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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1

ABSTRACT: The near-normalization of constitutive cytokine and matrix release following rescue by HPS1 transduction of HPM cells suggests that HPS-1 HuMCs may contribute to pulmonary fibrosis and constitute a target for therapeutic intervention. Microarray analysis of HPS-1 HuMCs and non-transduced HPM cells confirmed upregulation of differentially expressed genes involved in fibrogenesis and degranulation. Six HPS-1 patients and five healthy controls were studied following informed consent. One typical HPS-1 HuMC culture at 5-6 weeks was eventually overgrown by a population of smaller, rapidly dividing cells. Analysis of differential gene expression from 8 wk old control and HPS-1 HuMCs and HPM cells was performed using cDNA generated from cultured cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Arnold Kirshenbaum

PROVIDER: E-GEOD-83920 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1

Project description:The near-normalization of constitutive cytokine and matrix release following rescue by HPS1 transduction of HPM cells suggests that HPS-1 HuMCs may contribute to pulmonary fibrosis and constitute a target for therapeutic intervention. Microarray analysis of HPS-1 HuMCs and non-transduced HPM cells confirmed upregulation of differentially expressed genes involved in fibrogenesis and degranulation.

2016-07-01 | GSE83920 | GEO

The effects of herb-partitioned moxibustion on miRNA expression profiling in the colons of CD rats

Project description:Using the highly sensitive miRNA microarray, we screened differentially-expressed miRNAs in colons of normal control (NC) rats, model control (MC) rats and herb-partitioned moxibustion (HPM) rats. We found 40 miRNAs differentially expressed in CD rats’ colons compared with the NC rats, and HPM significantly regulated 26 miRNAs in colon tissues compared with the MC group. Furthermore, the quantitative real-time polymerase chain reaction results showed that down-regulated miR-147 and miR-205 in CD rats’ colons were both significantly up-regulated by HPM, with 2.64- and 3.72-folds increased respectively, indicating that miR-147 and miR-205 are the target genes of HPM in treating CD rats. In the study presented here, four samples from each group were used to screen the differentially-expressed miRNAs in colons of experimental CD rats and the target genes of HPM. Six colons from each group were further used to verify the target genes of HPM. Finally, miR-147 and miR-205 were experimentally validated to be target genes of HPM.

2015-01-31 | E-GEOD-65490 | biostudies-arrayexpress

DNA elimination analysis of scnRNA production-defective Tetrahymena

Project description:Analysis of genome-wide IES elimination of Late-scnRNA accumulation-defective cells inducates that Early-scnRNAs are sufficient to induce DNA elimination for a majority of IESs, whereas Late-scnRNAs are important for DNA elimination of some, mainly Type-B, IESs. new MACs of exconjugants were isolated from different mutants at 36 hpm, and the genomic DNA was analyzed by high-throughput sequencing

2015-06-15 | E-GEOD-68457 | biostudies-arrayexpress

The effects of herb-partitioned moxibustion on miRNA expression profiling in the colons of CD rats

2015-01-31 | GSE65490 | GEO

Porcine spleen_Haemophilus Parasuis infected_7days

Project description:Haemophilus parasuis(HPS) is a prominent swine pathogen that causes GlM-CM-$sser's disease characterized by fibrinous polyserositis, meningitis and arthritis; however, the molecular mechanisms underlying disease pathogenesis remains poorly understood, particularly the host counteraction to HPS invasion by the immune system. Here, we investigated the global expression changes in spleen following HPS infection using the Affymetrix Porcine Genechip.Our findings indicate previously unrecognized gene transcription changes in case of HPS infection in vivo and many presumed cascades in the study are clearly merit further investigation. Our data should provide new clues for immune response in mammals and identification of candidate genes related to HPS resistance. All animal tissue collection procedures were performed according to protocols approved by The Hubei Province, PR China for Biological Studies Animal Care and Use Committee. Piglets at 30 days old were determined to be HPS-free by serum indirect haemagglutination test before artificial bacterial challenges. Each piglet was intratracheally challenged with 5M-CM-^W108 colony-forming units (CFU) per millilitre of HPS strain 0165 (serotype 5) . A total of 5 piglets were challenged, and 5 pigs were used as controls. These two groups were raised in isolated facilities. Six microarrays were used in the experiment, corresponding to the RNAs from spleen tissues of three most severe piglets with fibrinous polyserositis, meningitis and arthritis after HPS infection and three controls.

