Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identify changes in gene expression during overexpression of the glycosyltransferase LARGE

ABSTRACT: alpha-dystroglycan is a component of the dystrophin associated glycoprotein complex that binds components of the extracellular matrix (including laminin, perlecan and neurexin) via its carbohydrate groups. Recently, a group of muscular dystrophies have been identified due to the aberrant glycosylation of this molecule (dystroglycanopathies). The overexpression of the glycosyltransferase LARGE in several cell lines results in alpha-dystroglycan hyperglycosylation and enhanced ligand binding. The glycan structures induced by LARGE overexpression are unknown. We have injected into mouse legs two LARGE constructs, one wild type and the second in which a DxD motif has been mutated to NNN as a control. We aim to identify genes unregulated during LARGE induced hyperglycosylation in order to gain insight into the enzymes involved in this process and ultimatley the nature of the glycans responsible for ligand binding. RNA preparations from two LARGE constructs, were sent to Microarray Core (E). One wild type and the second in which a DxD motif has been mutated to NNN as a control. The aim is to identify genes unregulated during LARGE induced hyperglycosylation in order to gain insight into the enzymes involved in this process and ultimatley the nature of the glycans responsible for ligand binding. The RNA was amplified, labeled, and hybridized to teh GLYCOv3 microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Steven Head

PROVIDER: E-GEOD-28932 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A novel germline variant in CSF3R highlights the potent oncogenic effects of loss of N-glycosylation and its implication for therapeutic intervention

Project description:Mutations in the colony stimulating factor 3 receptor (CSF3R) have been identified in the vast majority of patients with chronic neutrophilic leukemia and are present in other kinds of leukemia, such as AML. Herein, we study the function of novel germline variants in CSF3R at amino acid N610. These N610 substitutions are potently oncogenic and activate the receptor independently of its ligand, GCSF. These mutations activate the JAK-STAT signaling pathway and confer sensitivity to JAK inhibitors. The N610 residue is part of a consensus N-linked glycosylation motif in the receptor, usually linked to complex glycans, as shown by detailed mass spectrometry analysis. Further analysis demonstrates that N610 is the primary site of sialylation of the receptor. This study demonstrates that membrane-proximal N-linked glycosylation is critical for maintaining the ligand dependence of the receptor. Mutation of the N610 site prevents membrane proximal N-glycosylation of CSF3R, which then drives ligand-independent neutrophil expansion. Kinase inhibitors block growth of cells with an N610 mutation. This study expands the repertoire of oncogenic mutations in CSF3R that are therapeutically targetable and provides insight into the function of glycans in receptor regulation.

2018-11-06 | PXD011118 | Pride

Glyco-gene expression in DP thymic T cells from control and mutant mice that carry a mutation in the ligand binding domain of Notch1

Project description:Dr. Stanley's laboratory is interested in determining how O-fucose glycans function in Notch receptor signaling and in modulating the interactions of Notch receptors with their ligands. We have generated mice carrying a point mutation in the ligand binding domain of Notch1 that reduces Notch ligand binding to mutant T cells. We wish to identify Notch target genes including glycosylation genes with altered expression in DP thymic T cells from mutant and control mice.

2011-04-29 | GSE28936 | GEO

High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells

Project description:Synthetic riboswitches mediating ligand-dependent RNA cleavage or splicing-modulation represent elegant tools to control gene expression in various applications, including next-generation gene therapy. However, due to the limited understanding of context-dependent structure-function relationships, the identification of functional riboswitches requires large-scale-screening of aptamer-effector-domain designs, which is hampered by the lack of suitable cellular high-throughput methods. Here we describe a fast and broadly applicable method to functionally screen complex riboswitch libraries (~1.8x104 constructs) by cDNA-amplicon-sequencing in transiently transfected and stimulated human cells. The self-barcoding nature of each construct enables quantification of differential mRNA levels without additional pre-selection or cDNA-manipulation steps. We apply this method to engineer tetracycline- and guanine-responsive ON- and OFF-switches based on hammerhead, hepatitis-delta-virus and Twister ribozymes as well as U1-snRNP polyadenylation-dependent RNA devices. In summary, our method enables fast and efficient high-throughput riboswitch identification, thereby overcoming a major hurdle in the development cascade for therapeutically applicable gene switches. DOI:10.1038/s41467-020-14491-x

2020-02-05 | GSE143466 | GEO

Aflibercept or Bevacizumab as Second-line Treatment of RAS Mutated Metastatic Colorectal Cancer

