TestChip Expression data of skeletal muscle from of HRT users and non-users
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE6378 | GEO | 2007/11/19
SECONDARY ACCESSION(S): PRJNA99605
REPOSITORIES: GEO
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Project description:Modification of Gene Expression of Skeletal Muscle in Response to postmenopause with or without Hormone Replacement Therapy. Even though menopause is often accompanied with first signs of age-associated changes in muscle structure and function, the effects of hormone replacement therapy (HRT) or menopause-related decline in estrogen production in the muscles of postmenopausal women is not well understood. We have used a randomized double-blinded study design together with an explorative microarray experiment to characterize possible effects of continuous, combined HRT and estrogen deprivation on the skeletal muscle of fifteen early postmenopausal women from which 10 used HRT and 5 used placebo for 12-months in a douple-blinded design. Keywords: time course analysis from HRT users and non-users comparison of gene expression in skeletal muscle of healthy postmenopausel women using HRT (n=10) vs not-using HRT (n=5)
2007-11-12 | E-GEOD-6348 | biostudies-arrayexpress
Project description:Modification of Gene Expression of Skeletal Muscle in Response to postmenopause with or without Hormone Replacement Therapy. Even though menopause is often accompanied with first signs of age-associated changes in muscle structure and function, the effects of hormone replacement therapy (HRT) or menopause-related decline in estrogen production in the muscles of postmenopausal women is not well understood. We have used a randomized double-blinded study design together with an explorative microarray experiment to characterize possible effects of continuous, combined HRT and estrogen deprivation on the skeletal muscle of fifteen early postmenopausal women from which 10 used HRT and 5 used placebo for 12-months in a douple-blinded design. Keywords: time course analysis from HRT users and non-users
2007-11-12 | GSE6348 | GEO
Project description:The American Women's Health Initiative study published in July 2002 caused considerable concern among hormone replacement therapy (HRT) users and prescribers in many countries. This study is an exploratory research comparing the genome wide expression profile in whole blood samples according to HRT use. Within the Norwegian Women and Cancer study, 100 postmenopausal women (50 HRT users and 50 non-HRT users) born between 1943 and 1949 with normal to high body mass index and no other medication use were selected. After total RNA extraction, amplification and labelling, the samples were hybridized together with a common reference (Universal human reference RNA, Stratagen) to Agilent Human 1A oligoarrays (G4110b, Agilent Technologies, Palo Alto, CA) containing 20,173 unique genes. Differentially expressed genes were used to build a classifier using the nearest shrunken centroids method (PAM). Then, we tested the significant changes in single genes by different methods like t-test, Significance Analysis of Microarrays (SAM) and Bayesian ANOVA analysis (BAM). Results did not reveal any distinct gene list which predicted accurately HRT exposure (error rate = 0.45). Classifier performance slightly improved (error rate = 0.29) including only women who were using continuous combined HRT treatment. According to the small amplitude of expression alterations observed after HRT use in whole blood, large sample sizes are needed to identify significant single genes differentially expressed. However, significant enrichments in biologic process of genes with small changes after HRT use were observed (e.g. receptor and transporter activities, immune response, frizzled signalling pathway, actin filament organization, glycogen metabolism). Experiment Overall Design: Indirect design with Stratagene reference Experiment Overall Design: 47 non HRT users and 42 HRT users Experiment Overall Design: No technical replicates
2007-11-28 | E-GEOD-3492 | biostudies-arrayexpress
Project description:Women’s aging is characterized by menopausal loss of ovarian function, which has been suggested as a contributing factor to aging-related muscle deterioration and predisposes to the metabolic dysfunctions. However, the underlying molecular mechanisms have remained unknown. To identify mechanisms, we utilized muscle samples from 24 pre- and postmenopausal women, established proteome-wide profiles and identified upstream regulators and downstream cellular pathways associated with the differences in age, menopausal status and use of hormone replacement therapy (HRT). None of the premenopausal women used hormonal medication while the postmenopausal women were monozygotic twin-sister pairs who were either current HRT users or had never used HRT. The proteomic analyses resulted in the quantification of 762 muscle proteins of which 158 were for the first time associated with female muscle aging. The Ingenuity Pathway Analysis pinpointed 17β-estradiol as a potential upstream regulator of the observed differences in the major downstream pathways including dysregulated cell death and glycolysis pathways. The results increase knowledge on the factors related to skeletal muscle signaling and aging. This is of importance, since the role of female sex hormones in the regulation of muscle cell signaling has been under appreciated and scarcely studied as compared to vast amount of data on male sex hormones and skeletal muscle. Our results clearly demonstrate the also female sex hormones and HRT should be considered as potential active players and an intervention targets to promote women’s muscular health.
