Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA sequencing of two protein phosphatases(ppm2 and ppm5) knockouts in Plasmodium berghei to study their role in the parasite's sexual development

ABSTRACT: To identify protein phosphatases (PP) that are essential during asexual blood stage development in Plasmodium berghei, we attempted systematic deletion of the 30 P. berghei PP genes using double homologous recombination. Of these, we performed strand-specific RNA-sequencing (RNA-Seq) analysis for 2 myristoylated PP mutants _ppm2 and _ppm5 lines across relevant lifestages ( activated gametocyte and schizont stages in both _ppm2 and _ppm5 and ookinete stage in _ppm5 alone). Two to four biological replicates each for _ppm2, _ppm5 and wild-type parasites were processed into strand-specific RNA-seq libraries and sequenced in Illumina Hiseq platform using 100-bp paired end chemistry.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Plasmodium berghei

SUBMITTER: Abhinay Ramaprasad

PROVIDER: E-MTAB-2215 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Analysis of transcriptional response to Plasmodium berghei ANKA infection in cerebral malaria susceptible C57BL/6 mouse brains as well as cerebral malaria resistant BXH2 mice which carry a severe hypomorphic Irf8-R294C allele. Interferon Regulatory Factor 8 (IRF8) is required for development, maturation and expression of anti-microbial defenses of myeloid cells. BXH2 mice harbor a loss-of-function allele at Irf8 (Irf8-R294C) that causes susceptibility to infection with intracellular pathogens, including Mycobacterium tuberculosis. We report that XH2 are completely resistant to the development of cerebral malaria following Plasmodium berghei ANKA infection. Comparative transcriptional profiling of brain RNA as well as chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) was used to identify IRF8-regulated genes whose expression is associated with pathological acute neuroinflammation. Genes up-regulated by infection were strongly enriched for IRF8 binding sites, suggesting that IRF8 acts as a transcriptional activator in inflammatory programs. These lists were enriched for myeloid-specific pathways, including interferon responses, antigen presentation and Th1 polarizing cytokines. We show that inactivation of several of these downstream target genes confers protection against experimental cerebral malaria. We also report strong overlap between genes bound and regulated by IRF8 during cerebral malaria and genes regulated in the lungs of M. tuberculosis infected mice. This IRF8-dependent network contains several genes recently identified as risk factors in acute and chronic human inflammatory conditions. In summary, this work defines a common core of IRF8-bound genes forming a critical inflammatory host-response network. Comparison of whole brain transcript profiles for wildype C57BL/6 mice versus severely hypomorphic Irf8-R294C BXH2 mice following experimental infection with Plasmodium berghei ANKA (d7). Baseline (d0) profiles are also compared. Pleaes note that each sample record represents 2-4 replicates and sample data table contains mean, standard error of the mean (SEM), and quality for the replicates. The non_normalized data matrix contains raw data for each replicate (total 12 samples).

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RNA sequencing of two protein phosphatases(ppm2 and ppm5) knockouts in Plasmodium berghei to study their role in the parasite's sexual development

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