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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cellular and molecular response to ruthenium(II)-arene complex with substituted picolinato ligand in HeLa cells

ABSTRACT: Ruthenium(II)-arene complexes are promising drug candidates for therapy of solid tumors. We have previously shown that ruthenium(II)-arene complex [Ru(η6-p-cymene)(L7)Cl] (RuT7) exerts cytotoxic effects in a panel of cancer cell lines (J. Organomet. Chem. 2014, 749, 343–349). In this study we analyzed in vitro cellular response and performed whole-transcriptome microarray gene expression analysis in HeLa cells in order to understand the cellular and molecular mechanism of response to RuT7 complex. Results on biological action of ruthenium complex obtained on cellular level were reflected on molecular level as well. Analysis of functional categories and signaling and biochemical pathways that are associated with HeLa cells' response to ruthenium complex revealed that RuT7 complex leads HeLa cells through intrinsic (mitochondrial) apoptotic pathway, via indirect DNA damage made by action of reactive oxygen species and through direct DNA binding of RuT7. Performed molecular toxicity analysis has shown that RuT7 has fewer associated toxicity profiles than cisplatin. Altogether these results provide the basis for development of RuT7 in animal and pre-clinical studies as a potential drug candidate. We hybridized each condition (control, RuT7 and CDDP) at each time point (12 h and 24 h) in triplicate, for a total of 18 samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Miljana Tanic

PROVIDER: E-GEOD-72905 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cellular and molecular response to ruthenium(II)-arene complex with substituted picolinato ligand in HeLa cells

Project description:Ruthenium(II)-arene complexes are promising drug candidates for therapy of solid tumors. We have previously shown that ruthenium(II)-arene complex [Ru(η6-p-cymene)(L7)Cl] (RuT7) exerts cytotoxic effects in a panel of cancer cell lines (J. Organomet. Chem. 2014, 749, 343–349). In this study we analyzed in vitro cellular response and performed whole-transcriptome microarray gene expression analysis in HeLa cells in order to understand the cellular and molecular mechanism of response to RuT7 complex. Results on biological action of ruthenium complex obtained on cellular level were reflected on molecular level as well. Analysis of functional categories and signaling and biochemical pathways that are associated with HeLa cells' response to ruthenium complex revealed that RuT7 complex leads HeLa cells through intrinsic (mitochondrial) apoptotic pathway, via indirect DNA damage made by action of reactive oxygen species and through direct DNA binding of RuT7. Performed molecular toxicity analysis has shown that RuT7 has fewer associated toxicity profiles than cisplatin. Altogether these results provide the basis for development of RuT7 in animal and pre-clinical studies as a potential drug candidate.

2015-09-11 | GSE72905 | GEO

mRNA sequencing identifies differential gene expresssion profiles between ASCC3 knock-down cells and control cells

Project description:We sequenced mRNAs from HeLa cells transduced with either scrambled shRNA or shRNA targeting ASCC3. The results have shown differential gene expression in ASCC3 knockdown cells, suggesting a regulatory role for ASCC3 in certain cellular pathway. mRNA from HeLa cells transduced with either scrambled shRNA (ni) or shRNA targeting ASCC3 (ai) were harvested and used for deep sequencing by Illumina HiSeq 2000 sequencing instruments.

2013-06-15 | E-GEOD-47399 | biostudies-arrayexpress

Comparative effect of DON and plant or microbial biotransformation of DON on gene expression of piglets jejunal explants

Project description:Deoxynivalenol (DON) is a frequent mycotoxin in grains, produced by Fusarium fungi, which demonstre multiple side effects such as modulation of immune responses, reduced feed intake and weight gain or impairment of the intestinal barrier function. Among animal species, pigs are the best model for humans and are very sensitive to DON. In wheat, DON can be conjugated to glucose to form DON-3-Î²-D-glucoside (D3G). Some bacteria isolated from digestive tracts or soil, are also able to de-epoxydize or epimerize DON to metabolites such as deepoxy-deoxynivalenol (DOM-1) or 3-epi-deoxynivalenol (epi-DON). The toxicity of these DON metabolites is poorly documented. By the way of ingestion, the intestine is the first organ exposed to these molecules and so constitute a relevant model. The aim of this study was to compare the intestinal toxicity of three DON metabolites (D3G, DOM-1 and epi-DON) with the one of DON. Intestinal explants from 6 pigs were treated with 10mM DON, D3G, DOM-1 or epi-DON for 4 hours and transcriptomic analysis was performed using an âAgilent Porcinet 60Kâ. Jejunal explants from 4 piglets aged of 5 weeks were sampled and exposed in vitro to differents molecules (DON, D3G, DOM-1 & 3-epi-DON) at 10ÂµM during 4h. Then RNA was extracted.

2016-07-20 | E-GEOD-66918 | biostudies-arrayexpress

Modulation of gene expression induced by cylindrospermopsin in human intestinal Caco-2 cells

Project description:Cylindrospermopsin (CYN) is a cyanotoxin that has been recognised as an emerging potential public health risk. Although CYN toxicity has been demonstrated, the mechanisms involved have not been fully characterised. To identify some key pathways related to this toxicity, we studied the transcriptomic profile of human intestinal Caco-2 cells exposed to a sub-toxic concentration of CYN (1.6 M-BM-5M for 24hrs) using a non-targeted approach. CYN was shown to modulate different biological functions which were related to growth arrest (with down-regulation of cdkn1a and uhrf1 genes), and DNA recombination and repair (with up-regulation of aptx and pms2 genes). Our main results reported an increased expression of some histone-modifying enzymes (histone acetyl and methyltransferases MYST1, KAT5 and EHMT2) involved in chromatin remodelling, which is essential for initiating transcription. We also detected greater levels of acetylated histone H2A (Lys5) and dimethylated histone H3 (Lys4), two products of these enzymes. In conclusion, CYN overexpressed proteins involved in DNA damage repair and transcription, including modifications of nucleosomal histones. Our results highlighted some new cell processes induced by CYN. Modulation of gene expression in differentiated Caco-2 cells was measured at 24 hours after exposure to doses of 0 and 1.6 M-BM-5M of cylindrospermopsin. Six independent experiments were performed, but only 11 samples (5 controls and 6 exposed to cylindrospermopsin) had an RNA quality indicator M-bM-^IM-% 9 and were used for the microarray experiments.

