Myoepithelial cell perturbations in BRCA mutation carriers and in DCIS (ductal carcinoma in situ)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA454004 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7074670.fastq.gz | Fastqsanger.gz | |||
| SRR7074680.fastq.gz | Fastqsanger.gz | |||
| SRR7074671.fastq.gz | Fastqsanger.gz | |||
| SRR7074681.fastq.gz | Fastqsanger.gz | |||
| SRR7074672.fastq.gz | Fastqsanger.gz |
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Project description:We describe the gene expression profiles and enhancer landscape of normal myoepithelial cells and perturbations of these in BRCA1 and BRCA2 mutation carriers and in DCIS. We identified a myoepithelial transcription regulatory network orchestrated by p63 and TCF7 and defined the genomic targets of these transcription factors by ChIP-seq. While the majority of myoepithelial cells co-express p63 and TCF7 in normal breast of healthy women, the frequency of these cells is significantly lower in BRCA1 mutation carriers and in DCIS. Downregulation of p63 in MCF10DCIS cells leads to loss of myoepithelial cells and invasive tumors, whereas overexpression of TCF7 enhances tumor growth. Our findings suggest that loss of normal myoepithelial cell function facilitates in situ to invasive carcinoma transition and it may also enhance tumor initiation in BRCA mutation carriers.
2021-04-27 | GSE113795 | GEO
Project description:We describe the gene expression profiles and enhancer landscape of normal myoepithelial cells and perturbations of these in BRCA1 and BRCA2 mutation carriers and in DCIS. We identified a myoepithelial transcription regulatory network orchestrated by p63 and TCF7 and defined the genomic targets of these transcription factors by ChIP-seq. While the majority of myoepithelial cells co-express p63 and TCF7 in normal breast of healthy women, the frequency of these cells is significantly lower in BRCA1 mutation carriers and in DCIS. Downregulation of p63 in MCF10DCIS cells leads to loss of myoepithelial cells and invasive tumors, whereas overexpression of TCF7 enhances tumor growth. Our findings suggest that loss of normal myoepithelial cell function facilitates in situ to invasive carcinoma transition and it may also enhance tumor initiation in BRCA mutation carriers.
2019-08-20 | GSE113909 | GEO
Project description:Myoepithelial cell perturbations in BRCA mutation carriers and in DCIS (ductal carcinoma in situ)
| PRJNA454454 | ENA
Project description:There are currently no screening methods for high grade ovarian cancer (HGOC) that guarantee effective early detection for high risk women such as germline BRCA mutation carriers. Therefore, the standard-of-care remains risk reducing salpingo-oophorectomy (RRSO) around age 40. Proximal liquid biopsy has been shown to be a promising source of biomarkers, but sensitivity has not yet qualified for clinical implementation. We report the discriminant performance of a novel proteomic classifier for detection of HGOC in high-risk population, and the safety and feasibility of simplified utero-tubal lavage (UtL) as a method for sampling proximal liquid biopsy.The training set included 93 women with high-risk for HGOC (BRCA1 and BRCA2 mutation carriers), including: 16 HGOC patients and 77 asymptomatic women, who donated UtL liquid biopsies, in 3 Israeli medical centers (Biomarkers for Early Detection of Ovarian Cancer Using Uterine Lavage (BEDOCA); ClinicalTrials.gov Identifier: NCT03150121). The proteome of the microvesicle fraction of the samples was profiled by mass spectrometry and a classifier was developed using logistic regression. An independent cohort of 104 BRCA mutation carriers was used as validation. Safety information was collected for all women who opted to UtL in a clinic setting.
