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RNA-seq experiment to investigate the effect sulforaphane metabolism in HepG2 cells (human hepatocellular carcinoma cell lines). Cells treated with sulforaphane were compared against untreated cells in three different glucose environments: no glucose, basal and high glucose, to study the transcriptional effect of sulforaphane on liver cells at different metabolic states.

ABSTRACT: Over the past six years, literature has shown that sulforaphane (SF) can affect a wide range of genes involved in central metabolism, such as glycolysis, pentose phosphate pathway, TCA cycle, lipid biosynthesis and oxidation. In this experiment, RNA sequencing was performed on HepG2 cells in three glucose environments: no glucos (0 mM), basal (5 mM), and high glucose (25 mM). These environments represent fasting, healthy and insulin-resistant hepatocytes, treated with physiological concentrations (10 µM) SF for 24 h. Differential expression analysis is performed to determine the effect of SF on the transcriptional changes in three different metabolic states in the liver. This experiment addresses the following questions: 1) how do the NRF2 target genes respond under different metabolic states?, and 2) does SF affects the gene expression of genes linked to central metabolism in hepatocytes under different metabolic states?

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Perla Rey

PROVIDER: E-MTAB-12851 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-seq experiment to investigate the impact of sulforaphane metabolism in HepG2 cells. Cells with NRF2 knockdown treated with sulforaphane were compared to untreated cells with NRF2 knock-down. Similarly, wild type cells treated with sulforaphane were compared to untreated cells.

Project description:This study aims to assess whether genes involved in central metabolism induced by Sulforaphane, SF, are mediated through the transcription factor NRF2. A time course RNA-seq experiment was performed, where RNA is extracted after 3, 9, and 24 hours SF treatment. This experiment tests the following hypotheses: 1) The transcriptional changes induced by SF at early time points will affect genes involved in the antioxidant response machinery of the cell. 2) The transcriptional changes induced by SF at 24 h will affect genes involved in central metabolism. This is a follow up from a previous study of the effect of SF on HepG2 cells under different glucose environment (see E-MTAB-12851).

2024-03-30 | E-MTAB-12858 | biostudies-arrayexpress

Suppression of LPS-induced transcription and cytokine secretion by the dietary isothiocyanate sulforaphane

Project description:Consumption of a diet rich in cruciferous vegetables is associated with decreased risk of developing non-communicable chronic disease. It has been proposed that biologically active isothiocyanates (ITCs) obtained from these vegetables, such as sulforaphane (SF) derived from broccoli, are responsible for mediating health benefits via multiple mechanisms of action. ITCs have been shown to suppress the levels of several LPS-induced pro-inflammatory cytokines that are biomarkers for chronic inflammatory conditions, and which have been associated with the development of both cancer and cardiovascular disease. In patients suffering from chronic inflammatory diseases, LPS is elevated in circulation to levels reaching around 1ng/ml. In the current study, we demonstrate that SF suppresses global changes in gene expression induced by LPS exposure (1ng/ml) in human THP-1 cells at a physiologically achievable concentration of 5 micromolar. These results illustrate the profound effect that SF can have at concentrations achievable through the consumption of broccoli in suppressing TLR4-mediated inflammatory pathways.

2014-12-03 | E-MEXP-3931 | biostudies-arrayexpress

Expression data from H295R cells where NRSF/REST or SF-1 were knocked down

Project description:SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed. NRSF/REST is a transcriptional repressor that represses expression of neuronal genes in non-neural tissues. Some data suggest that SF-1 and NRSF/REST can functionally interact in adrenocortical cancer cells. We studied gene expression profiles using Affymetrix microarrays in the H295R/TR SF-1 adrenocortical cancer cell line. In this cell line, SF-1 expression can be increased in a doxycycline-dependent manner (Mol. Endocrinol. 21: 2968–2987, 2007). The effects of a control siRNA and sRNAs specific for SF-1 and for NRSF/REST (in basal or increased SF-1 expression conditions) on gene expression were measured. In H295R/TR SF-1 cells SF-1 and NRSF/REST (in conditions of basal and increased SF-1 dosage) expression were knocked down by Amaxa nucleofection. RNA was extracted and hybridized to Human Gene 1.0 ST Affymetrix microarrays.

2013-08-01 | E-GEOD-43033 | biostudies-arrayexpress

Expression data from H295R cells in basal conditions/overexpressing SF-1

Project description:SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed. We studied gene expression profiles using Affymetrix microarrays in the H295R/TR SF-1 adrenocortical cancer cell line, where SF-1 expression can be increased in a doxycycline-dependent manner (Mol. Endocrinol. 21: 2968–2987, 2007) H295R/TR SF-1 cells were cultured either in basal conditions or with doxycycline (Dox) added to the culture medium for 72 hours. RNA was extracted and hybridized to HG-U133 Plus 2.0 Affymetrix microarrays.

