LPX
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33403 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3420040_1.fastq.gz | Fastqsanger.gz | |||
| ERR3420040_2.fastq.gz | Fastqsanger.gz | |||
| ERR3420050_1.fastq.gz | Fastqsanger.gz | |||
| ERR3420050_2.fastq.gz | Fastqsanger.gz | |||
| ERR3420060_1.fastq.gz | Fastqsanger.gz |
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Project description:Gonorrhea occurs at high incidence worldwide and has a major impact on reproductive and neonatal health worldwide. Alarmingly, with each new antibiotic introduced for gonorrhea, resistance has emerged, including resistance to penicillin, tetracycline, fluoroquinolones, and recently the third-generation cephalosporins. Treatment options are currently seriously limited and the development of a gonorrhea vaccine is a critical, longterm solution to this problem. Progress on gonorrhea vaccines has been slow, however, in part due to the high number of surface molecules in Neisseria gonorrhoeae (GC) that undergo phase or antigenic variation and a lack of understanding of protective responses. Gonorrhea vaccine development can therefore benefit from a comprehensive, unbiased approach for antigen discovery. Here we identified cell envelop proteins from Neisseria gonorrhoeae exposed to physiology relevant conditions: presence of human serum, iron limitation and anaerobic growth.
2016-05-09 | PXD001944 | Pride
Project description:Drug resistance (DR) is a phenomenon characterized by the tolerance of a disease to pharmaceutical treatment. In cancer patients, DR is one of the main challenges that limit the therapeutic potential of the existing treatments. Therefore, overcoming DR by restoring the sensitivity of cancer cells would be greatly beneficial. In this context, mathematical modeling can be used to provide novel therapeutic strategies that maximize the efficiency of anti-cancer agents and potentially overcome DR. In this paper, we present a new multiscale model devoted to the interaction of potential treatments with multiple myeloma (MM) development. In this model, MM cells are represented as individual objects that move, divide, and die by apoptosis. The fate of each cell depends on intracellular and extracellular regulation, as well as the administered treatment. The model is used to explore the combined effects of a tyrosine-kinase inhibitor (TKI) with a pentose phosphate pathway (PPP) inhibitor. We use numerical simulations to tailor effective and safe treatment regimens that may eradicate the MM tumors. The model suggests that an interval for the daily dose of the PPP inhibitor can maximize the responsiveness of MM cells to the treatment with TKIs. Then, it demonstrates that the combination of high-dose pulsatile TKI treatment with high-dose daily PPP inhibitor therapy can potentially eradicate the tumor.The predictions of numerical simulations using such a model can be considered as testable hypotheses in future pre-clinical experiments and clinical studies.
2020-01-09 | MODEL1912170004 | BioModels
Project description:A mathematical model was designed to explore the co-interaction of gonorrhea and HIV in the presence of antiretroviral therapy and gonorrhea treatment. Qualitative and comprehensive mathematical techniques have been used to analyse the model.
2020-07-09 | MODEL1812040004 | BioModels
Project description:CDK9 is the kinase subunit of P-TEFb that enables RNA polymerase (Pol) II to transit from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to the lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9’s activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb’s loss of activity, only the simultaneous inhibition of CDK9 and MYC can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy. ChIP-seq of Pol II in HeLa cells before or after i-CDk9 treatment
2015-06-17 | E-GEOD-60953 | biostudies-arrayexpress
Project description:FGFR signalling is one of the most prominent pathways involved in cell growth and development, as well as cancer progression. FGFR1 amplification occurs in approximately 20% of all squamous cell lung carcinomas (SCC) - one of the most common subtypes of non-small cell lung carcinoma (NSCLC), indicating FGFR as a potential target for the new anti-cancer therapies. However, acquired resistance to this type of therapies remains a clinical issue. Here, we investigated the NSCLC cell lines response and potential mechanism of acquired resistance to novel selective FGFR inhibitor CPL304110. We found that despite significant genomic differences between CPL304110-sensitive cell lines, their resistant variants were characterized by upregulated p38 expression/phosphorylation, as well as enhanced expression of genes involved in MAPK signalling. We revealed that p38 inhibition restored sensitivity to CPL304110 in these cells. Moreover, overexpression of this kinase in parental cells led to impaired response to FGFR inhibition, thus confirming that p38 MAPK is a driver of resistance to a novel FGFR inhibitor. Taken together, our results provide an insight into the potential direction for NSCLC targeted therapy.
2021-11-23 | GSE189268 | GEO
Project description:Studies investigating the causes of autism spectrum disorder (ASD) point to genetic as well as epigenetic mechanisms of the disease. Identification of epigenetic processes that contribute to ASD development and progression is of major importance and may lead to the development of novel therapeutic strategies. Here we identify the bromodomain and extra-terminal domain containing transcriptional regulators (BETs) as epigenetic drivers of an ASD-like disorder in mice. We found that the pharmacological suppression of the BET proteins by a novel, highly selective and brain-permeable inhibitor, I-BET858, leads to selective suppression of neuronal gene expression followed by the development of an autism-like syndrome in mice. Many of the I-BET858 affected genes have been linked to ASD in humans thus suggesting the key role of the BET-controlled gene network in ASD. Our studies also suggest that environmental factors controlling BET proteins or their target genes may contribute to the epigenetic mechanism of ASD. There are 24 total samples. There are two timepoints, 2 and 12 hours. Triplicates were performed for each treatment. Control samples were prepared by treating with DMSO for each of the timepoints.
