To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE156964 | GEO | 2020/08/28
REPOSITORIES: GEO
Similar Datasets
Project description:Cancer associated fibroblast mRNA profiles were generated from Control and NetrinG1 KO fibroblast lines, with controls done in duplicate and KOs in triplicate. Comparing the mRNA profiles of CON and NetrinG1 KO CAFs, we observed a reversion of many pro-tumor genes and associated pathways upon ablation of NetrinG1 in CAFs.
2020-08-28 | GSE156962 | GEO
Project description:Purpose: To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1. Methods: Cancer associated fibroblast mRNA profiles were generated from Control and NetrinG1 KO fibroblast lines, with controls done in duplicate and KOs in triplicate. Results: Comparing the mRNA profiles of CON and NetrinG1 KO CAFs, we observed a reversion of many pro-tumor genes and associated pathways upon ablation of NetrinG1 in CAFs. Conclusions: Loss of NetrinG1 in CAFs results in normalization of CAF gene signatures.
2020-08-28 | GSE156963 | GEO
Project description:To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1.
| PRJNA659658 | ENA
Project description:To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1. [Microarray]
| PRJNA659655 | ENA
Project description:To determine the differentially expressed genes in cancer associated fibroblasts upon ablation of the glutamatergic synapse protein NetrinG1. [RNA-Seq]
| PRJNA659668 | ENA
Project description:The assembly and function of presynaptic nerve terminals relies on evolutionarily conserved proteins. A small number of presynaptic proteins occurs only in vertebrates. These proteins may add specialized functions to certain synapses, thus increasing synaptic heterogeneity. Here, we show that the vertebrate-specific synaptic vesicle (SV) protein mover is differentially distributed in the forebrain and cerebellum of the adult mouse. Using a quantitative immunofluorescence approach, we compare the expression of mover to the expression of the general SV marker synaptophysin in 16 brain areas. We find that mover is particularly abundant in the septal nuclei (SNu), ventral pallidum (VPa), amygdala and hippocampus. Within the hippocampus, mover is predominantly associated with excitatory synapses. Its levels are low in layers that receive afferent input from the entorhinal cortex, and high in layers harboring intra-hippocampal circuits. In contrast, mover levels are high in all nuclei of the amygdala, and mover is associated with inhibitory synapses in the medioposterior amygdala. Our data reveal a striking heterogeneity in the abundance of mover on three levels, i.e., between brain areas, within individual brain areas and between synapse types. This distribution suggests a role for mover in providing specialization to subsets of synapses, thereby contributing to the functional diversity of brain areas.
| S-EPMC6053503 | biostudies-literature
Project description:Rhizomania is one of the most devastating sugar beet diseases. It is caused by Beet necrotic yellow vein virus (BNYVV), which induces abnormal rootlet proliferation. To understand better the physiological and molecular basis of the disorder, transcriptome analysis was performed by restriction fragment differential display polymerase chain reaction (RFDD-PCR), which provided differential gene expression profiles between non-infected and infected sugar beet roots. Two distinct viral isolates were used to detect specific or general virus-induced genes. Differentially expressed genes were selected and identified by sequence analysis, followed by reverse Northern and reverse transcriptase PCR experiments. These latter analyses of different plants (Beta vulgaris and Beta macrocarpa) infected under distinct standardized conditions revealed specific and variable expressions. Candidate genes were linked to cell development, metabolism, defence signalling and oxidative stress. In addition, the expression of already characterized genes linked to defence response (pathogenesis-related protein genes), auxin signalling and cell elongation was also studied to further examine some aspects of the disease. Differential expression was retrieved in both B. vulgaris and B. macrocarpa. However, some candidate genes were found to be deregulated in only one plant species, suggesting differential response to BNYVV or specific responses to the BNYVV vector.
