CYPTAM - PacBio SMRT sequencing
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001004224 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Dataset contains CYP2D6 sequencing data of 566 individuals who used tamoxifen as adjuvant breast cancer therapy. Phenotype data consists of the ratio between the metabolites endoxifen and desmethyltamoxifen (Metabolic ratio (MR)) as a proxy for CYP2D6 enzyme activity. Each sample is linked to one bam-file containing the CYP2D6 sequence.
| EGAD00001005972 | EGA
Project description:Background: Current reports suggest that a certain minimum plasma concentration of (Z)-endoxifen is required for breast cancer patient to benefit from tamoxifen therapy. A reliable prediction of which patients are at risk for insufficient exposure to (Z)-endoxifen would be relevant for optimizing treatment, e.g. by adjusting the dose, from the very beginning. The objective of this study was to search for new DNA variants that could be helpful in the preemptive prediction of impaired tamoxifen to endoxifen metabolism. Methods: The molecular ratio (MR) was defined as (Z)-endoxifen plasma concentration divided by the sum of concentrations of tamoxifen and other measured metabolites. The MR of 0.0146, previously delineated as corresponding to (Z)-endoxifen 6 ng/ml efficacy threshold level, was adopted as a cut-off value in a genome-wide association study (GWAS) comprising 287 breast cancer patients receiving tamoxifen 20 mg daily. Multivariate binary logistic regression was used for the pre-selection of variables that showed independent impact on MR and to develop models predictive for MR value below the threshold. Results: In total, 13 GWAS-selected single nucleotide polymorphisms (SNPs) located outside the CYP2D6 gene and two known CYP2D6 variants were significantly associated with the MR value below 0.0146. The strongest association was observed for rs8138080 in WBP2NL (p = 1.78 x 10-15). The minor allele of six SNPs was associated with a decreased risk of impaired tamoxifen metabolism. CYP2D6 genotype was found by Nagelkerke pseudo-R2 to explain 42.7% of a total variation observed in MR, while rs8138080 alone explained 33.7% of this variability. Two alternative models for MR prediction have been developed. The prediction accuracy of Model 1, including rs7245, rs6950784 and rs1320308 in addition to CYP2D6 genotype, was considerably higher than predictive performance of CYP2D6 genotype alone (AUC increase from 0.758 to 0.879). The AUC of 0.830 achieved for the Model 2, developed with the same three SNPs as in Model 1 and rs8138080 instead of CYP2D6 genotype, makes it an interesting, simplified alternative to the costly and time-consuming testing of full CYP2D6 genotype. Conclusions: The four novel SNPs, tested alone or in addition to CYP2D6 genotype, improved the prediction of impaired tamoxifen to endoxifen metabolism, allowing for adjustments in dosing regimen before the treatment begins.
2019-09-18 | GSE129162 | GEO
Project description:The global burden of tuberculosis (TB) is aggravated by the continuously increasing emergence of drug resistance, highlighting the need for innovative therapeutic options. The concept of host-directed therapy (HDT) as adjunctive to classical antibacterial therapy with antibiotics represents a novel and promising approach for treating TB. Here, we have focused on repurposing the clinically used anticancer drug tamoxifen, which was identified as a molecule with strong host-directed activity against intracellular Mycobacterium tuberculosis (Mtb). Using a primary human macrophage Mtb infection model, we demonstrate the potential of tamoxifen against drug-sensitive as well as drug-resistant Mtb bacteria. The therapeutic effect of tamoxifen was confirmed in an in vivo TB model based on Mycobacterium marinum infection of zebrafish larvae. Tamoxifen had no direct antimicrobial effects at the concentrations used, confirming that tamoxifen acted as an HDT drug. Furthermore, we demonstrate that the antimycobacterial effect of tamoxifen is independent of its well-known target the estrogen receptor (ER) pathway, but instead acts by modulating autophagy, in particular the lysosomal pathway. Through RNA sequencing and microscopic colocalization studies, we show that tamoxifen stimulates lysosomal activation and increases the localization of mycobacteria in lysosomes both in vitro and in vivo, while inhibition of lysosomal activity during tamoxifen treatment partly restores mycobacterial survival. Thus, our work highlights the HDT potential of tamoxifen and proposes it as a repurposed molecule for the treatment of TB.
