EGAS00001000387-sc-20131009 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001000670 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:A potential and very serious side effect of treating IBD with antiTNFa therapies (the current
gold standard) is the development of systemic lupus erythematosis (SLE). This side effect is
rare and unpredictable. Out of several thousand cases having received treatment, the
University of Calgary have accumulated 12 individuals with full phenotyping and novel
serological antibody discovery panel data. We propose to exome sequence these samples in
an effort to identify rare highly-penetrant variants that could be underlying this severe
phenotype.
| EGAS00001000387 | EGA
Project description:AAmiodarone is an antiarrhythmic drug and representatively induce pulmonary phospholipidosis. Amiodarone-induced toxicity has been a serious unpredictable side effect of the treatment and an important clinical problem. Possible causes include allergic, cytotoxic or immunologic reactions to this agent. We examined the consequences of the mechanism of amiodarone-induced pulmonary toxicity gene expression in BEAS-2B cells, huma bronchial cell line, by microarray. The expression of these genes are potential biomarker of amiodarone-induced pulmonary toxicity. Also, We provide a clue about mechanism of pulmonary toxic action by these clinical chemotherapeutic agents.
2011-01-10 | GSE20582 | GEO
Project description:Methotrexate (MTX) has been widely used for the treatment of a variety of tumors as well as for inflammatory diseases and rheumatoid arthritis (RA). MTX-induced toxicity has been a serious unpredictable side effect of the treatment and an important clinical problem. Possible causes include allergic, cytotoxic or immunologic reactions to this agent. We examined the consequences of the mechanism of MTX-induced pulmonary toxicity gene expression in BEAS-2B cells, huma bronchial cell line, by microarray. The expression of these genes are potential biomarker of methotrexate-induced pulmonary toxicity. Also, We provide a clue about mechanism of pulmonary toxic action by these clinical chemotherapeutic agents. Keywords: 48h treatment, 0.144uM (dose), MTX
2008-12-06 | GSE9815 | GEO
Project description:Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease. It is thought that many common variant gene loci of weak effect act additively to predispose to common autoimmune diseases, while the contribution of rare variants remains unclear. Here we describe that rare coding variants in lupus-risk genes are present in most SLE patients and healthy controls. We demonstrate the functional consequences of rare and low frequency missense variants in the interacting proteins BLK and BANK, which are present alone, or in combination, in a substantial proportion of lupus patients. The rare variant found in patients, but not those found exclusively in controls, impair suppression of IRF and type-I IFN in human B cell lines and increase pathogenic lymphocytes in lupus-prone mice. Thus, rare gene variants are common in SLE and likely contribute to genetic risk.
2019-05-01 | GSE126307 | GEO
Project description:Pathological cardiac hypertrophy is featured by enhanced protein synthesis. Translation inhibition is effective in treating cardiac hypertrophy, yet with systematic side effect. We identified a cardiac-enriched LncRNA CARDINAL, when deleted, exacerbate transaortic constriction (TAC) induced hypertrophy.
2024-04-22 | GSE210982 | GEO
Project description:Pathological cardiac hypertrophy is featured by enhanced protein synthesis. Translation inhibition is effective in treating cardiac hypertrophy, yet with systematic side effect. We identified a cardiac-enriched LncRNA CARDINAL, when over-expressed in cardiomyocyte using AAV9 driven by cTNT promoter, ameliorate transaortic constriction (TAC) induced hypertrophy.
2024-04-22 | GSE210983 | GEO
Project description:AAmiodarone is an antiarrhythmic drug and representatively induce pulmonary phospholipidosis. Amiodarone-induced toxicity has been a serious unpredictable side effect of the treatment and an important clinical problem. Possible causes include allergic, cytotoxic or immunologic reactions to this agent. We examined the consequences of the mechanism of amiodarone-induced pulmonary toxicity gene expression in BEAS-2B cells, huma bronchial cell line, by microarray. The expression of these genes are potential biomarker of amiodarone-induced pulmonary toxicity. Also, We provide a clue about mechanism of pulmonary toxic action by these clinical chemotherapeutic agents. BEAS-2B cells were seeded and after incubation for 24 h at 37C, the cells were treated with 29.388 μM(IC20) amiodarone for 48 h. And after total RNA isolation, gene expression analysis was conducted using a 44-k whole human genome microarray. Labeling and hybridization were performed using a FairPlay microarray labeling kit, followed by the coupling of Cy3 (controls) or Cy5 (treated samples) dye. The hybridized slides were scanned using a GenePix 4000B microarray scanner, and the images were analyzed using GenePix 4.1 software to obtain gene expression ratios. The fluorescence intensity of each spot was calculated by local median background subtraction. We then used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000. A significance analysis of microarray (SAM) was performed for genes with significant changes in expression.
