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Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium.

ABSTRACT: Cadmium (Cd²?) is a known nephrotoxin causing tubular necrosis during acute exposure and potentially contributing to renal failure in chronic long-term exposure. To investigate changes in global gene expression elicited by cadmium, an in-vitro exposure system was developed from cultures of human renal epithelial cells derived from cortical tissue obtained from nephrectomies. These cultures exhibit many of the qualities of proximal tubule cells. Using these cells, a study was performed to determine the cadmium-induced global gene expression changes after short-term (1 day, 9, 27, and 45 ?M) and long-term cadmium exposure (13 days, 4.5, 9, and 27 ?M). These studies revealed fundamental differences in the types of genes expressed during each of these time points. The obtained data was further analyzed using regression to identify cadmium toxicity responsive genes. Regression analysis showed 403 genes were induced and 522 genes were repressed by Cd²? within 1 day, and 366 and 517 genes were induced and repressed, respectively, after 13 days. We developed a gene set enrichment analysis method to identify the cadmium induced pathways that are unique in comparison to traditional approaches. The perturbation of global gene expression by various Cd²? concentrations and multiple time points enabled us to study the transcriptional dynamics and gene interaction using a mutual information-based network model. The most prominent network module consisted of INHBA, KIF20A, DNAJA4, AKAP12, ZFAND2A, AKR1B10, SCL7A11, and AKR1C1.

SUBMITTER: Garrett SH

PROVIDER: S-EPMC3552673 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium.

Garrett Scott H SH Clarke Kaitlin K Sens Donald A DA Deng Youping Y Somji Seema S Zhang Ke K KK

BMC medical genomics 20130123

Cadmium (Cd²⁺) is a known nephrotoxin causing tubular necrosis during acute exposure and potentially contributing to renal failure in chronic long-term exposure. To investigate changes in global gene expression elicited by cadmium, an in-vitro exposure system was developed from cultures of human renal epithelial cells derived from cortical tissue obtained from nephrectomies. These cultures exhibit many of the qualities of proximal tubule cells. Using these cells, a study was performed to determi ...[more]

PMID: 23369406

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Project description:Circadian variability in kidney function is well recognized but is often ignored as a potential confounding variable in physiological experiments. Here, we have created a data resource consisting of expression levels for mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. Small-sample RNA sequencing was applied to microdissected S1 proximal convoluted tubules and S2 proximal straight tubules. After stringent filtering, the data were analyzed using JTK-Cycle to detect periodicity. The data set is provided as a user-friendly webpage at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox2/. In proximal convoluted tubules, 234 transcripts varied in a circadian manner (4.0% of the total). In proximal straight tubules, 334 transcripts varied in a circadian manner (5.3%). Transcripts previously known to be associated with corticosteroid action and with increased flow were found to be overrepresented among circadian transcripts peaking during the "dark" portion of the day [zeitgeber time (ZT)14-22], corresponding to peak levels of corticosterone and glomerular filtration rate in mice. To ask whether there is a time-of-day dependence of protein abundances in the kidney, we carried out LC-MS/MS-based proteomics in whole mouse kidneys at ZT12 and ZT0. The full data set (n = 6,546 proteins) is available at https://esbl.nhlbi.nih.gov/Databases/Circadian-Proteome/. Overall, 293 proteins were differentially expressed between ZT12 and ZT0 (197 proteins greater at ZT12 and 96 proteins greater at ZT0). Among the regulated proteins, only nine proteins were found to be periodic in the RNA-sequencing analysis, suggesting a high level of posttranscriptional regulation of protein abundances.NEW & NOTEWORTHY Circadian variation in gene expression can be an important determinant in the regulation of kidney function. The authors used RNA-sequencing transcriptomics and LC-MS/MS-based proteomics to identify gene products expressed in a periodic manner. The data were used to construct user-friendly web resources.