| S-EPMC6640463 | biostudies-literature
Project description:In this study, we integrated the gene expression data of sepsis to reveal more precise genome-wide expression signature to shed light on the pathological mechanism of sepsis. Differentially expressed genes via integrating five microarray datasets from the Gene Expression Omnibus database were obtained. The gene function and involved pathways of differentially expressed genes (DEGs) were detected by GeneCodis3. Transcription factors (TFs) targeting top 20 dysregulated DEGs (including up- and downregulated genes) were found based on the TRANSFAC. A total of 1339 DEGs were detected including 788 upregulated and 551 downregulated genes. These genes were mostly involved in DNA-dependent transcription regulation, blood coagulation, and innate immune response, pathogenic escherichia coli infection, epithelial cell signaling in helicobacter pylori infection, and chemokine signaling pathway. TFs bioinformatic analysis of 20 DEGs generated 374 pairs of TF-target gene involving 47 TFs. At last, we found that five top ten upregulated DEGs (S100A8, S100A9, S100A12, PGLYRP1 and MMP9) and three downregulated DEGs (ZNF84, CYB561A3 and BST1) were under the regulation of three hub TFs of Pax-4, POU2F1, and Nkx2-5. The identified eight DEGs may be regarded as the diagnosis marker and drug target for sepsis.
| S-EPMC5428098 | biostudies-literature
Project description:Microarray analysis on total retinal RNA from 15 day old Sirt6 wild-type (WT) and knock-out (KO) mice. The retina is one of the major energy consuming tissues within the body. In this context, synaptic transmission between light-excited rod photoreceptors and downstream ON-bipolar neurons is a highly demanding energy consuming process. Sirtuin 6 (SIRT6), a NAD-dependent deacylase, plays a key role in regulating glucose metabolism. In this study, we demonstrate that SIRT6 is highly expressed in the retina, controlling levels of histone H3K9 and H3K56 acetylation. Notably, despite apparent normal histology, SIRT6 deficiency caused major retinal transmission defects concomitant to changes in expression of glycolytic genes and glutamate receptors, as well as elevated levels of apoptosis in inner retina cells. Our results identify SIRT6 as a critical modulator of retinal function, likely through its effects on chromatin. Microarray analysis of total retinal RNA from 15 day old Sirt6 wild-type (WT) and knock-out (KO) mice with 3 replicates in each condition using the Affymetrix Mouse Gene 2.1 ST array (transcript (gene) version).
2014-07-30 | E-GEOD-56563 | biostudies-arrayexpress
Project description:Background: Lower-grade glioma (LGG) is the most common histology identified in gliomas, a heterogeneous tumor that may develop into high-grade malignant glioma that seriously shortens patient survival time. Recent studies reported that glutamatergic synapses might play an essential role in the progress of gliomas. However, the role of glutamatergic synapse-related biomarkers in LGG has not been systemically researched yet. Methods: The mRNA expression data of glioma and normal brain tissue were obtained from The Cancer Genome Atlas database and Genotype-Tissue Expression, respectively, and the Chinese Glioma Genome Atlas database was used as a validation set. Difference analysis was performed to evaluate the expression pattern of glutamatergic synapse-related genes (GSRGs) in LGG. The least absolute shrinkage and selection operator (LASSO) Cox regression was applied to construct the glutamatergic synapse-related risk signature (GSRS), and the risk score of each LGG sample was calculated based on the coefficients and expression value of selected GSRGs. Univariate and multivariate Cox regression analyses were used to investigate the prognostic value of risk score. Immunity profile and single-sample gene set enrichment analysis (ssGSEA) were performed to explore the association between risk score and the characters of tumor microenvironment in LGG. Gene set variation analysis (GSVA) was performed to investigate the potential pathways related to GSRS. The HPA database and real-time PCR were used to identify the expression of hub genes identified in GSRS. Results: A total of 22 genes of 39 GSRGs were found differentially expressed among normal and LGG samples. Through the LASSO algorithm, 14-genes GSRS constructed were associated with the prognosis and clinicopathological features of patients with LGG. Furthermore, the risk score level was significantly positively correlated with the infiltrating level of immunosuppressive cells, including M2 macrophages and regulatory T cells. GSVA identified a series of cancer-related pathways related to GSRS, such as P13K-AKT and P53 pathways. Moreover, ATAD1, NLGN2, OXTR, and TNR, hub genes identified in GSRS, were considered as potential prognostic biomarkers in LGG. Conclusion: A 14-genes GSRS was constructed and verified in this study. We provided a novel insight into the role of GSRS in LGG through a series of bioinformatics methods.
| S-EPMC8581158 | biostudies-literature