Dataset Information

The Effect of the Menstrual Cycle on the Normal Human Breast

ABSTRACT:

The Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center [www.komentissuebank.iu.edu] (KTB) was established expressly for the prospective collection of normal, healthy breast tissue from volunteer donors. Blood is also obtained from donors at the time of donation and is processed for serum, plasma and peripheral blood leukocyte DNA. Specimens are annotated and data includes age, race, ethnicity, personal health history, family cancer history, medication usage at the time of donation, and breast cancer risk factors.

Premenopausal donors to the KTB were identified by a query of the Bank's database. Hematoxylin and eosin stained sections of the formalin-fixed paraffin-embedded tissue of the identified donors were reviewed and tissue was graded on the basis of the abundance of epithelium within the section. Only tissue containing abundant epithelium was considered for this study. Based on dates, the specimens of nine women in the follicular phase of the menstrual cycle and five in the luteal phase were chosen. Six donors using hormonal contraception at the time of donation were also included. Whole blood obtained from 19 of the 20 donors at the time of tissue donation was available and it was processed for serum. Estradiol, estriol, luteinizing hormone and progesterone concentrations were determined by the Indiana University Health Pathology Laboratory using a Beckman Unicel DxI 800 Immunoassay System. The phase of the menstrual cycle was verified by serum progesterone concentration. The epithelium of these 20 specimens was microdissected from multiple 8 micron frozen tissue sections. Total RNA extracted from the tissue was subsequently depleted of rRNA via locked nucleic acid probes. This enabled profiling of both poly-A and non-poly-A RNA species. Barcoded cDNA libraries from the 20 normal breast epithelia were prepared and sequenced on an Applied Biosystems (AB) SOLiD3 or SOLiD 4 platform. RNA-seq reads for each sample were then mapped to the human genome (hg19) using the LifeScope software version 2.5.1 (Life Technologies, Foster City, CA) and BAM (Binary Alignment/Map) files generated. Read counts for each gene were derived from the output BAM files using the RefSeq database (UCSC Genome Brower) as the gene model.

PROVIDER: phs000644 | dbGaP |

SECONDARY ACCESSION(S): PRJNA213366PRJNA213365

REPOSITORIES: dbGaP

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Dataset's files

Source:

			Action	DRS
	GapExchange_phs000644.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs000644.Breast_MenstrualCycleEffect.v1.p1.MULTI.pdf	Pdf
	manifest_phs000644.Breast_MenstrualCycleEffect.v1.p1.c1.DS-BRCA-PUB-MDS.pdf	Pdf
	datadict_v2.xsl	Other

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Project description:The Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center [<a href="www.komentissuebank.iu.edu" target="_blank">www.komentissuebank.iu.edu</a>] (KTB) was established expressly for the prospective collection of normal, healthy breast tissue from volunteer donors. Blood is also obtained from donors at the time of donation and is processed for serum, plasma and peripheral blood leukocyte DNA. Specimens are annotated and data includes age, race, ethnicity, personal health history, family cancer history, medication usage at the time of donation, and breast cancer risk factors. Premenopausal donors to the KTB were identified by a query of the Bank's database. Hematoxylin and eosin stained sections of the formalin-fixed paraffin-embedded tissue of the identified donors were reviewed and tissue was graded on the basis of the abundance of epithelium within the section. Only tissue containing abundant epithelium was considered for this study. Based on dates, the specimens of nine women in the follicular phase of the menstrual cycle and five in the luteal phase were chosen. Six donors using hormonal contraception at the time of donation were also included. Whole blood obtained from 19 of the 20 donors at the time of tissue donation was available and it was processed for serum. Estradiol, estriol, luteinizing hormone and progesterone concentrations were determined by the Indiana University Health Pathology Laboratory using a Beckman Unicel DxI 800 Immunoassay System. The phase of the menstrual cycle was verified by serum progesterone concentration. The epithelium of these 20 specimens was microdissected from multiple 8 micron frozen tissue sections. Total RNA extracted from the tissue was subsequently depleted of rRNA via locked nucleic acid probes. This enabled profiling of both poly-A and non-poly-A RNA species. Barcoded cDNA libraries from the 20 normal breast epithelia were prepared and sequenced on an Applied Biosystems (AB) SOLiD3 or SOLiD 4 platform. RNA-seq reads for each sample were then mapped to the human genome (hg19) using the LifeScope software version 2.5.1 (Life Technologies, Foster City, CA) and BAM (Binary Alignment/Map) files generated. Read counts for each gene were derived from the output BAM files using the RefSeq database (UCSC Genome Brower) as the gene model.

