Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human lung tissue

ABSTRACT: Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids. We have a particular interest in understanding how mucin type O-glycosylation is regulated. Mucin type O-glycosylation is controlled by the ppGalNAc-transferase multigene family. An estimated 23 iso-forms belong to this family, so the specific involvement of each individual iso-form in any given organ seems complex to understand. An initial attempt to comprehend how this multigene family regulates mucin type O-glycosylation, is to get insight into which iso-forms are expressed in different organs and cell types. For this reason we have generated monoclonal antibodies towards 7 iso-forms, and the list of ppGalNAc-T iso-form specific monoclonals is currently growing. We have done some immuno histochemistry on lung using the available monoclonals, but are keen on assessing the number of ppGalNAc-T's expressed in lung as determined this Glyco-array. We have focused on lung because a number of ppGalNAc-T acceptor polypeptides, belonging to the mucin gene family, are expressed in this organ. An RNA sample pooled from two independent adult human healthy lung tissue samples was analyzed

ORGANISM(S): Homo sapiens

SUBMITTER: Steven Head

PROVIDER: E-GEOD-25712 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Human lung tissue

Project description:Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids. We have a particular interest in understanding how mucin type O-glycosylation is regulated. Mucin type O-glycosylation is controlled by the ppGalNAc-transferase multigene family. An estimated 23 iso-forms belong to this family, so the specific involvement of each individual iso-form in any given organ seems complex to understand. An initial attempt to comprehend how this multigene family regulates mucin type O-glycosylation, is to get insight into which iso-forms are expressed in different organs and cell types. For this reason we have generated monoclonal antibodies towards 7 iso-forms, and the list of ppGalNAc-T iso-form specific monoclonals is currently growing. We have done some immuno histochemistry on lung using the available monoclonals, but are keen on assessing the number of ppGalNAc-T's expressed in lung as determined this Glyco-array. We have focused on lung because a number of ppGalNAc-T acceptor polypeptides, belonging to the mucin gene family, are expressed in this organ.

2010-11-30 | GSE25712 | GEO

Pancreatic tumor cell lines

Project description:Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids. RNA samples from two human pancreatic cell lines. The relevance of the variable expression levels of isoforms belonging to the polypeptide GalNAc-transferase gene-family is still a puzzle to us. The polypeptide GalNAc-transferase gene family is estimated to contain 24 gene-members all participating in the initiation of mucin-type O-glycosylation. It has become apparent that each of these individual isoforms have different tissue distribution profiles and kinetic capabilities. Mucin-type O-glycosylation is thus controlled, and dependent upon the repetoir of expressed GalNAc-transferases in any given organ and cell type at any given time. We have been trying to contribute to the understanding of the ordered process controlling mucin-type O-glycosylation in both normal and malignant models, and are currently investigating a pancreatic cell line model in the lab. The pancreatic tumor cell line ASPC-1 has been found to possess low metastatic potential in mouse models, in contrast to the pancreatic tumor cell line Suit-T2 possessing high metastatic potential. Immunohistochemical analysis of both cell lines, ASPC-1 and Suit-T2, using our monoclonal antibodies to 7 isoforms has revealed great differences in the expression profile of these 7 isoforms in theses two cell lines, and for instance GalNAc-T3 has been found to be highly expressed in Suit-T2 but completely lacking in ASPC-1. Two cell lines: ASPC-1 and Suit-T2 are analyzed with 3 independent replicate prepared for each cell line.

2010-12-11 | E-GEOD-26011 | biostudies-arrayexpress

Pancreatic tumor cell lines

Project description:Dr. Clausen's laboratory is interested in the structure, biosynthesis and genetic regulation of glycoconjugates, with a major focus on mucins. This laboratory is studying the glycosylation and secretion process of mucins and biological functions involving mucins. This lab is also interested in receptor modulation mediated by glycosylation or through glycosphingolipids. RNA samples from two human pancreatic cell lines. The relevance of the variable expression levels of isoforms belonging to the polypeptide GalNAc-transferase gene-family is still a puzzle to us. The polypeptide GalNAc-transferase gene family is estimated to contain 24 gene-members all participating in the initiation of mucin-type O-glycosylation. It has become apparent that each of these individual isoforms have different tissue distribution profiles and kinetic capabilities. Mucin-type O-glycosylation is thus controlled, and dependent upon the repetoir of expressed GalNAc-transferases in any given organ and cell type at any given time. We have been trying to contribute to the understanding of the ordered process controlling mucin-type O-glycosylation in both normal and malignant models, and are currently investigating a pancreatic cell line model in the lab. The pancreatic tumor cell line ASPC-1 has been found to possess low metastatic potential in mouse models, in contrast to the pancreatic tumor cell line Suit-T2 possessing high metastatic potential. Immunohistochemical analysis of both cell lines, ASPC-1 and Suit-T2, using our monoclonal antibodies to 7 isoforms has revealed great differences in the expression profile of these 7 isoforms in theses two cell lines, and for instance GalNAc-T3 has been found to be highly expressed in Suit-T2 but completely lacking in ASPC-1.

