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Exploratory analysis of the human breast DNA methylation profile upon soymilk

ABSTRACT: Exploratory analysis of the human breast DNA methylation profile upon soymilk

PROVIDER: PRJNA448840 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6944410_1.fastq.gz	Fastqsanger.gz
	SRR6944410_2.fastq.gz	Fastqsanger.gz
	SRR6944420_1.fastq.gz	Fastqsanger.gz
	SRR6944420_2.fastq.gz	Fastqsanger.gz
	SRR6944430_1.fastq.gz	Fastqsanger.gz

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Exploratory analysis of the human breast DNA methylation profile upon soymilk

Project description:Upon soy consumption, isoflavone metabolites attain bioactive concentrations in breast tissue possibly affecting health. Though in vitro epigenetic activity of soy metabolites has been described, the in vivo impact on the epigenome is largely unknown. Therefore, in this case-control study, the breast glandular tissue DNA methylome was explored in women undergoing an aesthetic breast reduction. After a run-in phase, 10 generally healthy Belgian or Dutch women received soymilk for 5 days. MethylCap-seq methylation profiles were compared with those of 10 matched controls. Isoflavones and their microbial metabolites were quantified in urine, serum, and glandular breast tissue (liquid chromatography-mass spectrometry) and 17β-estradiol in glandular breast tissue (immunoassay). Global DNA methylation levels were obtained for 6 cases and 5 controls using liquid chromatography-mass spectrometry. Although lower MethylCap-seq coverages were observed, mass spectrometry results and computational LINE-1 methylation analysis did not provide evidence supporting global methylation alterations upon treatment. At a false discovery rate of 0.05, no differentially methylated loci were identified. Moreover, a set of previously identified loci was specifically tested, but earlier reported results could not be validated. In conclusion, after a 5 day soymilk treatment, no epigenetic reprogramming in breast tissue could be found in this exploratory study.

2018-12-25 | GSE112727 | GEO

Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure.

Project description:Upon soy consumption, isoflavone metabolites attain bioactive concentrations in breast tissue possibly affecting health. Though in vitro epigenetic activity of soy metabolites has been described, the in vivo impact on the epigenome is largely unknown. Therefore, in this case-control study, the breast glandular tissue DNA methylome was explored in women undergoing an aesthetic breast reduction. After a run-in phase, 10 generally healthy Belgian or Dutch women received soymilk for 5 days. MethylCap-seq methylation profiles were compared with those of 10 matched controls. Isoflavones and their microbial metabolites were quantified in urine, serum, and glandular breast tissue (liquid chromatography-mass spectrometry) and 17?-estradiol in glandular breast tissue (immunoassay). Global DNA methylation levels were obtained for 6 cases and 5 controls using liquid chromatography-mass spectrometry. Although lower MethylCap-seq coverages were observed, mass spectrometry results and computational LINE-1 methylation analysis did not provide evidence supporting global methylation alterations upon treatment. At a false discovery rate of 0.05, no differentially methylated loci were identified. Moreover, a set of previously identified loci was specifically tested, but earlier reported results could not be validated. In conclusion, after a 5-day soymilk treatment, no major general epigenetic reprogramming in breast tissue could be found in this exploratory study.

| S-EPMC6133922 | biostudies-literature

Intratumoral heterogeneity of DNA methylation in an ovarian metastasis from lobular breast cancer

Project description:In lobular breast cancer, metachronous distant metastasis may become evident many years after primary tumor diagnosis and often affect the ovary. Little is known about tumor dormancy and intratumoral heterogeneity of DNA methylation in metastasis from lobular breast cancer. In this exploratory analysis, DNA methylation patterns were studied in six spacially separated regions of an ovarian metastasis from lobular breast cancer.

2021-12-01 | GSE144359 | GEO

DNA methylation profile for male SD Rats upon fructose treatment by RRBS

Project description:DNA methylation profile for male SD Rats upon fructose treatment by RRBS

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DNA methylation profile of triple negative breast cancer specific genes

Project description:DNA methylation profile of triple negative breast cancer specific genes

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Expression profile of MCF7 and T47D human breast cancer cell lines upon treatment with the BET bromodomian inhibitor JQ1

Project description:Expression profile of MCF7 and T47D human breast cancer cell lines upon treatment with the BET bromodomian inhibitor JQ1

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Assessing the immune profile of primary tumours upon combination of Anakinra with Doxorubicin+Zoledronic acid for the treatment of breast cancer bone metastasis in vivo

Project description:Genetic profile of immune cells was characterised in primary breast tumours upon treatment with Anakinra, Dox+Zol, Anakinra+Dox+Zol

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DNA methylation profile of triple negative breast cancer specific genes (study)

Project description:Purpose Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with no targeted treatment available. Our previous study identified 38 TNBC-specific genes with altered expression in tumour samples compared to normal samples. This study aimed to identify whether DNA methylation contributed to these gene expression changes in the same breast cancer cohort. Additionally, we aimed to identify a whole genome methylation profile that contributes to the progression from primary breast tumour to lymph node metastasis. Methods We used the DNA of 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues to perform 450K Illumina methylation arrays. The results were validated in an independent cohort of 70 primary TNBC samples. Results The gene expression of 16/38 TNBC-specific genes was associated with significantly altered methylation. Furthermore, altered methylation of 18 genes associated with lymph node metastasis was identified and validated in an independent cohort. Additionally, novel methylation changes between primary tumours and lymph node metastases, as well as those associated with survival were identified. Conclusion This study has shown that DNA methylation plays an important role in altered gene expression patterns of TNBC-specific genes and is the first study to perform whole genome DNA methylation analysis that includes matched lymph node metastases in this breast cancer subtype. This novel insight into the progression of TNBC to secondary cancers may provide potential prognostic indicators for this hard-to-treat breast cancer subtype. study cohort

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DNA methylation profile of triple negative breast cancer specific genes (validation)

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cDNA expression profiling of MDA-MB-231 breast cancer cells upon β-hydroxybutyrate treatment

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