2017-09-12 | PXD006446 | Pride
Project description:The American Women’s Health Initiative study published in July 2002 caused considerable concern among hormone replacement therapy (HRT) users and prescribers in many countries. This study is an exploratory research comparing the genome wide expression profile in whole blood samples according to HRT use. Within the Norwegian Women and Cancer study, 100 postmenopausal women (50 HRT users and 50 non-HRT users) born between 1943 and 1949 with normal to high body mass index and no other medication use were selected. After total RNA extraction, amplification and labelling, the samples were hybridized together with a common reference (Universal human reference RNA, Stratagen) to Agilent Human 1A oligoarrays (G4110b, Agilent Technologies, Palo Alto, CA) containing 20,173 unique genes. Differentially expressed genes were used to build a classifier using the nearest shrunken centroids method (PAM). Then, we tested the significant changes in single genes by different methods like t-test, Significance Analysis of Microarrays (SAM) and Bayesian ANOVA analysis (BAM). Results did not reveal any distinct gene list which predicted accurately HRT exposure (error rate = 0.45). Classifier performance slightly improved (error rate = 0.29) including only women who were using continuous combined HRT treatment. According to the small amplitude of expression alterations observed after HRT use in whole blood, large sample sizes are needed to identify significant single genes differentially expressed. However, significant enrichments in biologic process of genes with small changes after HRT use were observed (e.g. receptor and transporter activities, immune response, frizzled signalling pathway, actin filament organization, glycogen metabolism). Keywords: gene expression profile and exposure
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Project description:MicroRNAs regulate the biological aggressiveness of colorectal cancer (CRC) cells and might serve as potential prognostic factors and therapeutic targets. In this study, we therefore globally profiled microRNAs associated with aggressive growth in CRC cells, in an attempt to identify novel prognostic biomarkers in CRC patients. In detail, two different CRC cell lines (Caco-2 and HRT-18) with completely different growth rates and different E-cadherin expression were profiled for differences in more than 1000 human microRNAs by using microarray technology. Two-condition experiment, HRT-18 vs. Caco-2. Biological replicates: 3, independently grown and harvested. On each array, one BR of HRT-18 cells was directly compared to one BR of Caco-2 cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.
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Project description:Whole blood rather than purified peripheral blood mononuclear cells is likely to become the prime tissue using expression microarrays for disease predication or prognosis however excess of globin mRNA may reduce probe detection sensitivity. In our study, we assessed whether whole-blood or globin-reduced RNA gives the most robust and sensitive results to detect small gene expression changes in response to hormone replacement therapy exposure. Each sample (N = 12) were hybridized according to 3 different protocols: no globin reduction (controls), globin reduction using peptid nucleic acids (PNA) and using magnetic beads in the GlobinClear kit from Ambion. Finally, 7 and 4 technical replicates were conducted in no globin reduction and PNA groups, respectively. Both globin reduction approaches were mostly efficient at reducing globin RNA from cRNA. Samples processed by GlobinClear kit gave a very distinct gene expression profiles from the controls while samples processed with PNA gave an intermediary profile closest to the non globin reduction group with a slight increased sensitivity of transcript detection but a loss of reproducibility. Overall, no sign of higher sensitivity in detection of gene expression changes followed by hormone exposure was observed after globin reduction which was therefore judged not beneficial. Keywords: Groups comparaison To assess effect of globin reduction protocols on gene expression from whole-blood, we selected 12 postmenopausal women (6 HRT users and 6 non-HRT users) who were not using other medication than HRT at the time of blood sampling and in order to cover a wide body mass index (BMI) range in both HRT and non HRT users. The samples were also selected to contain the highest concentration of total extracted RNA. Each sample was hybridized according to 3 different protocols: no globin reduction (controls), globin reduction using PNAs, globin reduction using magnetic beads in the GlobinClear™ kit from Ambion. The reproducibility of the globin reduction method compared to the non globin reduction approach was investigated for the PNA method only since this method was the most effective and specific. We planned to conduct 7 technical replicates in each group (i.e. no globin reduction and PNA groups). During amplification process with PNA, 4 samples failed to reverse transcript long fragment of mRNA certainly due to inhibitory contamination and these arrays were therefore excluded from our analyses. One sample (sample 34) was amplified with PNA twice the same day to study technical reproducibility without amplification date effect. Finally, a total of 47 arrays were conducted including 7 and 4 technical replicates in no globin reduction and PNA group, respectively.
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Project description:Expression data of skeletal muscle from HRT users and non-users
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