2015-09-09 | E-GEOD-72149 | biostudies-arrayexpress
Project description:Pharmacodynamics of zoliflodacin and doxycycline in gonorrhea treatment
| PRJEB64051 | ENA
Project description:Neisseria gonorrhoeae is the causative agent of gonorrhea, a leading sexually transmitted disease with severe complications on reproductive health. The U.S. Centers for Disease Control and Prevention has categorized the public health threat induced by N. gonorrhoeae as “urgent”, due to the ease of transmission and the fast emergence of multi-drug resistant strains. The need for development of vaccines and understanding the underlying factors leading to antibiotic resistance is of utmost importance. The proteomic profiles of the 14 WHO N. gonorrhoeae reference strains have been compared to the WHO F reference strain using a mass spectrometry with tandem mass tags (TMT) labeling to analyze the cell envelope and the cytoplasmic fractions extracted from each strain. Identifying novel vaccine candidates and proteomic signatures for antimicrobial resistance will further our understanding of N. gonorrhoeae proteotypes, in relationship to their respective genotypes and phenotypes, and provide deep insights that will impact the development of preventive and therapeutic tools to combat gonorrhea.
2018-12-19 | PXD008412 | Pride
Project description:Background: Upregulation of H3K27me3 induced by EZH2 overexpression or somatic heterozygous mutations were implicated in lymphomagenesis. It has been demonstrated that several EZH2-target agents have notable therapeutic effects in EZH2-mutant B-cell lymphoma patients. Here we present a novel highly selective EZH2 inhibitor SHR2554 and possible combination strategy in diffuse large B cell lymphoma (DLBCL); Methods: Cell proliferation, cycle and apoptosis were analyzed by Cell Titer-Glo Luminescent Cell Viability Assay and flow cytometry. Western Blot was used to detect the regulatory protease in related signaling pathways and RNA-seq was conducted to assess transcriptome changes. Finally, CDX and PDX models were used to evaluate the synergistic anti-tumor effects of the combination in vivo; Results: The novel EZH2 inhibitor SHR2554 could inhibited proliferation, induced G1 phase arrest in EZH2-mutant DLBCL cell lines. The combination of EZH2 inhibitor SHR2554 with histone deacetylase (HDAC) inhibitor chidamide (hereafter referred as HBI8000) exerted synergistic anti-proliferative activity in vitro and in vivo. Gene expression profile analysis revealed dramatic inhibition of DNA replication process in combined treatment; Conclusions: SHR2554, a potent highly selective small molecule inhibitor of EZH2, inhibited EZH2-mutant DLBCL more significantly in vitro and in vivo. The combination of HDAC inhibitor HBI8000 with EZH2 inhibitor SHR2554 exhibited dramatically anti-tumor activity in both mutant and wild-type DLBCL, which may become potential therapeutic modality for the treatment of DLBCL patients.
2021-07-12 | GSE179792 | GEO
Project description:The immune response to Neisseria gonorrhoeae is poorly understood, but its extensive antigenic variability and resistance to complement are thought to allow it to evade destruction by the host’s immune defenses. We propose that N. gonorrhoeae also avoids inducing protective immune responses in the first place. We previously found that N. gonorrhoeae induces IL-17-dependent innate responses in mice and suppresses Th1/Th2-dependent adaptive responses in murine cells in vitro through the induction of TGF-β. In this study using a murine model of vaginal gonococcal infection, mice treated with anti-TGF-β antibody during primary infection showed accelerated clearance of N. gonorrhoeae with incipient development of Th1 and Th2 responses and diminished Th17 responses in genital tract tissue. Upon secondary reinfection, mice that had been treated with anti-TGF-β during primary infection showed anamnestic recall of both Th1 and Th2 responses, with the development of anti-gonococcal antibodies in serum and secretions, and enhanced resistance to reinfection. In knockout mouse strains defective in Th1 or Th2 responses, accelerated clearance of primary infection due to anti-TGF-β treatment was dependent on Th1 but not Th2 activity, whereas resistance to secondary infection resulting from anti-TGF-β treatment during primary infection was due to both Th1- and Th2-dependent memory responses. We propose that N. gonorrhoeae proactively elicits Th-17-driven innate responses that it can resist, and suppresses Th1/Th2-driven specific adaptive immunity that would protect the host. Blockade of TGF-β reverses this pattern of host immune responsiveness and facilitates the emergence of protective anti-gonococcal immunity. We only did microarray assay for wild-type mice with or without anti-TGF-b treatment. Experiment A: Totally there are three groups: Sham-infected mice without treatment; N.gonorrhoeae-infected with control IgG treatment; N.gonorrhoeae-infected with anti-TGF-β treatment. For each group, two mice were studied. Total RNA from mouse vagina were analysed. Experiment B: Totally there are three groups: Sham-reinfected mice without treatment; N.gonorrhoeae-reinfected with control IgG treatment; N.gonorrhoeae-reinfected with anti-TGF-β treatment. For each group, two mice were studied. Total RNA from mouse vagina were analysed.
2011-03-22 | E-GEOD-28055 | biostudies-arrayexpress