouse gene expression responses to the infection of different T. gondii strains at day 5 post intraperitoneal inoculation with 500 tachyzoites. The transcriptomes of mouse peritoneal cells showed that 1927, 1573, and 1009 transcripts were altered more than 2 fold by Type I, II and III infections, respectively, and majority of altered transcripts were shared. Overall transcription patterns were similar in Type I and Type II infections and both had greater changes than that of Type III. Quantification of parasite burden in mouse spleens showed that Type I was 1000 times higher than Type II, and Type II was 20 times higher than Type III. Fluorescence activated cell sorting revealed that Type I and II infections had comparable macrophage populations and both were higher than Type III infection. In addition, Type I infection had higher percentage of neutrophils than that of Type II and III. Taken together, these results suggested that there is a common gene expression response to T. gondii infection in mice. This response is further modified by parasite strain specific factors that determine their distinct virulence phenotypes. We analyzed mRNA from female CD1 outbred mice, 6-8 weeks old infected with Type I, II and III T. gondii strains. We used the Affymetrix Mouse Gene 1.0 ST platform. Raw array data was processed by Partek® Genomics SuiteTM software. Three replicates were performed for Type I-GT1 and Type III-CTG and two replicates for Type II- PTG.
2011-12-22 | E-GEOD-34416 | biostudies-arrayexpress
Project description:Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing, bioinformatic predictions with stem-loop real-time PCR analysis. Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belong to 284 families. There is strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil is the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and the end of conserved miRNAs. There is no significant M-bM-^@M-^\seed regionM-bM-^@M-^] at the first and ninth positions commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis are still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There are two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping a stringent conserved seed region with high active innovation in other place of miRNA mainly in the middle and the end, which are perfect for the parasite to perform its complex life style and for host changes. The present study represents the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as the miRNA studies of other related species such as Opisthorchis felineus and O. viverrini of human and animal health significance. Analysis of miRNA profile in parasite of C. sinensis
2010-09-03 | E-GEOD-22244 | biostudies-arrayexpress
Project description:Background: The identification of new high sensitivity and specificity markers for HCC are essential. We aimed to identify serum microRNAs for diagnosing hepatitis B virus (HBV) â??related HCC. Methods: Serum microRNA expression was investigated with four cohorts including 667 participants (261 HCC patients ,233 cirrhosi patients and 173 healthy controls), recruited between August 2010 and June 2013. First, An initial screening of miRNA expression by Illumina sequencing was performed using serum samples pooled from HCC patients and controls,respectively. Quantitative reverse-transcriptase polymerase chain reaction assay was then applied to evaluate the expression of selected microRNAs. A logistic regression model was constructed using a training cohort (n=357) and then validated using a cohort(n=241). The area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. Results: , We identified 8 miRNAs(hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p and hsa-miR-26a-5p.) formed a miRNA panel that provided a high diagnostic accuracy of HCC (AUC=0.887 and 0.879 for training and validation data set, respectively). The microRNA panel can also differentiate HCC from healthy (AUC =0.894) and cirrhosis (AUC = 0.892), respectively. Conclusions:We found a serum microRNAs panel that has considerable clinical value in diagnosing HCC. 9 serum samples pooled from 3 healthy control donors and 3 HCC patients, 3 cirrhosi patients treated at The First Affiliated Hospital of Soochow University were subjected to Illumina HiSeq 2000 deep sequencing to identify the miRNAs that were significantly differentially expressed.
2015-12-20 | E-GEOD-59418 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.
2016-06-01 | E-GEOD-72417 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE11437: Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array GSE11514: Expression QTL mapping of Toxoplasma gondii genes, Tachyzoite array Keywords: SuperSeries Refer to individual Series
2008-05-22 | E-GEOD-11515 | biostudies-arrayexpress
Project description:Toxoplasma gondii, a representative model organism of the phylum Apicomplexa, can infect almost all warm-blooded organisms including humans. Invasion of host cells in a host–parasite interaction is the key step necessary for T. gondii to complete its life cycle. Here, we investigate global proteomic changes based on TMT analysis in both the host cells (human foreskin fibroblasts, HFFs) and T. gondii during intracellular infection. A total of 3477 and 1434 proteins were quantified, of which 378 and 1100 proteins were differentially expressed (p-value<0.05 and ≥1.5-fold change)in Homo sapiens and T. gondii proteins, respectively. In HFF cells, Gene Ontology (GO) and KEGG pathway analyses revealed a large number of differentially expressed proteins (DEPs) enriched in metabolic processes and immune-associated signaling pathways, such as NF-κB, cAMP, and Rap1 signaling pathways. T. gondii DEPs involved in pathway analysis and GO annotations included cellular protein metabolic process, peptide metabolic process, and peptide biosynthetic processes and indicated that cell biosynthesis and metabolism were increased during T. gondii infection. These findings reveal new proteomic differences in the parasite–host interaction during T. gondii infection.