2022-11-29 | GSE178919 | GEO
Project description:After thawing, the mechanism of apoptosis advancing in human ES cells was invesitigated mainly by Gene conpath analysis. As time passed after thawing, nuclear fragmented cells increased more and more in cR-/mR- and cR+/mR-, but in cR+/mR+ and cR-/mR+, thawed cells formed cluster markedly, which was seen among three cell lines. Flow cytometry using TUNEL assay supported final colony formation ratio, which defined that such cell death was due to apoptosis. Gene map analysis 12 hours later after thawing of cR-/mR- showed activation of IL-1β & its receptor IL-1R and TGF-β & its receptor ACVR1C required for activation of caspase-8, initiation of caspase-8 and 10 and marked activation of ARHGDIB promoting actin reorganization comparing to cR+/mR+. Recovered cell lines in any condition did not lose proliferation and pluripotency regardless of ROCK inhibitor treatment. These results showed apoptotic events after thawing were more marked in cR- and advanced through autoenhanced cascaded mechanism followed by initiation of self-cytokain activity, and were suppressed by ROCK inhibitor Y-27632.
2011-11-15 | GSE21796 | GEO
Project description:After thawing, the mechanism of apoptosis advancing in human ES cells was invesitigated mainly by Gene conpath analysis. As time passed after thawing, nuclear fragmented cells increased more and more in cR-/mR- and cR+/mR-, but in cR+/mR+ and cR-/mR+, thawed cells formed cluster markedly, which was seen among three cell lines. Flow cytometry using TUNEL assay supported final colony formation ratio, which defined that such cell death was due to apoptosis. Gene map analysis 12 hours later after thawing of cR-/mR- showed activation of IL-1? & its receptor IL-1R and TGF-? & its receptor ACVR1C required for activation of caspase-8, initiation of caspase-8 and 10 and marked activation of ARHGDIB promoting actin reorganization comparing to cR+/mR+. Recovered cell lines in any condition did not lose proliferation and pluripotency regardless of ROCK inhibitor treatment.?These results showed apoptotic events after thawing were more marked in cR- and advanced through autoenhanced cascaded mechanism followed by initiation of self-cytokain activity, and were suppressed by ROCK inhibitor Y-27632. To investigate the protective mechanism caused by a novel cryo-technique of human embryonic stem (hES) cells using ROCK inhibitor Y-27632 against the cell death due to cryopreservation and thawing with Gene map analysis in addition to estimations of survival rate, apoptosis, undifferentiated states and pluripotency, the dissociated hES cells were cryopreserved in a freezing container in the following four conditions: addition of 10µM of Y-27632 to 1: cryoprotection solution and post-thawing medium (cR+/mR+), 2: only addition to cryoprotection (cR+/mR-), 3: only addition to post-thawing medium (cR-/mR+), 4: no addition to any medium (cR-/mR-).
2011-11-15 | E-GEOD-21796 | biostudies-arrayexpress
Project description:Knowledge of the genetic mechanisms underlying among-individual variation in response to environmental variables or treatment is important in many research areas; for example, acquaintance of the set of causal genetic variants for drug responses could revolutionize the field of personalized medicine. We used Drosophila melanogaster to investigate the genetic signature underlying variability in response to methylphenidate (MPH), a drug used in treatment of ADHD. We exposed a wild type D. melanogaster population to MPH or a control treatment and observed an increase in locomotor activity in individuals exposed to MPH. Whole-genome transcriptomic analyses revealed that the behavioral response to MPH was associated with abundant gene expression alterations. To confirm these patterns in a different genetic background, and to further advance knowledge on the genetic signature of drug response variability, we used a system of sequenced inbred lines, the Drosophila Genetic Reference Panel. Utilizing an integrative genomic approach we incorporated the transcriptomic data as well as gene interactions into the genomic analyses, from which we identified putative candidate genes for drug response variability. We successfully validated 70% of the investigated putative candidate genes by gene expression knockdown. Furthermore, we showed that MPH has cross generational behavioral- and transcriptomic effects.
