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MiRNA expression in healthy carriers of heterozygous BRCA1 mutation and healthy WT controls

ABSTRACT: In order to investigate whether carriers of BRCA1 heterozygous mutation show altered miRNA expression profiles, we established a panel of lymphoblastoid cell lines (LCLs) harboring either mutated or WT BRCA1 (control) and investigated their miRNA expression profiles. We were especially interested whether we find differences in miRNA expression between carriers of missense versus truncating mutation in BRCA1 gene.

ORGANISM(S): Mus musculus Rattus norvegicus Homo sapiens

PROVIDER: GSE60444 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA258279

REPOSITORIES: GEO

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miRNA expression in healthy carriers of heterozygous BRCA1 mutation and healthy WT controls

Project description:In order to investigate whether carriers of BRCA1 heterozygous mutation show altered miRNA expression profiles, we established a panel of lymphoblastoid cell lines (LCLs) harboring either mutated or WT BRCA1 (control) and investigated their miRNA expression profiles. We were especially interested whether we find differences in miRNA expression between carriers of missense versus truncating mutation in BRCA1 gene. We evaluated the miRNA expression in a panel of 21 non-treated lymphoblastoid cell lines (LCLs). Among them, 6 LCLs with WT BRCA1, 5 LCLs carrying missense mutation in BRCA1, and 10 LCLs harboring truncating mutation in BRCA1 were included in this study.

2015-12-31 | E-GEOD-60444 | biostudies-arrayexpress

Effect of BRCA1 heterozygous mutation on gene expression

Project description:In order to investigate whether carriers of BRCA1 heterozygous mutation show altered gene expression profiles, we used a whole genome microarray expression profiling of a panel of lymphoblastoid cell lines (LCLs) harboring either mutated or WT BRCA1 (control). We were especially interested whether we find differences in gene expression between carriers of missense versus truncating mutation in BRCA1 gene. We evaluated gene expression of a panel of 21 non-treated lymphoblastoid cell lines (LCLs). Among them, 6 LCLs with WT BRCA1, 5 LCLs carrying missense mutation in BRCA1, and 10 LCLs harboring truncating mutation in BRCA1 were included in this study.

2015-12-31 | E-GEOD-60396 | biostudies-arrayexpress

Effect of BRCA1 heterozygous mutation on gene expression

2015-12-31 | GSE60396 | GEO

Expression data from mammary epithelial cells from BRCA1 mutation carriers and non BRCA1 mutation carriers

Project description:Female BRCA1 mutation carriers have a nearly 80% probability of developing breast cancer during their life-time. We hypothesized that the breast epithelium at risk in BRCA1 mutation carriers harbors mammary epithelial cells (MECs) with altered proliferation and differentiation properties. Microarray studies revealed that PMEC colonies from BRCA1 mutation carriers anticipate expression profiles found in BRCA1-related tumors, and that the EGFR pathway is upregulated in BRCA1 mutation carriers compared ton non BRCA1 mutation carriers. Keywords: Class comparison and pathway analysis

2008-11-20 | GSE13671 | GEO

Expression data from mammary epithelial cells from BRCA1 mutation carriers and non BRCA1 mutation carriers

2008-11-19 | E-GEOD-13671 | biostudies-arrayexpress

Normal human mammary tissues from BRCA1 mutation carriers, non-BRCA1/2 mutation carriers and normal women

2009-08-01 | GSE17072 | GEO

Normal human mammary tissues from BRCA1 mutation carriers, non-BRCA1/2 mutation carriers and normal women

Project description:Gene expression profiles of normal human mammary tissue from BRCA1 mutation carriers, non-BRCA1/2 mutation carriers and normal women. RNA was prepared from normal breast tissue (confirmed by pathology) from reduction mammoplasties (n=5) and prophylactic mastectomies of known BRCA1 (n=7) and non-BRCA1/2 mutation carriers (n=8). non-BRCA1/2 carriers were individuals with a strong family history of breast cancer (kConFab Category 1 (http://www.kconfab.org/Collection/Eligibility.shtml) where no mutation in BRCA1 or BRCA2 has been identified in the family by high sensitivity testing (http://www.kconfab.org/Progress/Sensitivity.shtml) of any individual affected by breast or ovarian cancer. Normal breast samples refer to reduction mammoplasty specimens, where family history is generally not known. Microarray expression profiles were obtained from whole pre-neoplastic breast tissue from three categories of patient, as described in the summary. Samples were checked for keratin gene expression levels as a marker for epithelium tissue, and a number of samples were removed because two or more keratin genes lacked detectable expression (BeadStudio detection p-value 0.01). One other sample was removed because its expression profile appeared abnormal. Out of 36 samples initially profiled, 20 passed the quality filters and were used for the final analysis.

2009-08-01 | E-GEOD-17072 | biostudies-arrayexpress

Identification of BRCA1/2 mutation carriers using circulating microRNA profiles

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

Profiling BRCA1, BRCA2 and non-BRCA1/2 LCLs post-Irradiation

Project description:The functional consequences of missense variants in disease genes are difficult to predict. We assessed if gene expression profiles could distinguish between BRCA1 or BRCA2 pathogenic truncating and missense mutation carriers and familial breast cancer cases whose disease was not attributable to BRCA1 or BRCA2 mutations (BRCAX cases). 72 cell lines from affected women in high-risk breast-ovarian families were assayed after exposure to ionising irradiation, including 23 BRCA1 carriers, 22 BRCA2 carriers, and 27 BRCAX individuals. A subset of 10 BRCAX individuals carried rare BRCA1/2 sequence variants considered to be of low clinical significance (LCS). BRCA1 and BRCA2 mutation carriers had similar expression profiles, with some subclustering of missense mutation carriers. The majority of BRCAX individuals formed a distinct cluster, but BRCAX individuals with LCS variants had expression profiles similar to BRCA1/2 mutation carriers. Gaussian Process Classifier predicted BRCA1, BRCA2 and BRCAX status with a maximum of 62% accuracy, and prediction accuracy decreased with inclusion of BRCAX samples carrying an LCS variant, and inclusion of pathogenic missense carriers. Similarly, prediction of mutation status with gene lists derived using Support Vector Machines was good for BRCAX samples without an LCS variant (82-94%), poor for BRCAX with an LCS (40-50%), and improved for pathogenic BRCA1/2 mutation carriers when the gene list used for prediction was appropriate to mutation effect being tested (71-100%). This study indicates that mutation effect, and presence of rare variants possibly associated with a low risk of cancer, must be considered in the development of array-based assays of variant pathogenicity. Keywords: cell type comparison, stress response

2008-03-21 | GSE10905 | GEO

caArray_strue-00134: Identification of BRCA1 mutation carriers using oligonucleotide arrays

Project description:To determine if oligonucleotide arrays can be used to identify BRCA1 positive mutation carriers and to gain further insight into the role of BRCA1.

2016-12-08 | GSE91006 | GEO

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