2009-03-26 | E-GEOD-11787 | biostudies-arrayexpress

DNA elimination analysis of Tetrahymena cells defective in heterochromatin body formation

Project description:In the ciliated protozoan Tetrahymena, de novo heterochromatin body formation is accompanied by programmed DNA elimination. Here, we show that the novel heterochromatin body component Jub1p promotes heterochromatin body formation and dephosphorylation of the Heterochromatin Protein 1 (HP1)-like protein Pdd1p. Through the identification and mutagenesis of the phosphorylated residues of Pdd1p, we demonstrate that Pdd1p dephosphorylation promotes the electrostatic interaction between Pdd1p and RNA in vitro and heterochromatin body formation in vivo. We therefore suggest that heterochromatin bodies are assembled by the Pdd1p-RNA interaction. Jub1p and Pdd1p dephosphorylation are required for heterochromatin body formation and DNA elimination but not for local heterochromatin assembly, indicating that heterochromatin body of itself plays an essential role in DNA elimination. Micronuclei (MICs) and new macronuclei (MACs) of exconjugants were isolated from different mutants at 36 hpm, and the genomic DNA was analyzed by high-throughput sequencing.

2015-12-10 | E-GEOD-70082 | biostudies-arrayexpress

Porcine spleen_Haemophilus Parasuis infected_7days

Project description:Haemophilus parasuis(HPS) is a prominent swine pathogen that causes Glässer's disease characterized by fibrinous polyserositis, meningitis and arthritis; however, the molecular mechanisms underlying disease pathogenesis remains poorly understood, particularly the host counteraction to HPS invasion by the immune system. Here, we investigated the global expression changes in spleen following HPS infection using the Affymetrix Porcine Genechip.Our findings indicate previously unrecognized gene transcription changes in case of HPS infection in vivo and many presumed cascades in the study are clearly merit further investigation. Our data should provide new clues for immune response in mammals and identification of candidate genes related to HPS resistance.

2009-03-26 | GSE11787 | GEO

Analysis of Early-scnRNAs of Tetrahymena

Project description:scnRNAs co-IPed with Twi1p from wild-type cells @3 hpm

2016-04-02 | GSE79849 | GEO

EPIC-HPS

Project description:EPIC-HPS

| PRJNA684138 | ENA

Widespread monoallelic methylation of colorectal cancer associated tumour suppressor genes, including multiple Wnt pathway inhibitors, in Hyperplastic Polyposis Syndrome.

Project description:Hyperplastic Polyposis Syndrome (HPS) is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC). The majority of CRCs arising in HPS show a CpG island methylator phenotype (CIMP) that encompasses several common tumor suppressor genes, including regulators of DNA mismatch repair, and negative regulators of Wnt signaling. However, little is currently known about the CIMP status of premalignant polyp tissue in HPS or the temporal changes in CIMP profile associated with transition to malignancy. Using genomescale DNA methylation analysis of HPS polyp and disease-free tissue, we identified widespread coordinated DNA methylation changes, common to all HPS polyps examined. The majority of consistent changes involve low-intermediate (10-50%) methylation and include several tumour suppressor genes, including multiple negative regulators of Wnt signalling (SFRP-1, -2, -4, -5) and cell cycle regulation (eg. RASSF1). We also confirmed selective methylation of the RUNX1, CHFR, CDKN2A, and MLH-1 promoters previously described in HPS, but found no evidence for methylation of DNA mismatch repair genes MGMT or MSH-2 in premalignant polyps. Consistent and widespread methylation of the WT-1 tumour suppressor gene also appears to be a common feature of HPS. Interestingly, where tested the majority of methylation identified was localised to a single allele within the polyp tissue. These findings reveal that premalignant HPS is associated with coordinated, widespread intermediate levels of gene promoter methylation in several TS genes implicated in CRC, primarily restricted to one of two alleles. Transition to malignancy appears to be associated with widespread elevation of methylation at these sites. These findings warrant a further investigation of the potential for future development of novel methylation-based molecular assays for the prediction of HPS cases likely to transition to malignancy.

2014-12-01 | GSE34068 | GEO

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