2018-10-24 | GSE121643 | GEO
Project description:Tamoxifen, an antagonist to estrogen receptor (ER), is a first line drug used in breast cancer treatment. However, this therapy is complicated by the fact that a substantial number of patients exhibit either de novo or acquired resistance. To characterize the signaling mechanisms underlying the resistance to tamoxifen, we established a tamoxifen-resistant cell line by treating the MCF7 breast cancer cell line with tamoxifen for over 6 months. We showed that this cell line exhibited resistance to tamoxifen both in vitro and in vivo. In order to quantify the phosphorylation alterations associated with tamoxifen resistance, we performed SILAC-based quantitative phosphoproteomic profiling on the resistant and vehicle-treated sensitive cell lines where we identified >5,600 unique phosphopeptides. We found phosphorylation levels of 1,529 peptides were increased (>2 fold) and 409 peptides were decreased (<0.5-fold) in tamoxifen resistant cells compared to tamoxifen sensitive cells. Gene set enrichment analysis revealed that focal adhesion pathway was the top enriched signaling pathway activated in tamoxifen resistant cells. We observed hyperphosphorylation of the focal adhesion kinases FAK1 and FAK2 in the tamoxifen resistant cells. Of note, FAK2 was not only hyperphosphorylated but also transcriptionally upregulated in tamoxifen resistant cells. Suppression of FAK2 by specific siRNA knockdown could sensitize the resistant cells to the treatment of tamoxifen. We further showed that inhibiting FAK activity using the small molecule inhibitor PF562271 repressed cellular proliferation in vitro and tumor formation in vivo. More importantly, our survival analysis revealed that high expression of FAK2 significantly associated with short metastasis-free survival of ER-positive breast cancer patients treated with tamoxifen-based hormone therapy. Our studies suggest that FAK2 is a great potential target for the development of therapy for the treatment of hormone refractory breast cancers.
2016-05-25 | PXD001812 | Pride
Project description:The MR is an endocytic receptor, which plays an important role in serum homeostasis and antigen presentation. In this study, we firstly describe an important role of the MR as a direct regulator of CD8+ T cell activity. We could demonstrate that the presence of the MR on DCs impaired the cytotoxicity of activated CD8+ T cells both in vitro and in vivo. This regulatory effect was mediated by a direct interaction of the MR with CD45 on the T cells surface, which abolished CD45 activity. MR-mediated suppression of CD45 resulted in the up-regulation of the inhibitory molecule CTLA-4, which in turn was responsible for the reduced T cell activity. MR-mediated inactivation of CD45, up-regulation of CTLA-4 and T cell inactivation could be circumvented by increased signaling via CD28, which was achieved by DC maturation. These implications point out an important role of the MR in maintaining the balance between tolerance and immunity and might have pivotal implications for the development of vaccination strategies aimed at dampening adaptive immunity. DesTCR T cells were incubated with MR-deficient DCs in the presence of FcMR or isotype controls for the indicated time points. Afterwards, CD8+ T cells were isolated by cell sorting (FACSAria), and immediately lysed in Trizol (Invitrogen) before storage at -80°C for RNA isolation.
2016-08-23 | E-GEOD-45805 | biostudies-arrayexpress
Project description:The MR is an endocytic receptor, which plays an important role in serum homeostasis and antigen presentation. In this study, we firstly describe an important role of the MR as a direct regulator of CD8+ T cell activity. We could demonstrate that the presence of the MR on DCs impaired the cytotoxicity of activated CD8+ T cells both in vitro and in vivo. This regulatory effect was mediated by a direct interaction of the MR with CD45 on the T cells surface, which abolished CD45 activity. MR-mediated suppression of CD45 resulted in the up-regulation of the inhibitory molecule CTLA-4, which in turn was responsible for the reduced T cell activity. MR-mediated inactivation of CD45, up-regulation of CTLA-4 and T cell inactivation could be circumvented by increased signaling via CD28, which was achieved by DC maturation. These implications point out an important role of the MR in maintaining the balance between tolerance and immunity and might have pivotal implications for the development of vaccination strategies aimed at dampening adaptive immunity.
2016-08-23 | GSE45805 | GEO
Project description:Phenotypic cell-to-cell variability is central for microbial populations and contributes to cell function, stress adaptation and drug resistance. Gene-expression heterogeneity underpins this variability, but has been challenging to study genome-wide. Here, we report a novel approach which combines imaging of individual fission yeast cells with single-cell RNA sequencing (scRNA-seq) and Bayesian normalisation. We analyse >2000 single cells and >700 matching RNA controls in various environmental conditions that include reposnse to various stresses as well as growth and entry into stationary phase.
2018-11-14 | E-MTAB-6825 | biostudies-arrayexpress