Hsa-miR-375 in early breast cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Franz Zehentmayr
PROVIDER: E-GEOD-69951 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Purpose of the current study was to identify miRs that can differentiate between patients with and without local relapse after breast conserving therapy in early stage breast cancer, which is especially important in the context of individualized treatment selection.
2015-06-18 | GSE69951 | GEO
Project description:The productivity of plants and microalgae needs to be increased to feed the growing world population and to promote the development of a low-carbon economy. This goal can be achieved by improving photosynthesis via genetic engineering. In this study, we have employed the Modular Cloning strategy to overexpress the Calvin-Benson cycle (CBC) enzyme sedoheptulose-1,7 bisphosphatase (SBP1) up to 3-fold in the unicellular green alga Chlamydomonas reinhardtii. The protein derived from the nuclear transgene represented ~0.3% of total cell protein. Photosynthetic rate and growth were significantly increased in SBP1-overexpressing lines under high-light and high-CO2 conditions. Absolute quantification of the abundance of all other CBC enzymes by the QconCAT approach revealed no consistent differences between SBP1-overexpressing lines and the recipient strain. This analysis also revealed that the eleven CBC enzymes represent 11.9% of total cell protein in Chlamydomonas. Here the range of concentrations of CBC enzymes turned out to be much larger than estimated earlier, with a 128-fold difference between the most abundant CBC protein (rbcL) and the least abundant (triose phosphate isomerase). Accordingly, the concentrations of the CBC intermediates are often but not always higher than the binding site concentrations of the enzymes for which they act as substrates. The enzymes with highest substrate to binding site ratios might represent good candidates for overexpression in subsequent engineering steps.
2021-02-11 | PXD018833 | Pride
Project description:Human pluripotent stem cells (hPSCs) are now being used for both disease modeling and cell therapy. However, efficient homologous recombination (HR) is often crucial to develop isogenic control or reporter lines. Here we show that limited low dose irradiation (LDI) using either γ-ray or X-ray exposure (0.4 Gy) significantly enhances HR frequency, possibly through induction of DNA repair/recombination machinery including ataxia-telangiectasia mutated, Histone H2A.X and RAD51 proteins. LDI could also increase HR efficiency by over 30- fold when combined with the targeting tools zinc finger nucleases (ZFNs), transcription activatorâ??like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPRs). Whole exome sequencing confirmed that the LDI to hPSCs did not induce gross genomic alterations, or affect cellular viability. Irradiated and targeted lines were karyotypically normal and made all differentiated lineages that continued to express green fluorescent protein targeted at the AAVS1 locus. This simple method allows higher throughput of new targeted hPSC lines that are crucial for the research community as this growing field develops. 4 samples
2016-03-22 | E-GEOD-68328 | biostudies-arrayexpress
Project description:We wanted to test the effect on global gene expression of depleting the essential cell cycle regulator CtrA in order to determine the genes both indirectly and directly transcriptionally regulated by CtrA Gene expression changes in S. meliloti 1,2,4 and 6 hours post CtrA depletion Log-phase S. meliloti cultures carrying an IPTG-inducible allele of CtrA were split and transferred to growth media lacking IPTG (depletion) and with 1mM IPTG (control). Samples for RNA extraction were taken 1,2,4, and 6 hours after the start of the depletion experiment to monitor gene expression changes in the population after different periods of CtrA depletion.
2015-04-24 | E-GEOD-68218 | biostudies-arrayexpress
Project description:We profiled gene expression in synchronized cultures of Sinorhizobium meliloti treated with or without the nodule-specific cysteine-rich peptide 247. We compared gene expression between the two conditions at 5 timepoints (15, 30, 60, 90, 120) following the addition of the peptide A population of synchronized Sinorhizobium meliloti was subjected to two treatments (no treatment and treated with sublethal levels of the NCR247 peptide). A series of timepoints was taken to profile the gene expression in both populations.
2014-01-21 | E-GEOD-54244 | biostudies-arrayexpress
Project description:Growing interest in the cellular origins of different breast cancer subtypes has prompted investigations into the subpopulations of the normal breast epithelia and their differentiation hierarchy. Several groups have demonstrated a likely luminal-progenitor cell origin for basal-like breast cancer. However, the molecular and cellular mechanisms underlying why one breast cell type might be more susceptible to transformation are yet to be elucidated. To observe the molecular differences in the different cell subpopulation response to ionizing radiation (IR), we performed gene expression profiling of MUC1+-sorted and CD10+-sorted primary human mammary epithelial cell cultures. Transcriptional response was measured at 2 and 24 hr after treatment with 2 and 5 Gy IR using Illumina HumanHT-12 v4 Expression Beadchips. The complete sample cohort included time-point matched untreated (0 Gy) controls in a total of 5 individual patients. Our analyses indicated several cell-type specific differences in response to IR. RNA was extracted from MUC1+-sorted and CD10+-sorted primary human mammary epithelial cell cultures at 2 and 24 hr after treatment with 0, 2, and 5 Gy ionizing radiation (12 samples per patient), in a total of 5 individual patients.
