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Expression data from peripheral blood from healthy and predisposed individuals

ABSTRACT: Characterization of the underlying genetic defects in patients with a rare and peculiar phenotype is challenging. Here we have utilized whole genome expression profiling, and identified a homozygous germline mutation in the DDB2 gene in a patient with several facial tumors. The feasibility of using blood derived RNA, diminishing costs of the technology, and the limited number of samples needed provide this approach a powerful new tool that may substantially aid in such gene identification efforts. Keywords: disease vs control

ORGANISM(S): Homo sapiens

PROVIDER: GSE6351 | GEO | 2007/10/30

SECONDARY ACCESSION(S): PRJNA99621

REPOSITORIES: GEO

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Transcription profiling of human peripheral blood from healthy and predisposed individuals reveals a homozygouse germline mutation in the DDB2 gene in a patient with severe facial tumors

Project description:Characterization of the underlying genetic defects in patients with a rare and peculiar phenotype is challenging. Here we have utilized whole genome expression profiling, and identified a homozygous germline mutation in the DDB2 gene in a patient with several facial tumors. The feasibility of using blood derived RNA, diminishing costs of the technology, and the limited number of samples needed provide this approach a powerful new tool that may substantially aid in such gene identification efforts. Experiment Overall Design: RNA from patientâs and his parentsâ blood samples, as well as from twelve individuals available from other projects, were subjected to Human GeneChip U133 Plus 2.0 whole genome expression arrays (Affymetrix).

2008-06-14 | E-GEOD-6351 | biostudies-arrayexpress

Pancreatic Steatosis Associates With Impaired Insulin Secretion in Genetically Predisposed Individuals.

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Passage of transmissible cancers in the Tasmanian devil is due to a dominant, shared peptide motif and a limited repertoire of MHC-I allotypes

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DDB2 regulates gene expression in ovarian cancer cell lines

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DDB2 regulates gene expression in ovarian cancer cell lines

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METTL14 facilitates global genome repair and suppresses skin tumorigenesis

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Project description:Biofuel production from lignocellulosic waste and residues is a promising option to mitigate the environmental costs associated to energy production. However, the difficulty to cost-effectively overcome lignocellulose recalcitrance hampers a widespread application of such bioprocesses. Through an integrated approach, we focused on the factors affecting cellulose reactivity and their impact on downstream fermentation. Three cellulosic manufactured materials were characterized in details: facial tissue, Whatman paper, cotton pads. The model mesophilic cellulolytic bacterium Clostridium cellulolyticum was used to study colonization and metabolic patterns during fermentation of these materials. Facial tissue was extensively colonized and exhibited the fastest degradation and the highest ethanol-to-acetate ratio. Comparing facial tissue fermentation to Whatman paper fermentation by label-free quantitative shotgun proteomics and statistical analyses, 187 proteins showed a different behavior; higher concentration levels were detected for many enzymes from the carbohydrate central metabolic pathway; distinct patterns of expression levels were observed for carbohydratases degrading cellulose and hemicellulose. Overall, lower degrees of polymerization, lower crystallinity index, and the presence of hemicelluloses could explain the higher biological reactivity and bioethanol production yields.

2017-01-30 | PXD001051 | Pride

Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis [small RNA-seq]

Project description:We report the small RNA analysis of Arabidopsis plants deficient for the expression DDB2 involved in global genome repair using small RNA sequencing. In addition we performed RNA immunoprecipitation (RIP) of DDB2.

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Project description:The therapeutical efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the underlying molecular causes for this tumor specificity are not clear. Hence, stratification of patients based on DNA repair profiling is not sufficiently utilized for treatment selection. Using a combination of genetic, transcriptomic and imaging approaches, we identified factors that promote global genome nucleotide excision repair (GG-NER) of DNA-platinum adducts induced by oxaliplatin, but not by cisplatin. We show that oxaliplatin-DNA lesions are a poor substrate for GG-NER initiating factor XPC and that DDB2 and HMGA2 are required for efficient binding of XPC to oxaliplatin lesions and subsequent GG-NER initiation. Loss of DDB2 and HMGA2 therefore leads to hypersensitivity to oxaliplatin but not to cisplatin. As a result, low DDB2 levels in different colon cancer cells are associated with GG-NER deficiency and oxaliplatin hypersensitivity. Finally, we show that colon cancer patients with low DDB2 levels have a better prognosis after oxaliplatin treatment than patients with high DDB2 expression. We therefore propose that DDB2 is a promising predictive marker of oxaliplatin treatment efficiency in colon cancer.

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