2010-12-11 | GSE26011 | GEO

Identification of glycosyltransferases and glycosydases responsible for the synthesis/degradation of mucin O-glycans at the human ocular surface epithelium

Project description:The major focus of Dr. Argueso's research is to characterize the carbohydrate portion of the different mucins expressed by the ocular surface epithelia as well as the enzymes involved with their synthesis, and to determine whether the alteration of mucin glycosylation is associated with ocular surface disease. Highly glycosylated mucins on the ocular surface (cornea and conjunctiva) are the first line of defense of the eye against injury and infection. Changes in O-glycosylation of mucins may cause ocular surface disorders, such as dry eye. Gene expression patterns in the conjunctival epithelium of three normal subjects were analyzed. The three subjects have the same ABO-blood-group. For each donor, conjunctival cells were obtained by impression cytology. Conjunctival impression cytology was performed on each eye two times with a one-week interval. Conjunctival cells obtained from each individual were pooled and the RNA isolated. All three samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.

2011-03-02 | E-GEOD-27593 | biostudies-arrayexpress

Identification of glycosyltransferases and glycosydases responsible for the synthesis/degradation of mucin O-glycans at the human ocular surface epithelium

2011-03-02 | GSE27593 | GEO

Glycosite mapping and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Project description:Mucin-domain glycoproteins are densely O-glycosylated and play key roles in a host of biological functions. In particular, the T-cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, 3, 4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans, which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamic (MD) simulations of TIM-3 and 4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.

2023-09-27 | PXD039583 | Pride

Exploring glycosylation of mucins with O-glycodomain reporters expressed in glycoengineered HEK293 cells

Project description:Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of resistance to proteolytic digestion, and knowledge of positions of O-glycans is particularly limited for these regions. Mucin O-glycodomains are believed to contain important binding cues for endogenous lectin receptors and the microbiota, and it is important to develop strategies to characterize and produce these abundant molecules. Here, we took advantage of our recently developed glycoengineered cell-based platform for display and production of mucin TR reporters with custom designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom-up site-specific analysis for mapping O-glycosites in MUC2, MUC20, MUC21, PSGL-1, and Syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in HEK293 SimpleCells (Tn-glycoform). Interestingly, while all the sites in TRs derived from secreted mucins were almost fully occupied, positions in TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of the StcE and BT4244 glycoproteases, revealing a more restricted substrate specificities than reported. Finally, we used these for bottom-up analysis of isolated ovine submaxillary mucin (OSM) and identified the gene. The study provides insight into O-glycosylation of mucins and mucin-like domains and the strategies developed open up for wider analysis of native mucins.

2022-05-20 | PXD029885 | Pride

Early defects of airway mucin sialylation and of mucociliary clearance at the onset of lung pathogenesis in a pig model of cystic fibrosis

Project description:Chronic infection of the lungs by bacteria such as Pseudomonas aeruginosa plays an important role in the natural history of Cystic Fibrosis (CF). Altered mucin secretions and glycosylations are hallmarks of bacterial infections but their exact contributions to the development of chronic infection and/or inflammation remain to be established. We studied the lung environment in newborn CFTR-/- pigs, which closely mirrors the human CF phenotype at the levels of mucin glycosylation, mucociliary transport (MCT) and immune response to P. aeruginosa infections. We show an increased sialylation of mucins from the tracheal mucosa of CFTR-/- pigs, which is also associated to increased Pseudomonas aeruginosa adherence. RNA-seq analysis did not show any altered expression of inflammatory genes, nor of sialylation enzymes. CFTR-/- piglets were unable to clear P. aeruginosa from the airways, leading to increased bacteria time of residence in the airways. We propose that alterations in mucin sialylation and MCT directly contribute to the early development of a favorable environment for bacterial colonization of the CF airways in the absence of an intrinsic inflammation.

2020-06-01 | GSE99862 | GEO

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

Project description:Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and b1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD.

2024-06-19 | GSE262875 | GEO

Influence of inflammation on the expression and activity of glycosyltransferases in human bronchial mucosa

Project description:Bronchial inflammation is common in patients suffering from Cystic Fibrosis (CF) and is commonly responsible for mortality from CF. It is known that this inflammation has an influence over glycosylation events in bronchial mucins and abnormal glycosylation has been described in CF. These abnormalities can not be directly linked to CF, as the cells that secrete bronchial mucins do not express CFTR.

2011-03-02 | GSE27594 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data