Project description:The Biospecimen Pre-analytical Variables (BPV) Program is a National Cancer Institute-sponsored study to systematically assess the effects of pre-analytical factors on the molecular profile of biospecimens. A robust biospecimen collection infrastructure was established to prospectively collect biospecimens using rigorous standard operating procedures to control for most variables while introducing experimental conditions to study specific biospecimen handling issues, including the cold ischemic time (delay to formalin fixation), time in formalin, freezing methods, and storage temperatures and durations. RNA and DNA from biospecimens collected under these conditions was analyzed on multiple molecular platforms. The potential effects of these pre-analytical conditions on protein integrity and detection of metabolites were also examined. Data from this study will be used to develop evidence-based biospecimen standard operating procedures and best practices for fit-for-purpose collection, processing, and storage of biospecimens. The BPV Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following sub-studies below or in the "Substudies" box located on the right hand side of this top-level study page phs001304 BPV Cohort. The substudy links will be active once they are released by dbGaP. <ol> <li>Preanalytical Impacts on Global Metabolite Profiling - plasma (MassSpec by Metabolon) This study was to evaluate the impact of the storage temperature (s) (-80°C and LN2 vapor) and the length of storage on human plasma quality using LC-MS/MS (liquid-chromatography-mass spectrometry/mass spectrometry) based global metabolite profiling. The study includes 240 plasma samples collected from 40 donors.</li> <li>Investigate the effect of the delay to fixation on the proteome and phosphoproteome -FFPE (MassSpec by Caprion). The study is to do proteome and phosphoproteome analysis on Delay to fixation was carried out using FFPE tumor samples from colon and ovarian cancer patients comparing 2, 3, and 12hr delay to fixation to the 1hr time point. The study includes 100 samples 20 donors.</li> <li>Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling- Frozen tissue and plasma (MassSpec by Caprion). The study was to evaluate the effects of storage conditions on tumor specimens. Plasma samples from 40 cancer patients stored at two different temperatures (-80°C and LN2) for a given period (0-2, 6-8, and 12-14 months) were evaluated. Frozen kidney tumor samples from 20 patients were compared for effects of different snap frozen (dry ice vs. LN2) and storage temperatures (-80°C and LN2). The study includes 100 tissue and 240 plasma samples from 60 donors.</li> <li>Preanalytical Impacts on Genomic Sequencing by Next Generation Sequencing (NGS) technology (mRNA/miRNA and WES by Expression Analysis). The goal of the study is to determine the effects of cold ischemic delay-to-fixation (4 time points) and formalin preservation (FFPE) on the nature and quality of genomic profiles using the matched freshly frozen sample as the gold standard, which including WES, RNAseq. The study includes 395 samples from 37 donors.</li> <li>Preanalytical Impacts on Copy Number Variation (CNV) Detection by aCGH technology (aCGH by Georgetown University). This study was to use aCGH to evaluate the effect of variation in cold ischemia time and time in formalin fixation on CNV in DNA extracted from kidney cancer specimens. The study includes 235 samples from 40 donors.</li> <li>Evaluation of frozen conditions on mRNA profiling by TaqMan assay (mRNA expression by Georgetown University). This study was to utilize gene expression profiling, using custom TaqMan arrays, to compare the molecular profiles of RNA from frozen tumor samples collected using two freezing methods (dry ice or LN2), two storage temperatures (-80°C or LN2 vapor), as well as Optimal Cutting Temperature (OCT) compound and non-OCT embedded. The study includes 100 samples from 20 donors.</li> <li>mRNA signature for stratification by cold ischemia time (mRNA expression by IBBL). The study was to determine the effects of cold ischemic time (delay-to-fixation) and formalin preservation (FFPE) on mRNA detection by Taqman assay using tumor tissue specimens from kidney, colon and ovarian cancer patients. There are160 samples from 40 donors.</li> </ol> The Biospecimen PV cohort is utilized in the following dbGaP individual studies. To view molecular data, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page <a href="study.cgi?study_id=phs001304">phs001304</a> Biospecimen PV cohort. <ul> <li><a href="study.cgi?study_id=phs001634">phs001634</a> CIT mRNA</li> <li><a href="study.cgi?study_id=phs001635">phs001635</a> CNV aCGH</li> <li><a href="study.cgi?study_id=phs001636">phs001636</a> Fixation Delay</li> <li><a href="study.cgi?study_id=phs001637">phs001637</a> Global Metabolite Profiling</li> <li><a href="study.cgi?study_id=phs001638">phs001638</a> mRNA TaqMan</li> <li><a href="study.cgi?study_id=phs001639">phs001639</a> NGS</li> <li><a href="study.cgi?study_id=phs001640">phs001640</a> Tumor Storage</li> </ul>

Project description:The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from 5 time points of the estrous cycle (D0, D3, D8, D12, and D16) was performed to study the dynamics of endometrial gene expression. Endometrial biopsies were collected from five mares (Bavarian Warmblood) at the respective time points. Samples were divided and subjected to isolation of RNA for microarray analysis and analysis of tissue composition. Blood samples were collected to determine serum progesterone levels for every sample. Statistical analysis of microarray data revealed almost 10,000 differential probes corresponding to 4,996 differentially expressed genes. A cluster analysis based on gene expression profiles during the estrous cycle revealed 8 major gene expression profiles: mRNAs with highest levels 1) at D0, 2) from D0 to D3, 3) at D3, 4) from D3 to D8, 5) at D8, 6) from D8 to D12, 7) from D12 to D16, and 8) at D16. DAVID Functional Annotation Clustering revealed overrepresentation of distinct functional terms in different phases of the cycle, e.g. M-bM-^@M-^Xextracellular matrixM-bM-^@M-^Y and M-bM-^@M-^Xprotein transportM-bM-^@M-^Y during estrus, M-bM-^@M-^XDNA replication and M-bM-^@M-^Xcell cycleM-bM-^@M-^Y during early luteal phase, M-bM-^@M-^Xendoplasmic reticulumM-bM-^@M-^Y and M-bM-^@M-^Xprotein transportM-bM-^@M-^Y in the luteal phase, and M-bM-^@M-^Xinflammatory responseM-bM-^@M-^Y in the late luteal and follicular phase. Expression of selected genes of the expression clusters was validated by quantitative Real-time PCR (qPCR). This study provides new insights into global changes of equine endometrial gene expression during the estrous cycle. Equine endometrial tissue samples were collected at 5 time points during the sexual (estrous) cycle from 5 mares (5 biological replicates per time point) and analyzed with Agilent microarrays.

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The Effect of the Menstrual Cycle on the Normal Human Breast

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