2016-02-07 | E-GEOD-67595 | biostudies-arrayexpress
Project description:Deciduous and permanent human teeth represent a model system to study ageing of mesenchymal populations. Aging is tightly connected to self-renewal and proliferation and thus, mapping potential molecular differences in these characteristics between populations constitutes an important task. Specifically designed microarray panels were used. We have detected a number of molecules that were differentially expressed in dental pulp mesenchyme from deciduous and permanent teeth extracted from young children and adults, respectively. Among the differentially regulated genes HMGA2, a stem cell-associated marker, stood out as a remarkable example with a robust expression in deciduous pulp cells. In addition to this, we discovered that several proliferation-related genes, including CDC2A and CDK4, were up-regulated in deciduous pulp cells, while matrix genes COL1A1, fibronectin and several signaling molecules, such as VEGF, FGFr-1 and IGFr-1 were up-regulated in the pulp cells from permanent teeth. Taken together, our data suggest that deciduous pulp cells are more robust in self- renewal and proliferation, whereas adult dental pulp cells are more capable of signaling and matrix synthesis. The deciduous teeth were collected from 3-12-year-old children (N=8), whereas the permanent teeth were collected from adults, 19-52 years of age (N=8). The tooth was mechanically separated into two halves to remove all soft tissue in the pulp. The pulp tissue was digested and the dissociated cells were passed through cell strainer and plated with culture medium. The cells were then passaged at 90% confluency to a 10 cm dish for expansion. RNA was extracted from passage one cells with the Qiagen RNeasy Mini Kit. Microarray analysis was performed using PIQORTM Stem Cell Microarray chip (Miltenyi Biotech), which is comprised of 942 relevant genes for stem/progenitor cells and key genes for cell differentiation, to identify gene sets that are differentially expressed between cells in the deciduous and adult teeth. A total of 1 μg RNA for each sample was used for amplification and further analysis with the PIQORTM stem cell microarray chip (Miltenyi Biotec), followed by detection with a laser scanner (Agilent Technologies). In total, 8 comparisons were performed with dataset consisting of two microarrays, each containing a total of 11 slides with signal intensities within the R/Bioconductor statistical framework. The Linear Model for Microarray Data package (Limma) was used to pre-process the raw data, perform quality controls and estimate statistical significance. Expression intensities were background-corrected using a convolution of normal and exponential distributions with an offset of 50, which were then normalized within every slide using loess normalization. We analyzed the red and green channels separately using the mixed model method and different groups were quantile-normalized separately. The correlation was computed between the two channels for the same spot. Differentially expressed genes were identified by computing the contrasts, fitting to a linear model, performing the hypothesis tests, and correcting for multiple testing by performing the false discovery rate using the Benjamini-Hochberg correction.
2014-09-01 | E-GEOD-58668 | biostudies-arrayexpress
Project description:While multiple studies have reported the accelerated evolution of brain gene expression in the human lineage, the mechanisms underlying such change remain poorly understood. Here we address this issue from a developmental perspective, by analyzing mRNA and microRNA (miRNA) expression in two brain regions within macaques, chimpanzees and humans throughout their lifespan. We find that developmental profiles of trans-regulators, such as miRNA, as well as their target genes, show the fastest rates of human-specific evolutionary change. Changes in expression of a few key regulators may be a major driving force behind human brain evolution. Human, chimpanzee and rhesus macaque post-mortem brain samples from the prefrontal cortex and cerebellar cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to B72.
2011-12-09 | E-GEOD-29356 | biostudies-arrayexpress
Project description:Cereblon (CRBN), a substrate receptor of the E3 ubiquitin ligase complex CRL4CRBN, is the target of the immunomodulatory drugs lenalidomide and pomalidomide. Recently, it was demonstrated that binding of these drugs to CRBN promotes the ubiquitination and subsequent degradation of two common substrates, transcription factors Aiolos and Ikaros. Here we report that the pleiotropic pathway modifier CC-122, a new chemical entity termed pleiotropic pathway modifier binds CRBN and promotes degradation of Aiolos and Ikaros in diffuse large B-cell lymphoma (DLBCL) and T cells in vitro, in vivo and in patients, resulting in both cell autonomous as well as immunostimulatory effects. In DLBCL cell lines, CC-122-induced degradation or shRNA mediated knockdown of Aiolos and Ikaros correlates with increased transcription of interferon stimulated genes (ISGs) independent of interferon α, β, γ production and/or secretion and results in apoptosis in both ABC and GCB-DLBCL cell lines. Our results provide mechanistic insight into the cell of origin independent anti-lymphoma activity of CC-122, in contrast to the ABC subtype selective activity of lenalidomide. Microarray analysis of the OCI-LY10 activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL) cell line treated with the compound CC-122 for 18 hours
2015-11-26 | E-GEOD-75420 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2011-06-30 | E-GEOD-30107 | biostudies-arrayexpress