Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA553069 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. In epigenome-wide analyses we identified 58 differentially methylated CpG sites associated with breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer (q-value < 0.05), using linear mixed effects models adjusted for history of breast biopsy, age, age of the baby, cell type proportion estimates, array chip, and subject as random effect. Nearly all sites associated with breast cancer diagnosis were hypomethylated in cases compared with controls, and CpG sites were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has promise as a biospecimen for prospective assessment of disease risk, and for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.
2019-12-06 | GSE133918 | GEO
Project description:Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk. Of all these fluids, only breast milk provides access to a large volume of breast tissue, in the form of exfoliated epithelial cells, and to the local breast environment, in the form of molecules in the milk. Thus, analysis of breast milk is a non-invasive method with significant potential for assessing BC risk. Here we analyzed human breast milk by mass spectrometry (MS)-based proteomics to build a biomarker signature for early detection of BC. Ten milk samples from 8 women provided 5 paired-groups (cancer versus control) for analysis of differentially expressed proteins: 2 within woman comparisons (milk from a diseased breast versus a healthy breast of the same woman) and 3 across women comparisons (milk from a woman with cancer versus a woman without cancer). Despite a wide range in the time between milk donation and cancer diagnosis (cancer diagnosis occurred from 1 month before to 24 months after milk donation), the levels of some proteins differed significantly between cancer and control in several of the 5 comparison groups. These pilot data are supportive of the idea that molecular analysis of breast milk will identify proteins informative for early detection and accurate assessment of BC risk, and warrant further research.
2017-12-18 | PXD007066 | Pride
Project description:We used Affymetrix microarrays to investigate gene expression changes in somatic cells from breast-milk extracted from women suffering from mastitis and taking a daily dose of three capsules with ~50 mg of a freeze-dried probiotic (~109 CFU of L. salivarius PS2 strain) for 21 days. Healthy women were subjected to the same treatment for comparison. The aim of this work was to determine whether the daily intake of a probiotic strain for a total of 21 days exerted any modulatory effects, at the level of gene expression, in somatic cells from breast-milk in women with mastitis. Women were divided into 2 groups: mastitis and healthy. Total RNA was extracted from breast-milk isolated cells obtained from 10 participants (7 women from the mastitis group and 3 women from the healthy group) at day 0 (initial) and after 21 days (final) to compare differential gene expression between the groups. Differential gene expression after 21 days of the study for each group: mastitis and healthy
2015-01-21 | E-GEOD-65152 | biostudies-arrayexpress
Project description:Breast milk is a complex liquid that enriched in immunological components and affect the development of the infant immune system. Exosomes, the membranous vesicles of endocytic origin, are ubiquitously in various body fluids which can mediate intercellular communication. MicroRNAs (miRNAs), a well-defined group of non-coding small RNAs, in human breast milk are packaged inside exosomes. Here, we present the identification of miRNAs in human breast milk exosomes using deep sequencing technology. We found that the immune-related miRNAs are enriched in breast milk exosomes, and are resistant to the general harsh conditions. Four small RNA libraries in human breast milk exosomes from four healthy women (30 +/- 0.9 years old, primiparity) when the infant were aged at 60 days were sequenced.
2011-12-21 | E-GEOD-32253 | biostudies-arrayexpress
Project description:Breast Cancer (BC) is one of the most common cancers and one of the most common causes for cancer- related mortality. Discovery of protein biomarkers associated with cancer, is considered as important for early diagnosis and prediction of the cancer risk. Protein biomarkers could be investigated by large-scale protein investigation or proteomics, using mass spectrometry (MS)- based techniques. Our group applies MS-based proteomics to study the protein pattern in human breast milk from women with BC and controls and investigates the alterations and dysregula-tions of breast milk proteins in comparison pairs of BC versus control. These dysregulated pro-teins might be considered as potential future biomarkers of BC. Identification of potential bi-omarkers in breast milk may benefit young women without BC, but who could collect the milk for future assessment of BC risk. Previously we identified several dysregulated proteins in dif-ferent sets of human breast milk samples from BC patients and controls using gel-based protein separation coupled with MS. Here, we performed two-dimensional polyacrylamide gel electro-phoresis (2D-PAGE) coupled with nano-liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) in a small-scale study on a set of 6 human breast milk samples (3 BC samples vs. 3 controls) and we identified several dysregulated proteins which have potential roles in cancer progression and might be considered as potential BC biomarkers in the future.
2023-10-20 | PXD040188 | Pride
Project description:We used Affymetrix microarrays to investigate gene expression changes in somatic cells from breast-milk extracted from women suffering from mastitis and taking a daily dose of three capsules with ~50 mg of a freeze-dried probiotic (~109 CFU of L. salivarius PS2 strain) for 21 days. Healthy women were subjected to the same treatment for comparison.
2015-01-21 | GSE65152 | GEO
Project description:Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis, we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an epigenome-wide association study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip and subject as random effect. We identified 58 differentially methylated CpG sites associated with a subsequent breast cancer diagnosis (q-value <0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.
| S-EPMC7068171 | biostudies-literature
Project description:By using the cutting-edge technology of high-resolution LC-MS/MS, we do not only investigate the proteome of breast milk samples but also the glycoproteome. What’s more, the purpose of our research is to investigate the feasibility of breastfeeding of COVID-19 puerperant women which is closer to the clinical demand. Last but not least, we collected in detailed information of puerperant woman as well as their breast milk samples in different stages.
2021-03-16 | PXD024776 |
Project description:Breast Cancer (BC) remains a major cause of mortality, and early detection is considered important for reducing BC-associated deaths. Early detection of BC is challenging in young women, due to the limitations of mammography on the dense breast tissue of young women. We recently reported results of a pilot study, using one-dimensional polyacrylamide gel electrophoresis (1D-PAGE)-based mass spectrometry (MS) to investigate differences in milk proteins from women with and without BC. Here, we applied two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)-based MS to compare the protein pattern in milk from the breasts of a single woman who was diagnosed with BC in one breast 24 months after donating her mil. Statistically different gel spots were picked for protein digestion followed by nanoLC-MS/MS analysis. The upregulated proteins in BC versus control are alpha-amylase, gelsolin isoform a precursor, alpha-2-glycoprotein 1 zinc isoform CRA_b partial, apoptosis-inducing factor 2 and vitronectin. Several proteins were downregulated in the milk of the breast later diagnosed with cancer as compared to the milk from the healthy breast, including different isoforms of albumin, cholesterol esterase, different isoforms of lactoferrin, different proteins from the casein family and different isoforms of lysozyme. Results warrant further studies to determine the usefulness of these milk proteins for assessing risk and detecting occult disease.
2018-06-25 | PXD009860 | Pride
Project description:Breast milk is a complex liquid that enriched in immunological components and affect the development of the infant immune system. Exosomes, the membranous vesicles of endocytic origin, are ubiquitously in various body fluids which can mediate intercellular communication. MicroRNAs (miRNAs), a well-defined group of non-coding small RNAs, in human breast milk are packaged inside exosomes. Here, we present the identification of miRNAs in human breast milk exosomes using deep sequencing technology. We found that the immune-related miRNAs are enriched in breast milk exosomes, and are resistant to the general harsh conditions.
2011-12-21 | GSE32253 | GEO