Gene expression and epigenetic changes by furan in rat liver

Chen, Tao; Williams, Tim D.; Mally, Angela; Hamberger, Carolin; Mirbahai, Leda; Hickling, Kevin; Chipman, J.K.

doi:10.1016/j.tox.2011.10.020

Cited by 41 publications

(31 citation statements)

References 30 publications

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“…COBRA has been widely used for confirming methylation results obtained by microarray analysis [12,24]. Here the COBRA assay was used to validate the reliability of the methylation microarray analysis and to screen for fetal methylation biomarkers.…”

Section: Resultsmentioning

confidence: 99%

Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray

Yin

Zhang

et al. 2012

BMC Med Genomics

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Background The noninvasive prenatal diagnosis procedures that are currently used to detect genetic diseases do not achieve desirable levels of sensitivity and specificity. Recently, fetal methylated DNA biomarkers in maternal peripheral blood have been explored for the noninvasive prenatal detection of genetic disorders. However, such efforts have covered only chromosomal aneuploidy, and fetal methylated DNA biomarkers in maternal whole blood for detecting single-gene diseases remain to be discovered. Methods To address this issue, we systematically screened significantly hypermethylated genes in fetal tissues and compared them with maternal peripheral blood potential in an attempt to detect fetal genes in maternal peripheral blood. First, the methylated-CpG island recovery assay combined with a CpG island array was performed for four fetus-toward placental tissues and the corresponding maternal peripheral bloods. Subsequently, direct bisulfite sequencing and combined bisulfite restriction analysis (COBRA) were carried out to validate the methylation status of the hypermethylated genes that were identified by the microarray analysis. Results Three hundred and ten significantly hypermethylated genes in the placental tissues were detected by microarray. From the top 15 hypermethylated genes detected by microarray, two were selected for sequencing validation in placental tissue and chorionic villus samples and four were selected for COBRA validation in four placental tissues, ten amniotic fluids and five chorionic villus samples. The six selected genes were confirmed to be hypermethylated in placental tissue and chorionic villus samples, but methylation of the genes could not be detected in the amniotic fluids. Conclusions Of the many hypermethylated genes and methylation sites that were found in the fetal tissues, some have great potential to be developed into molecular markers for noninvasive prenatal diagnosis of monogenic disorders. Further clinical studies are warranted to confirm these findings.

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Section: Resultsmentioning

confidence: 99%

Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray

Yin

Zhang

et al. 2012

BMC Med Genomics

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“…Genomic DNA hypo-methylation is also thought to provide a molecular mechanism for the role of hypoxia in hepatocellular carcinoma (Liu et al, 2011). Hypo-methylation has also been reported as a result of exposure to furan and has been linked to tumors induced by this carcinogen (Chen et al, 2012). On the other hand, cadmium has been found to increase global gene methylation in the liver of rats and this effect has been linked to increased apoptosis and the onset of neoplastic lesions (Wang et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Effect of chronic heroin and cocaine administration on global DNA methylation in brain and liver

et al. 2013

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“…Thus, miR-16 plays a role in the regulation of the biological activity of this compound [172]. Other compound such as furan, found in heated food items, also modified miRNA expression in Sprague Dawley rat liver [173]. Based on these observations, miRNA may play an important role in diet response.…”

Section: Mirnamentioning

confidence: 99%

The Use of Transcriptomics to Unveil the Role of Nutrients in Mammalian Liver

Osada

2013

ISRN Nutrition

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Liver is the organ primarily responding to diet, and it is crucial in determining plasma carbohydrate, protein, and lipid levels. In addition, it is mainly responsible for transformation of xenobiotics. For these reasons, it has been a target of transcriptomic analyses. In this review, we have covered the works dealing with the response of mammalian liver to different nutritional stimuli such as fasting/feeding, caloric restriction, dietary carbohydrate, cholesterol, fat, protein, bile acid, salt, vitamin, and oligoelement contents. Quality of fats or proteins has been equally addressed, and has the influence of minor dietary components. Other compounds, not purely nutritional as those represented by alcohol and food additives, have been included due to their relevance in processed food. The influence has been studied not only on mRNA but also on miRNA. The wide scope of the technology clearly reflects that any simple intervention has profound changes in many metabolic parameters and that there is a synergy in response when more compounds are included in the intervention. Standardized arrays to systematically test the same genes in all studies and analyzing data to establish patterns of response are required, particularly for RNA sequencing. Moreover, RNA is a valuable, easy-screening ally but always requires further confirmation.

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Gene expression and epigenetic changes by furan in rat liver

Cited by 41 publications

References 30 publications

Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray

Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray

Effect of chronic heroin and cocaine administration on global DNA methylation in brain and liver

The Use of Transcriptomics to Unveil the Role of Nutrients in Mammalian Liver

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