2022-09-13 | PXD030390 | Pride
Project description:The development of non-invasive primary cancer preventive measures in humans require a thorough understanding of the initial cancer-driving molecular mechanisms. High grade serous extra-uterine M llerian cancers (HGSEMC; formerly classified as ovarian/tubal/peritoneal cancer) present at a very late stage and less than 40% of women survive 5 years. Although the recent TCGA initiatives revealed key molecular changes in established cancers, very little is known about the initial molecular alterations in cancer development. Analysis of normal tissue at extensively high risk prior to the development of any microscopic alterations is critical. BRCA1/2 mutation carriers have an up to 30 40 fold increased risk to develop ovarian cancer, preferentially HGSEMC. Despite a plethora of evidence linking mutations in BRCA1 or BRCA2 to cancer development the core components such as organ specificity (i.e. to breast and Fallopian Tube) are still missing. The Fallopian Tube of BRCA mutation carriers offers a unique opportunity to study carcinogenesis because these cancers originate only from the distal (i.e. fimbrial) end of the Fallopian Tube (which is in close proximity to the ovary), and not from the proximal end (which is close to the uterus). The ovary which is in extreme close proximity to the fimbriae provides an excellent soil for cancer cells which are likely shed from the fimbriae and once the cancer has been discovered the big bulk of tumour is usually present on the ovary and hence the majority of HGSEMC are also referred to as ovarian cancer . To study the earliest steps of human carcinogenesis we performed epigenome-wide DNA methylation (DNAme) analyses (using the Illumina 450k DNA methylation bead-array assay assessing DNAme at ~480 000 CpG sites) in 215 microscopic normal Fallopian Tube samples of BRCA1/2 mutation carriers (n=56) and controls (n=59) who had their tubes/ovaries removed for prophylactic or other reasons, respectively (for 52 and 49 individuals respectively we analysed both fimbrial and proximal Fallopian Tubes). In order to adjust for any epigenetic effects which are not of immediate importance to the carcinogenic process, for each volunteer we analysed both the fimbrial (at risk) and the proximal (non at risk) portion of the tubes separately. Formalin fixed paraffin embedded (FFPE) tissue blocks were retrieved from UCL Biobank (NC09.13). Histopathological features of fimbrial and proximal section of Fallopian Tube from BRCA carriers and control cases were carefully examined. Cases negative for serous tubal intraepithelial carcinoma (STIC) lesions were chosen for DNA isolation to characterize pre-cancer epigenetic changes. For DNA isolation, a core of 3 x 0.6 mm was taken from each block representing fimbrial and proximal end of fallopian tubes from both BRCA carriers and matched control cases. The DNA was isolated using QIAamp(r) DNA FFPE Tissue Kit as per manufacturer's protocol with minor modifications (Dewaxing for 4 hours in xylene and proteinase digestion performed overnight, other procedures were as per the instructions). DNA was quantified using Nandrop and restored using the Infinium FFPE DNA Restore Kit and then 200 nanogram of DNA was bisulfite converted using the EZ DNA Methylation-Gold(tm) and subjected to methylation analysis on the Illumina Infinium Human Methylation450 BeadChip.
2016-05-19 | E-GEOD-74845 | biostudies-arrayexpress
Project description:The development of non-invasive primary cancer preventive measures in humans require a thorough understanding of the initial cancer-driving molecular mechanisms. High grade serous extra-uterine M llerian cancers (HGSEMC; formerly classified as ovarian/tubal/peritoneal cancer) present at a very late stage and less than 40% of women survive 5 years. Although the recent TCGA initiatives revealed key molecular changes in established cancers, very little is known about the initial molecular alterations in cancer development. Analysis of normal tissue at extensively high risk prior to the development of any microscopic alterations is critical. BRCA1/2 mutation carriers have an up to 30 40 fold increased risk to develop ovarian cancer, preferentially HGSEMC. Despite a plethora of evidence linking mutations in BRCA1 or BRCA2 to cancer development the core components such as organ specificity (i.e. to breast and Fallopian Tube) are still missing. The Fallopian Tube of BRCA mutation carriers offers a unique opportunity to study carcinogenesis because these cancers originate only from the distal (i.e. fimbrial) end of the Fallopian Tube (which is in close proximity to the ovary), and not from the proximal end (which is close to the uterus). The ovary which is in extreme close proximity to the fimbriae provides an excellent soil for cancer cells which are likely shed from the fimbriae and once the cancer has been discovered the big bulk of tumour is usually present on the ovary and hence the majority of HGSEMC are also referred to as ovarian cancer . To study the earliest steps of human carcinogenesis we performed epigenome-wide DNA methylation (DNAme) analyses (using the Illumina 450k DNA methylation bead-array assay assessing DNAme at ~480 000 CpG sites) in 215 microscopic normal Fallopian Tube samples of BRCA1/2 mutation carriers (n=56) and controls (n=59) who had their tubes/ovaries removed for prophylactic or other reasons, respectively (for 52 and 49 individuals respectively we analysed both fimbrial and proximal Fallopian Tubes). In order to adjust for any epigenetic effects which are not of immediate importance to the carcinogenic process, for each volunteer we analysed both the fimbrial (at risk) and the proximal (non at risk) portion of the tubes separately.
