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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole blood derived cadmium responsive miRNome

ABSTRACT: Purpose: Cadmium is a nonessential heavy metal and a well known toxic agent. Cadmium is known to alter the gene expression and signaling but the role of miRNAs during Cadmium exposure is not understood. Methods: Mice were treated with 100 mg/ ml cadmium chloride for 120 days and accumulation of cadmium in blood and organs are confirmed by GFAAS. Subsequently, the total RNA was isolated from the whole blood and small RNA sequencing was executed in Illumina HiSeq 1000. Results: The reads were annotated to the mice genome and miRNAs in miRbase using miRDeep* and novel miRNAs were also predicted. The differential expression was studied by DeSeq Conclusions: This is the first report to reveal the cadmium responsive miRNome. These candidate miRNAs can serve as biomarkers for cadmium Whole blood small RNA profiles of control and cadmium exposed mice generated by deep sequencing using Illumina HiSeq 1000

ORGANISM(S): Mus musculus

SUBMITTER: Velmurugan Ganesan

PROVIDER: E-GEOD-73744 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Whole blood derived cadmium responsive miRNome

Project description:Purpose: Cadmium is a nonessential heavy metal and a well known toxic agent. Cadmium is known to alter the gene expression and signaling but the role of miRNAs during Cadmium exposure is not understood. Methods: Mice were treated with 100 mg/ ml cadmium chloride for 120 days and accumulation of cadmium in blood and organs are confirmed by GFAAS. Subsequently, the total RNA was isolated from the whole blood and small RNA sequencing was executed in Illumina HiSeq 1000. Results: The reads were annotated to the mice genome and miRNAs in miRbase using miRDeep* and novel miRNAs were also predicted. The differential expression was studied by DeSeq Conclusions: This is the first report to reveal the cadmium responsive miRNome. These candidate miRNAs can serve as biomarkers for cadmium

2015-11-01 | GSE73744 | GEO

Expression profiling of small, noncoding RNAs in physiologically hypertrophied rat hearts

Project description:Purpose: Different studies revealed the importance of microRNAs (miRNAs) in pathological hypertrophy but their role during physiological hypertrophy is largely unexplored. Hence, this study is aimed at revealing the global expression profile of miRNAs during physiological cardiac hypertrophy. Methods: Chronic swimming protocol continuously for eight weeks resulted in induction of physiological hypertrophy in rats and histopathology revealed the absence of tissue damage, apoptosis or fibrosis. Subsequently, the total RNA was isolated and small RNA sequencing was executed in Illumina HiSeq 2000. Results: Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during physiological hypertrophy. The expression profile of the significantly differentially expressed miRNAs were validated by qPCR. Conclusions: This is the first report to reveal the involvement of a large number of apoptotic miRNAs during physiological cardiac hypertrophy including the previously unknown cardiac players like miR-99, miR-100, miR-191, miR-181 and miR-19. Our data indicates that regulation of these apoptotic miRNAs can be one of the major key factor in determining pathological or physiological hypertrophy by controlling apoptosis, fibrosis and cell death mechanisms. Heart small RNA profiles of 16-week old control and physiologically hypertrophied wistar rat were generated by deep sequencing using Illumina HiSeq 2000

2015-10-31 | E-GEOD-62883 | biostudies-arrayexpress

Transcription profiling of rat adult testes treated with 3 mg/kg b.w. cadmium chloride via i.p.

Project description:This is a study to explore the transcriptional changes after cadmium treatment in adult rat testes at three time points (control--0 hour, 8 hour and 4 day). Cadmium is an environmental toxicant that is known to affect the male reproductive system. It disrupts the blood-testis barrier irreversibly, and affects the Sertoli-germ cells adhesion, causing germ cell depletion from the seminiferous epithelium. Experiment Overall Design: Adult Sprague-Dawley rats treated with a single dose of cadmium chloride at 3 mg/kg b.w. by i.p. and terminated after 8 hours (n=2) and 20 hours (n=2). Testes from cadmium-treated rats and untreated (control, 0 hour, n=3) rats were harvested and total RNA were prepared. Standard Affymetrix genechip procedures were followed for the subsequent experiments. Data were analysed in MAS 5.0 and GeneSpring 7.2.

