Ontology highlight
ABSTRACT:
PROVIDER: PRJNA523838 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8627360_1.fastq.gz | Fastqsanger.gz | |||
| SRR8627360_2.fastq.gz | Fastqsanger.gz | |||
| SRR8627370_1.fastq.gz | Fastqsanger.gz | |||
| SRR8627370_2.fastq.gz | Fastqsanger.gz | |||
| SRR8627380_1.fastq.gz | Fastqsanger.gz |
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Project description:Cetuximab, erlotinib, and panitumumab are all recently FDA approved epidermal growth factor receptor (EGFR) inhibitors that treat a wide variety of tumor types, such as colon, lung, and head and neck. Blockade of the EGFR results in inhibition of multiple downstream pathways, leading to slowed tumor growth. In addition, these inhibitors may enhance anti-tumor immune responses through uncharacterized mechanisms. While producing significant responses in many settings, EGFR inhibitors also result in significant skin toxicity (rash) in a high percentage of patients. Multiple studies have correlated the presence and severity of rash with clinical response. Unfortunately, severe rash can often lead to dose delays, reductions, or even discontinuation of EGFR inhibitors, thus limiting their efficacy. The mechanism of both the rash and its correlation with tumor response is poorly understood. Skin biopsies display a robust leukocyte infiltrate, but a systematic analysis of the type of infiltrating leukocytes, activation state, or homing receptor expression has not been performed. Chemokines and chemokine receptors control leukocyte trafficking to the skin and other tissue sites, and defined receptor profiles for skin-, gut-, and lung-homing leukocytes are well established. In this study, the investigators propose to evaluate the homing phenotype of leukocytes from peripheral blood and skin biopsies of patients receiving EGFR inhibitors. The investigators will use RNA microarrays to evaluate the expression of chemokines and other key genes regulated in skin during treatment. The investigators will utilize in vitro methods to investigate effects of EGFR inhibitors on imprinting of T cell tissue-specific homing receptors. The investigators will examine correlations among the pathologic data, clinical findings, and tumor response. If validated, peripheral blood evaluation could potentially be used as a predictive indicator for patients receiving EGFR inhibitors. This study may also identify novel targets for limiting skin toxicity while receiving EGFR inhibitors, thus allowing maximal dosing and clinical response from these agents.
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Project description:Combining RNA-seq with ATAC-seq, we screened the open chromatin of dairy goat mammary epithelial cells during lactation and then integrated human lysozyme into various open regions using the CRISPR/Cas9 system. A comparison of lysozyme gene expression and integration efficiency showed that chromatin accessibility at target sites was significantly positively correlated with gene insertion efficiency, and the insertion of foreign genes into highly accessible chromatin regions could enhance its expression.
2023-12-01 | GSE225654 | GEO
Project description:Abstract: Proteins contribute to a major part of the organic nitrogen in forest soils. This nitrogen is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released nitrogen are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic nitrogen from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates. Firoz Shah, Francois Rineau, Björn Canbäck, Tomas Johansson and Anders Tunlid (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus (submitted)
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Project description:Paneth cells are the primary, and possibly the sole, source of lysozyme in the intestinal lumen. Mice lacking the Paneth cell lysozyme gene, Lyz1, had diminished NLR signaling and basal inflammation, and were further protected from experimental colitis. Protection depended on an enhanced goblet and tuft cell program that was driven by IL13-IL4Ra-Stat6 signaling and required an expansion of lysozyme-sensitive mucolytic bacteria. Forced ectopic lysozyme production in colonic epithelium suppressed these bacteria and exacerbated colitis. Single cell RNA-seq of Lyz1 KO lamina propria revealed an activated ILC2 profile towards cytokine production. One lysozymesensitive species, Ruminococcus gnavus , when processed by lysozyme, induced a pro-inflammatory response, while non-processed R. gnavus stimulated IL13 production in lymphocytes. Consistent with a role of lysozyme for cell-wall processing in the inflammatory response, Lyz1 KO microbiota was anti-colitogenic in lysozymedeficient hosts but colitogenic in lysozyme-sufficient hosts. Thus, Paneth cell lysozyme regulates inflammatory tone by modulating mucosal response to specific bacterial groups.
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Project description:Purpose: The phosphoinositide 3-kinase (PI3K) pathway is fundamental for cell proliferation and survival and is frequently altered and activated in neoplasia, including carcinomas of the lung. In this study we investigated the potential of targeting the catalytic class IA PI3K isoforms in small cell lung cancer (SCLC), which is the most aggressive of all lung cancer types. Experimental Design: The expression of PI3K isoforms in patient specimens was analyzed. The effects on SCLC cell survival and downstream signaling were determined following PI3K isoform inhibition by selective inhibitors or down-regulation by small interfering RNA. Results: Over-expression of the PI3K isoforms p110 -alpha and p110-alpha was shown by immunohistochemistry in primary SCLC tissue samples. Targeting the PI3K p110 -alpha with RNA interference (RNAi) or selective pharmacological inhibitors resulted in strongly affected cell proliferation of SCLC cells in vitro and in vivo, while targeting p110-alph was less effective. Inhibition of p110 -alpha also resulted in increased apoptosis and autophagy, which was accompanied by decreased phosphorylation of Akt and components of the mammalian target of rapamycin (mTOR) pathway, such as the ribosomal S6 protein, and the eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1). A DNA microarray analysis revealed that p110-alpha inhibition profoundly affected the balance of pro- and anti-apoptotic Bcl-2 family proteins. Finally, p110 -alpha inhibition led to impaired SCLC tumor formation and vascularization in vivo. Conclusion: Together our data demonstrate the key involvement of the PI3K isoform p110 -alpha in multiple tumor-promoting processes in SCLC. 3 control samples, 3 samples for two treaments
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