2016-05-19 | GSE74845 | GEO
Project description:Myoepithelial cells play key roles in normal mammary gland development and in limiting pre-invasive to invasive breast tumor progression, yet their differentiation and perturbation in ductal carcinoma in situ (DCIS) are poorly understood. Here, we investigated myoepithelial cells in normal breast tissues of BRCA1 and BRCA2 germline mutation carriers and in non-carrier controls, and in sporadic DCIS. We found that in the normal breast of non-carriers, myoepithelial cells frequently co-express the p63 and TCF7 transcription factors and that p63 and TCF7 show overlapping chromatin peaks associated with differentiated myoepithelium-specific genes. In contrast, in normal breast tissues of BRCA1 mutation carriers the frequency of p63+TCF7+ myoepithelial cells is significantly decreased and p63 and TCF7 chromatin peaks do not overlap. These myoepithelial perturbations in normal breast tissues of BRCA1 germline mutation carriers may play a role in their higher risk of breast cancer. The fraction of p63+TCF7+ myoepithelial cells is also significantly decreased in DCIS, which may be associated with invasive progression.
| S-EPMC6744561 | biostudies-literature
Project description:Identifying germline BRCA1/2 mutation carriers is vital for reducing their risk of breast and ovarian cancer; however, many carriers are not referred for genetic testing. While population-wide testing is not feasible, a cheap functional screen for phenotypic ‘BRCAness’ could guide efforts for focused genetic counseling and improve cancer prevention and early detection. The aim of this study was to derive a serum-based miRNA panel to identify BRCA1/2 mutation carriers among healthy controls. We performed a diagnostic biomarker study based on serum samples collected between by six international cohorts. Serum samples from 653 healthy women with known mutation status of BRCA1 and BRCA2 were used in the analysis. All individuals had no history of prior cancer or any detected malignancies for at least 12 months after sample collection. Among the study population, 350 (53.6%) subjects had BRCA mutations and 303 (46.4%) were BRCA1/2 – wild-type. In all individuals, we isolated and quantified miRNAs expression using RNA-sequencing. Variable selection based on differential expression analysis on merged, batch adjusted cohorts was performed to identify a set of miRNAs associated with BRCA mutation carrier status.
2023-05-02 | GSE226445 | GEO
Project description:cDNA aCGH study of pure DCIS (breast duct carcinoma in situ) without invasive tumor, DCIS associated with IDC (breast invasive duct carcinoma) and its IDC component 23 patients: 6 pure DCIS without invasive cancer and no history of invasive cancer, 17 DCIS associated with IDC. Out of the latter 1 tumor had only enough DCIS (#16) for aCGH and one - IDC (#23) Keywords: Comparative clinical study
2009-02-01 | GSE10197 | GEO
Project description:Purpose:Triple negative breast cancer (TNBC) commonly metastasizes to the brain and predicts poor prognosis with limited therapeutic options. TNBC frequently harbors BRCA mutations translating to platinum sensitivity; platinum response may be augmented by additional suppression of DNA repair mechanisms through poly(ADP-ribose)polymerase (PARP) inhibition. We evaluated brain penetrance and efficacy of Carboplatin +/- the PARP inhibitor ABT888, and investigated gene expression changes in murine intracranial (IC) TNBC models stratified by BRCA and molecular subtype status. Experimental design:Athymic mice were inoculated intra-cerebrally with BRCA-mutant: SUM149 (basal), MDA-MB-436 (claudin-low), or BRCA-wild-type: MDA-MB-468 (basal), MDA-MB-231BR (claudin-low) TNBC cells and treated with PBS control (IP, weekly), Carboplatin (50mg/kg/week, IP), ABT888 (25mg/kg/day, OG), or their combination. DNA-damage (?-H2AX) and apoptosis (cleaved-Caspase-3(cC3)) were assessed via IHC of IC tumors. Gene expression of BRCA-mutant IC tumors was measured. Results: Carboplatin+/-ABT888 significantly improved survival in BRCA-mutant IC models compared to control, but did not improve survival in BRCA-wild-type IC models. Carboplatin+ABT888 revealed a modest survival advantage versus Carboplatin in BRCA-mutant models. ABT888 yielded a marginal survival benefit in the MDA-MB-436 but not in the SUM149 model. BRCA-mutant SUM149 expression of ?-H2AX and cC3 proteins was elevated in all treatment groups compared to Control, while BRCA-wild-type MDA-MB-468 cC3 expression did not increase with treatment. Carboplatin treatment induced common gene expression changes in BRCA-mutant models.Conclusions: Carboplatin+/-ABT888 improves survival in BRCA-mutant IC TNBC models with corresponding DNA damage and gene expression changes. Combination therapy represents a promising treatment strategy for patients with TNBC brain metastases warranting further clinical investigation. reference x sample
2015-05-12 | E-GEOD-55399 | biostudies-arrayexpress