2008-06-16 | E-GEOD-9480 | biostudies-arrayexpress

Cadmium specific proteomic responses of Pseudomonas aeruginosa san ai

Project description:Pseudomonas aeruginosa san ai resists a high concentration of up to 7.2 mM of cadmium. Leaving biomass of P. aeruginosa san ai exposed to sub-lethal concentration of cadmium (0.9 mM) adsorbed 75% of added cadmium after 48 hours, while remaining 25% in culture supernatant was adsorbed by exopollysaccaryde, implying a large biosorption potential of leaving biomass and its exopollysaccaryde. Inner cell response on the protein level was investigated by shotgun proteomics approach based on liquid chromatography and tandem mass spectrometry coupled with bioinformatics to identify proteins in complex protein fractions obtained by size exclusion chromatography used to preserve native forms of metalloproteins and protein complexes. Using this approach a total of 59 proteins were observed as up-regulated in cadmium- amended culture. Almost a third of the total number of up-regulated were metalloproteins. P. aeruginosa san ai developed a complex mechanism to adapt to cadmium, based on: extracellular biosorption, bioaccumulation, the formation of biofilm, controlled siderophore production, enhanced respiration and modified protein profile. An increased abundance of proteins involved in cell energy metabolism, amino acid metabolism, cell motility and posttranslational modifications, primarily based on thiol-disulfide exchange, were observed. Enhanced oxygen consumption of biomass in cadmium- amended culture versus control was found. Our results signify that P. aeruginosa san ai has a great potential for application in bioremediation of cadmium polluted sites.

2022-05-19 | PXD008020 | Pride

Global gene expression analysis of six cadmium-transformed UROtsa cell isolates

Project description:The immortalized human urothelial cell line, UROtsa, was transformed in six parallel cultures with continual passaging in1 µM Cd+2 until the cells were able to attain the ability to form colonies in soft agar and subcutaneous tumors in nude mice. The gene expression profiles between cadmium-transformed and control samples were compared and the differentially expressed genes were identified. Six independent Cadmium-transformed UROtsa cell cultures, three control UROtsa cell cultures

2011-01-25 | E-GEOD-26828 | biostudies-arrayexpress

miRNA-99 family diverges physiological cardiac hypertrophy to pathological cardiac hypertrophy

Project description:Purpose: The physiological cardiac hypertrophy is an adaptive condition that does not associate with myocyte cell death while pathological hypertrophy is a maladaptive condition associated with myocyte cell death. Alpha-2 macroglobulin (Î±-2M) an acute phase protein induces cardiac hypertrophy via the ERK1,2 and PI3K/Akt signaling. This study is aimed at exploring the miRNome of Î±-2M induced hypertrophied cardiomyocytes and to understand the role of miRNAs in determination of pathological and physiological hypertrophy. Methods: Hypertrophy was induced in H9c2 cardiomyoblasts using alpha-2 macroglobulin. The induction of hypertrophy is confirmed by microscopy and gene expression studies. Subsequently, the total RNA was isolated and small RNA sequencing was executed in Illumina HiSeq 2000. Results: Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during hypertrophy. Among the differentially expressed candidates, miR-99 family (miR-99a, miR-99b and miR-100) showed significant downregulation upon Î±-2M treatment while isoproterenol treatment (pathological hypertrophy) upregulated their expression. The binding site for Egr1 transcription factor was identified in the promoter region of miR-99 family, and interestingly all miRNAs with Egr1 binding site proven by ChIP-Seq were downregulated during physiological hypertrophy Conclusions: The results proved Egr-1 mediated regulation of miR-99 family determines the uniqueness of pathological and physiological hypertrophy. Upregulated miR-99 expression during pathological hypertrophy suggests that it can be a valuable diagnostic marker and potential therapeutic target for cardiac hypertrophy and heart failure. Small RNA profiles of control and hypertrophied cardiomyocyte H9c2 cells were generated by deep sequencing using Illumina HiSeq 2000