2013-08-01 | E-GEOD-43032 | biostudies-arrayexpress

Effect of PY-ITC and sulforaphane on gene expression of PC3 and PNT1A prostate cells in the presence and absence of the PI3K inhibitor LY294002

Project description:Non cancerous PNT1A and cancerous PC3 prostate cells were treated with a novel isothiocyanate (PY-ITC) and compared to sulforaphane (SF), an isothiocyanate (ITC) derived from broccoli. Treatments with these ITCs were performed in the presence and absence on the PI3K inhibitor LY294002.

2013-04-24 | E-MEXP-3640 | biostudies-arrayexpress

Identification of SF-1 genomic binding sites in conditions of basal and increased dosage in the H295R adrenocortical tumor cell line

Project description:The goal of this study was to identify genomic binding sites of the SF-1 nuclear receptor under conditions of basal and increased dosage in the H295R human adrenocortical tumor cell line. 14 samples: input DNA (2 replicates) - SF-1 ChIP Millipore antibody basal SF-1 dosage (3 replicates) - SF-1 ChIP Millipore antibody increased SF-1 dosage (3 replicates) - SF-1 ChIP Perseus antibody basal SF-1 dosage (3 replicates) - SF-1 ChIP Perseus antibody increased SF-1 dosage (3 replicates)

2013-08-01 | E-GEOD-44220 | biostudies-arrayexpress

Epigenomic profiling in visceral white adipose tissue of offspring of mice exposed to late gestational sleep fragmentation

Project description:Background: Late gestational sleep fragmentation (LG-SF) is one of the major perturbations associated with sleep apnea and other sleep disorders during pregnancy. Objectives: To investigate the effects of late LG-SF on the epigenome of visceral white adipose tissue (VWAT) in the offspring. Methods: Time-pregnant mice were exposed to LG-SF or control sleep (LG-SC) conditions during the last 6 days of gestation. We performed large-scale DNA methylation analyses using MeDIP coupled to microarrays (MeDIP-chip) in VWAT of 24-week-old LG-SF and LG-SC offspring (n=8 mice/group). Univariate multiple-testing adjusted statistical analyses were applied to identify differentially methylated regions (DMRs) between the groups. DMRs were mapped to their corresponding genes, and tested for potential overlaps with biological pathways and gene networks. Results: We detected 2148 DMRs between LG-SF and LG-SC groups (p< 0.0001, MAT algorithm). A large proportion of the DMR-associated genes have reported functions that are altered in obesity and metabolic syndrome. Overrepresented pathways and gene networks were related to metabolic regulation and inflammatory response. Conclusions: Our findings show a major role for epigenomic regulation of pathways associated to metabolic processes and inflammatory response in VWAT. Furthermore, LG-SF-induced epigenetic alterations appear to increase the susceptibility to obesity and metabolic syndrome in the offspring. 16 mouse VWAT samples were analyzed by MeDIP coupled to microarray analysis: Offspring of mothers exposed to late-gestational sleep fragmentation (n=8, LG-SF group) and offspring of mothers mouse exposed to normal sleep conditions (n=8, LG-SC group)

2015-04-02 | E-GEOD-63208 | biostudies-arrayexpress

Transcription profiling of human CaCo-2 cells following various iron treatments

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2008-01-19 | E-GEOD-3573 | biostudies-arrayexpress

Identification of NRSF/REST genomic binding sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line

Project description:The goal of this study was to identify genomic binding sites of the NRSF/REST transcription factor under conditions of basal and increased SF-1 dosage in the H295R human adrenocortical tumor cell line. 4 samples: input DNA (2 replicates) - NRSF/REST ChIP basal SF-1 dosage - NRSF/REST ChIP increased SF-1 dosage

2013-08-01 | E-GEOD-49014 | biostudies-arrayexpress

Identification of chromatin regulatory sites in conditions of basal and increased SF-1 dosage in the H295R adrenocortical tumor cell line

Project description:The goal of this study was to identify chromatin regulatory sites by FAIRE-seq under conditions of basal and increased dosage of transcription factor SF-1 in the H295R human adrenocortical tumor cell line. 4 samples: input DNA in basal SF-1 expression conditions - FAIRE-seq in basal SF-1 expression conditions - input DNA in SF-1 overexpression conditions - FAIRE-seq in SF-1 overexpression conditions

2013-08-01 | E-GEOD-44221 | biostudies-arrayexpress

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