Project description:Colorectal cancer is the third most frequent neoplasm after prostate and lung in man and breast and lung cancers in woman from Western Countries. The intensive study of predictive factors has strongly ameliorated the therapeutic flow-chart of metastatic colorectal cancer (mCRC) by allowing the selection of patients who benefit from specific therapies. In this context, the assessment of RAS (N- and K-) oncogene mutations is able to predict the response to anti-EGFR agents being mutated RAS mCRC patients resistant to these drugs. In this group of patients the use of anti-angiogenic drugs (bevacizumab and aflibercept) is predominant. Still to date there are no studies to guide oncologists in the selection of the best anti-angiogenic drug (bevacizumab beyond progression vs aflibercept) after failure of the first-line chemotherapy in RAS-M mCRC patients. The present is the first observational, pragmatic, prospective study aimed to report outcomes of mCRC patients treated with folfiri plus bevacizumab versus folfiri plus aflibercept in second-line treatment of mRAS mCRC. Furthermore, the serum levels of angiopoietin-1 (Ang-1), angiopoietin-2 (Ang-2), vascular endothelial growth factor-A and C (VEGF-A and C), stromal cell-derived factor-1 (SDF-1), platelet-derived growth factor beta (PDGF-β), basic fibroblast growth factor (bFGF), interleukin-8 (IL-8), chemokine (C-C motif) ligand 2 (CCL2), and chemokine (C-C motif) ligand 5 (CCL5) and Placental Growth Factor (PlGF), will be evaluated before starting second-line chemotherapy with bevacizumab or aflibercept in order to evidence any pattern related to response and/or prognosis. The hypothesis is that knowledge of eventual unbalance of these factors could help to select the best anti-angiogenic drug in second-line treatment of mRAS mCRC patients.

| 2339938 | ecrin-mdr-crc

Homo sapiens

Project description:Function of chemokine (CXC motif) ligand 12 in periodontal ligament fibroblasts

| PRJNA227089 | ENA

Analysis of the purified RNA samples to confirm that Notch pathway activation inhibits apoptosis in uterine leiomyomas leading to fibroid growth

Project description:Uterine leiomyomas are the most common benign tumor in humans causing significant morbidity with vaginal bleeding, pelvic pressure and pain. Histologically, leiomyomas show a large degree of extracellular matrix disorganization. I am working with a colleague who recently found Notch pathway gene expression were clearly altered in fibroids (“Differential expression of the Notch signal transduction pathway: ligands, receptors and Numb in uterine leiomyomas vs. myometrium,” G. Christman, H. Tang, I. Ahmad, J. Stribley, Fertility and Sterility, Volume 88, Supp 1, S72, September 2007). Glycosaminoglycan expression was found to be over-expressed in uterine leiomyomas compared to myometrial samples (Fertility and Sterility, Vol 88 Supp 1, S106, September, 2007), but glycosyltransferase and glycosidase expression has not been reported. We have purified RNA samples from paired uterine leiomyoma and normal myometrium from a previous clinical study. Dr. Domino's laboratory hypothesis is that Notch pathway activation inhibits apoptosis in uterine leiomyomas leading to fibroid growth. Notch ligands are fucosylated glycans. The bulk of a fibroid is the extracellular matrix yet little has been studied on leiomyocyte expression of enzymes that model glycans in the extracellular matrix.

2011-04-29 | GSE28945 | GEO

Analysis of bovine leukocyte antigen (BoLA)-associated peptides by LC-MS

Project description:An increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is in general challenging due to the poly-specificity nature of the data. We here outline a general pipeline for dealing with this challenge, and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in-silico models. We illustrate the approach here in the context of MHCI molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in-vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T cell epitopes.

2017-11-20 | PXD008151 | Pride

Analysis of gene expression with the Hmga2 allelic series.

Project description:In this study, we introduced a series of expression constructs into a mouse lung cancer cell line (482N1): (1) a control short hairpin RNA (shluc) plus the empty expression vector (empty); (2) an shRNA targeting Hmga2 (shHmga2) plus empty; (3) shHmga2 plus an expression vector for the full-length Hmga2 cDNA with the shRNA site mutated (shHmga2 wt); (4) shHmga2 plus the full-length shRNA-mutated Hmga2 with let-7 sites in the 3' UTR mutated (shHmga2 m7); (5) shHmga2 plus the full-length shRNA-mutated Hmga2 with the start codon mutated (shHmga2 ATG wt); and (6) shHmga2 plus the full-length shRNA-mutated Hmga2 with the start codon and let-7 sites mutated (shHmga2 ATG m7).

2013-09-18 | GSE50932 | GEO

AR and ERG ChIP-seq in presence or absence of PRMT5

Project description:Replicates of ChIP seq data using AR and ERG antibodies from VCaP cell lines harboring inducible shRNA constructs for PRMT5 (3 independent, sh1, sh2, sh3) and 1 non targeting control (NTC), all sample stimulated with ligand, either DHT or R1881

2016-05-20 | GSE79128 | GEO