Project description:Increasing demand for river water now conflicts with an increasing desire to maintain riparian ecosystems. Efficiently managing river flows for riparian vegetation requires an understanding of the time scale of flow effects, but this information is limited by the absence of long-term studies of vegetation change in response to flow variation. To investigate the influence of short- and long-term flow variability and dam operation on riparian vegetation, we determined the occurrence of 107 plant species in 133 permanent plots of known inundating discharge along the Gunnison River in Colorado on five different occasions between 1990 and 2013. Individual species moved up and down the gradient of inundating discharge coincident with increases and decreases in mean annual flow, and the correlations between flow and species occurrence were strongest when flows were weighted by time before vegetation sampling with a median half-life of 1.5 years. Some tall, rhizomatous, perennial species, however, responded to flows on a longer time scale. Logistic regression of species occurrence showed a significant relation with inundation duration for 70 out of 107 species. Plot species richness and total vegetative cover decreased in association with desiccation at low inundation durations and with fluvial disturbance at high inundation durations. Within-plot similarity in species occurrence between years decreased strongly with increasing inundation duration. Moderate inundation durations were dominated by tall, rhizomatous, perennial herbs, including invasive Phalaris arundinacea (reed canary grass). Over the 23-year study period, species richness declined, and the proportion of rhizomatous perennials increased, consistent with the hypothesis that decreases in flow peaks and increases in low flows caused by flow regulation have decreased establishment opportunities for disturbance-dependent species. In summary, annual-scale changes in vegetation were strongly influenced by flow variation, and decadal-scale changes were influenced by decreases in fluvial disturbance from upstream flow regulation beginning decades prior to the onset of this study.

Project description:BackgroundChronic exposure to low cadmium (Cd) levels produces urinary excretion of low molecular weight proteins, which is considered the critical effect of Cd exposure. However, the mechanisms involved in Cd-induced proteinuria are not entirely clear. Therefore, the present study was designed to evaluate the possible role of megalin and cubilin (important endocytic receptors in proximal tubule cells) and angiotensin II type 1 (AT1) receptor on Cd-induced microalbuminuria.MethodsFour groups of female Wistar rats were studied. Control (CT) group, vehicle-treated rats; LOS group, rats treated with losartan (an AT1 antagonist) from weeks 5 to 8 (10 mg/kg/day by gavage); Cd group, rats subchronically exposed to Cd (3 mg/kg/day by gavage) during 8 weeks, and Cd + LOS group, rats treated with Cd for 8 weeks and LOS from weeks 5-8. Kidney Cd content, glomerular function (evaluated by creatinine clearance and plasma creatinine), kidney injury and tubular function (evaluated by Kim-1 expression, urinary excretion of N-acetyl-β-D-glucosaminidase (NAG) and glucose, and microalbuminuria), oxidative stress (measured by lipid peroxidation and NAD(P)H oxidase activity), mRNA levels of megalin, expressions of megalin and cubilin (by confocal microscopy) and AT1 receptor (by Western blot), were measured in the different experimental groups. Data were analyzed by one-way ANOVA or Kruskal-Wallis test using GraphPad Prism 5 software (Version 5.00). P < 0.05 was considered statistically significant.ResultsAdministration of Cd (Cd and Cd + LOS groups) increased renal Cd content. LOS-treatment decreased Cd-induced microalbuminuria without changes in: plasma creatinine, creatinine clearance, urinary NAG and glucose, oxidative stress, mRNA levels of megalin and cubilin, neither protein expression of megalin nor AT1 receptor, in the different experimental groups studied. However, Cd exposure did induce the expression of the tubular injury marker Kim-1 and decreased cubilin protein levels in proximal tubule cells whereas LOS-treatment restored cubilin levels and suppressed Kim-1 expression.ConclusionLOS treatment decreased microalbuminuria induced by Cd apparently through a cubilin receptor-dependent mechanism but independent of megalin.

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Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium.

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Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium.

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