2021-05-10 | PXD021736 | Pride
Project description:The population structure of Toxoplasma gondii includes three highly prevalent clonal lineages, types I, II, and III, which differ greatly in virulence in the mouse model. Previous studies have implicated a family of serine threonine protein kinases found in rhoptries (ROPs) as important in mediating virulence differences between types I vs. III and II vs. III. Here, we explored the genetic basis of differences in virulence between the highly virulent type I lineage and moderately virulent type II based on a new genetic cross and linkage mapping. Genome-wide association revealed a single quantitative trait locus controls the > 4 log difference in lethality between these strains. Neither ROP16 nor ROP18, previously implicated in virulence differences in T. gondii, were found to contribute to differences between types I and II. Instead, the major virulence locus contained a cluster of pseudokinases denoted as rhoptry protein 5 (ROP5); this locus contains a tandem cluster of polymorphic alleles that differed in expression levels between strains. ROP5 alleles contained only part of the catalytic triad of canonical S/T kinases, and consistent with this they lack demonstrable kinase activity in vitro. Genetic disruption of the rop5 locus in the type I lineage lead to a > 5 log increase in the lethal dose, and surviving mice developed lasting immunity and were protected from an otherwise lethal challenge. These findings reveal that amplification of a polymorphic cluster of pseudokinases plays an important role in pathogenesis of toxoplasmosis in the mouse model. We used a new genotyping protocol based on hybridization of parental and recombinant progeny genomic DNA (gDNA) to Affymetrix gene arrays constructed for T. gondii (http://ancillary.toxodb.org/docs/Array-Tutorial.html). We identified 1,603 single feature polymorphisms (SFP) based on probes that successfully discriminated perfect match (type II) from mismatch (type I) hybridization across all clones and provided reliable SFP markers for this cross.
2011-05-03 | E-GEOD-24905 | biostudies-arrayexpress
Project description:Toxoplasma gondii pathogenesis includes the invasion of host cells by extracellular parasites (tachyzoites), replication of intracellular tachyzoites, and differentiation to a latent bradyzoite stage. Whole genome expression profiling was carried out using the newly developed Affymetrix ToxoGeneChip (GeneChip Tgondiia520372) in order to analyze the ~8,000 predicted genes in the T. gondii genome of mutants and wild-type, allowing for full-scale expression profiling during bradyzoite differentiation in vitro. RNA from mutant and wild-type parasites was extracted and hybridized to the ToxoGeneChip. We harvested extracellular tachyzoites from freshly lysed fibroblasts (ET, 0h), intracellular tachyzoites (IT, 24h post-invasion) and parasites subjected to bradyzoite growth conditions for 72h (B72, 72h of induction). Extracellular parasites from freshly lysed fibroblasts were harvested for the seven mutant parasite lines (12K, 13P, B7, 11P, 11K, 7K and P11) and mutant parasites subjected to bradyzoite differentiation conditions for 72h. For a few samples we also harvested parasites 11h post egress of host cells. A time course was carried out with wild-type: parasites subjected to bradyzoite growth conditions for 24h, 36h and 48h.
2010-07-27 | E-GEOD-23174 | biostudies-arrayexpress
Project description:MS/MS dataset for proteogenomics study of Toxoplasma gondii. The dataset was searched against the official v9 gene model from ToxoDB, and the alternate panels of proteins predicted from RNA-SEQ evidences.
2015-02-09 | PXD000297 | Pride
Project description:A Toxoplasma gondii infection during pregnancy can result in spontaneous abortion, preterm labor, or congenital fetal defects. The decidual immune system plays a critical role in regulating the immune micro-environment and in the induction of immune tolerance. To better understand the factors that mediate the decidual immune response associated with the T. gondii infection, a large-scale study employing TMT proteomics was conducted to characterize the differential decidual immune proteomes from infected and uninfected human decidual immune cells samples. The decidual immune cells from 105 human voluntary abortion tissues were purified, and of the 5510 unique proteins identified, 181 proteins were found to be differentially abundant (>1.2-fold cutoff, P＜0.05) in the T. gondii-infected decidual immune cells. 11 proteins of 181 differentially expressed proteins associated with trophoblast invasion, placental development, intrauterine fetal growth, and immune tolerance were verified using a quantitative real-time polymerase chain reaction and western blotting. This systematic research identified a broad range of immune factors in human decidual immune cells, shedding a new insight into the decidual immune molecular mechanism for abnormal pregnancy outcomes associated with T. gondii infection.
2018-07-27 | PXD008448 | Pride