2015-11-01 | E-GEOD-73597 | biostudies-arrayexpress

Identifying the impact of cadmium stress on the pneumococcal metalloproteome

Project description:The toxicity of the heavy metal cadmium is well established. However, the molecular basis for how this toxicity perturbs cellular viability is still not well understood. This project investigates the cellular and molecular impacts of cadmium stress in the bacterial pathogen, Streptococcus pneumoniae. We find that cadmium depletes cellular manganese and zinc stores, leading to disruption of metalloproteins and the corresponding biochemical pathways. Furthermore, the over-accumulation of cadmium within the cells appears to facilitate mismetallation events, whereby native metal cofactors are displaced by cadmium, leading to reduced or abrogated enzymatic activity. These metalloproteomic analyses have been conducted in conjunction with transcriptomics and metabolomics to elucidate the global impacts of cadmium stress within a prokaryotic organism.

2021-06-25 | PXD021643 | Pride

Interleukin-27 treated human macrophages induce the expression of novel miRNAs which may mediate anti-viral properties (RNA-seq)

Project description:In this study, we hypothesized that IL-27 could induce the expression of novel miRNAs in macrophages which may have functional relevance in terms of anti-viral activity. In this study, primary monocytes were differentiated into macrophages using M-CSF (M-Mac) or with a combination of M-CSF and IL-27 (I-Mac) for seven days. Following this, total RNA was extracted from these cells and deep sequencing was performed, in parallel with gene expression microarrays. Using the novel miRNA discovery software, miRDeep, seven novel miRNAs were discovered in the macrophages, four of which were expressed higher in I-Mac (miRNAs 2.1, 8.1, 9.1 and 14.2) whilst three were detected in both M-Mac and I-Mac (miRNAs 9.3, 13.6 and 15.8). The expression of six of the seven novel miRNAs was highly correlated with qRT-PCR using specific primer/probes designed for the novel miRNAs. Gene expression microarray further demonstrated that a number of genes were potentially targeted by these differentially expressed novel miRNAs. screening novel and known miRNAs which may have antiviral properties in 2 different treatments in 2 donors.

2013-03-29 | E-GEOD-44953 | biostudies-arrayexpress

cadmium-mirna-cadmium stress on suspension cells.

Project description:rs06-03_cd-mirna - cadmium-mirna - trancriptional and post-transcriptional response to cadmium. - After 5 days of grown in a fresh medium (5% PCV at day0), CdCl2 was added to tested cells (Cad) to a final concentration of 200uM. Nothing was added to control cells (Tem). After 12 and 24 hours of growth +/- cadmium, cells were harvested and frozen in liquid nitrogen. 4 dye-swap - treated vs untreated comparison

2012-03-25 | E-GEOD-36627 | biostudies-arrayexpress

Transcription profiling of rat primary hepatocyte in culture after low dose and short incubation time of cadmium in primary

Project description:The study was performed using primary rat hepatocyte in culture from 4 adult male Sprague-Dawley rats to investigate the changes in gene expression under low dose (4Î¼M) and short exposure (3hrs) of cadmium chloride. By comparing the gene expression profiles of control and cadmium-treated cells, the most dramatic and significant changes were for those genes associated with transcriptional regulation, antioxidant response and control of protein integrity. Changes in other genes involved in cellular physiological responses such as inflammation, growth and apoptosis were also observed. Results were further confirmed by quantitative real time polymerase chain reaction (qRT-PCR). Experiment Overall Design: Primary hepatocytes from four rats were isolated using the collagenase-hyaluronidase perfusion and digestion method. The cells of greater than 85% viability were used in this study. The cells were plated at 90% confluency on culture dishes coated with collagen and maintained in Waymouth's medium containing BSA for 4hrs prior to an overnight incubation with BSA free Waymouth's medium. Control samples and cadmium-treated samples from individual rats were hybridized to RAE 230A arrays (n=4 and 8 microarrays); data were generated and analyzed.

2009-03-07 | E-GEOD-8013 | biostudies-arrayexpress

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