2011-01-10 | E-GEOD-20582 | biostudies-arrayexpress
Project description:Methotrexate (MTX) has been widely used for the treatment of a variety of tumors as well as for inflammatory diseases and rheumatoid arthritis (RA). MTX-induced toxicity has been a serious unpredictable side effect of the treatment and an important clinical problem. Possible causes include allergic, cytotoxic or immunologic reactions to this agent. We examined the consequences of the mechanism of MTX-induced pulmonary toxicity gene expression in BEAS-2B cells, huma bronchial cell line, by microarray. The expression of these genes are potential biomarker of methotrexate-induced pulmonary toxicity. Also, We provide a clue about mechanism of pulmonary toxic action by these clinical chemotherapeutic agents. Experiment Overall Design: BEAS-2B cells were seeded and after incubation for 24 h at 37C, the cells were treated with 0.144 ?M(IC20) MTX for 48 h. And after total RNA isolation, gene expression analysis was conducted using a 44-k whole human genome microarray. Labeling and hybridization were performed using a FairPlay microarray labeling kit, followed by the coupling of Cy3 (controls) or Cy5 (treated samples) dye. The hybridized slides were scanned using a GenePix 4000B microarray scanner, and the images were analyzed using GenePix 4.1 software to obtain gene expression ratios. The fluorescence intensity of each spot was calculated by local median background subtraction. We then used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000. A significance analysis of microarray (SAM) was performed for genes with significant changes in expression.
2008-12-12 | E-GEOD-9815 | biostudies-arrayexpress
Project description:Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease. It is thought that many common variant gene loci of weak effect act additively to predispose to common autoimmune diseases, while the contribution of rare variants remains unclear. Here we describe that rare coding variants in lupus-risk genes are present in most SLE patients and healthy controls. We demonstrate the functional consequences of rare and low frequency missense variants in the interacting proteins BLK and BANK1, which are present alone, or in combination, in a substantial proportion of lupus patients. The rare variants found in patients, but not those found exclusively in controls, impair suppression of IRF5 and type-I IFN in human B cell lines and increase pathogenic lymphocytes in lupus-prone mice. Thus, rare gene variants are common in SLE and likely contribute to genetic risk.
| EGAS00001003548 | EGA
Project description:<p>Autism spectrum disorder (ASD) is highly heritable with recent sibling recurrence risk estimates of 19% overall and 26% in males. The heritable phenotype of hyperserotonemia, or elevated levels of platelet serotonin (5HT), in ~35% of people with ASD is a well-established biomarker. The efficacy of drugs like risperidone and potent serotonin transporter inhibitors at treating behaviors related to Insistence on Sameness, along with evidence of the contribution of hyperserotonemia to autism susceptibility collectively support the hypothesis that dysfunction in the 5HT system is a significant etiological target for investigation of the genetic component to autism. ASD genetic architecture is complex; common variants of large effect do not contribute substantially to overall ASD risk, but there are clearly common variants with small effects and rare genetic/genomic variation of larger effect among ASD genetic risk factors. The NIH ARRA Autism Sequencing Consortium, including Dr. Sutcliffe and Dr. Cook among others, has initiated exome sequencing studies to identify more of the rare variants contributing to ASD. Data from our group and others reveal numerous rare <i>de novo</i> and inherited sequence mutations, and the number of <i>de novo</i> and other functional mutations that are found to affect molecules encoding 5HT signaling and its regulation further reinforces our hypothesis that regulation of serotonin levels is important in autism genetic susceptibility. Integrin receptor signaling pathways were prominently featured among identified de novo mutations, thus defining a set of interrelated gene networks that control 5HT signaling. We propose to extend our findings to date by conducting exome sequencing on ACE subjects, for whom we also have 5HT biochemical data, to identify rare variants (including CNVs) in 5HT-related gene networks. In total we propose to have exome sequencing completed on 523 samples. The purpose of the proposed research is two-fold: 1) we will conduct more extensive investigations to determine the support for the hypothesis that genetic variation at genes regulating platelet serotonin levels affect susceptibility to ASD and 2) we will combine the exome sequence data from these studies with sequence data for autism being accumulated in a variety of other research projects to further the goal of identifying and characterizing the genetic component to ASD.</p>
| phs000712 | dbGaP