2014-03-11 | E-GEOD-55723 | biostudies-arrayexpress

Effects of Ars2 or DGCR8 siRNA on gene expression

Project description:Ars2 is a component of the nuclear cap-binding complex that is required for cellular proliferation and contributes to microRNA biogenesis. Arrays were performed to determine the repertoire of genes that change following knock-down of Ars2. Knock-down of DGCR8 was also performed to determine which changes in Ars2 knock-down cells resulted from defects in microRNA expression. 9 samples were analyzed including: three biological replicates of control siRNA-transfected HeLa cells, HeLa cells transfected with three independent siRNAs targeting Ars2, or HeLa cells transfected with three independent siRNAs targeting DGCR8.

2012-02-01 | E-GEOD-34679 | biostudies-arrayexpress

Effects of Ars2 or DGCR8 siRNA on microRNA expression

Project description:Ars2 is a component of the nuclear cap-binding complex that is required for cellular proliferation and contributes to microRNA biogenesis. Arrays were performed to determine the repertoire of microRNAs that change following knock-down of Ars2. Knock-down of DGCR8 was also performed to determine which microRNAs were expressed and had half-lives short enough to significantly decrease over the duration of the experiment. 9 samples were analyzed including: three biological replicates of control siRNA-transfected HeLa cells, HeLa cells transfected with three independent siRNAs targeting Ars2, or HeLa cells transfected with three independent siRNAs targeting DGCR8.

2012-02-01 | E-GEOD-34680 | biostudies-arrayexpress

Kidney toxicity in miR-155-/- mice

Project description:The development of nephrotoxicity limits the maximum achievable dosage and treatment intervals for cisplatin chemotherapy. Therefore, identifying mechanisms that regulate this toxicity could offer novel methods to optimize cisplatin delivery. MicroRNAs are capable of regulating many different genes, and can influence diverse cellular processes, including cell death and apoptosis. We previously observed miR-155 to be highly increased following ischemic or toxic injury to the kidneys and, therefore, sought to determine whether mice deficient in miR-155 would respond differently to kidney injury. miR-155-/- mice (B6.Cg-Mir155tm1.1Rsky/J originally purchased from The Jackson Laboratory) and age- and weight-matched C57BL/6 (wild type) mice (Charles River Laboratories) were used in this study. Mice were injected with one single 20mg/kg dose of cisplatin. Kidney tissues were collected at 0, 24, 48, and 72 hours i.p. with saline-injected mice as control. Total RNA extracted from the kidney tissues were used for gene expression analysis with Agilent Mouse whole genome 4x44k v2 array.

2014-08-05 | E-GEOD-57292 | biostudies-arrayexpress

Genome-wide binding profiles of the B-Myb-MuvB complex in HeLa cells

Project description:To identify genomic regions bound by B-Myb and LIN9 (a subunit of the MuvB complex), we performed ChIP-Sequencing (ChIP-Seq) using chromatin from proliferating HeLa cells in which we can detect a robust association between B-Myb and subunits of the MuvB complex. This analysis allowed us identify late cell cycle or G2/M expressed genes as specific targets of the B-Myb-MuvB complex. Examination of B-Myb and LIN9 binding in asynchronously growing HeLa cells

2012-01-25 | E-GEOD-27030 | biostudies-arrayexpress

Gene expression signatures in uteri from nuclear and membrane effects of Estradiol on Estrogen receptor ERÎ±

Project description:To further study gene expression regulated by 17b-estradiol in uteri, we have employed whole gene microarray profiling to identify genes specifically regulated by the Estrogen receptor ERÎ± localized either at the plasma membrane or in the nucleus. Two mice models have been used, the mice named ERa-AF2Â° (named AF2_KO and on C57BL6/J background) in which 7 aminoacids have been deleted in the AF2 domain and the mice C451A-ERa (named MISS_KO and on C57BL6/N background) mutated for the C451 into Ala on ERa. Control littermates were used for each mutant mice respectively name AF2_WT or MISS_WT. 17b-estradiol induced gene expression in uteri from ovariectomized mice was measured after 6 hours exposure to 0 (PLB) and 8Âµg/kg of 17b-estradiol (E2) injected subcutaneously in castor oil.

2014-07-01 | E-GEOD-53237 | biostudies-arrayexpress

Muscle Transcriptomic Investigation of Late Fetal Development Identifies Candidate Genes for Key Roles in Piglet Maturity

Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows). To assay for changes in gene expression during piglet maturity, mRNA was isolated from 61 fetal skeletal muscle samples with 8 different conditions: two fetal gestational ages (90 or 110 days of gestation), associated with four genotypes (two extreme breeds for mortality at birth (MS and LW) and two crossed breeds (MSLW and LWMS)). MS fetuses are known to have a better survival at birth than LW fetuses. An understanding of maturity is possible with the comparison between the fetal gestational ages and between the two extreme breeds. The impact of parental genotypes is studied with the presence of crossed fetuses. After quality control and normalization, only 61 samples were conserved (represented here).

2014-09-19 | E-GEOD-56301 | biostudies-arrayexpress

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