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Gene expression differences among human natural killer cells and recombinant expression hosts

ABSTRACT: This study was designed to identify gene expression differences in activatable cells used to test therapeutic monoclonal antibody efficacy in vitro. We characterized the types of glycans attached to CD16a that were expressed by four cell types and compared these compositional differences to gene expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE153738 | GEO | 2020/12/10

REPOSITORIES: GEO

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Gene expression differences among human natural killer cells and recombinant expression hosts

Project description:Gene expression differences among human natural killer cells and recombinant expression hosts

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Transcriptomic profiles of Candida albicans grown in the presence or absence of mucin glycans

Project description:We use high-throughput sequencing to profile the response of the opportunistic fungal pathogen Candida albicans to mucins and mucin-glycans from the mucosal niche. We find that C. albicans undergoes a genome-wide phenotypic shift in response to mucins and their attached glycans suppressing virulence-associated pathways.

2022-01-03 | GSE192826 | GEO

Transcriptomic profiles of Pseudomonas aeruginosa PAO1 grown in the presence or absence of mucins or mucin-glycans

Project description:We use high-throughput sequencing to profile the response of the opportunistic mucosal pathogen Pseudomonas aeruginosa to mucins and mucin-glycans from the mucosal niche. We find that P. aeruginosa undergoes a genome-wide phenotypic shift in response to mucins and their attached glycans. Specifically, nearly all virulence pathways are downregulated in response to these host-produced factors. This study provides a framework for understanding how the host environment regulates bacterial function.

2019-10-20 | GSE136097 | GEO

Transcriptomic profiles of Pseudomonas aeruginosa PA14 grown in the presence or absence of mucins or mucin-glycans

2020-08-28 | GSE156995 | GEO

Free glycans derived from O-mannosylated glycoproteins suggest the presence of an O-glycoprotein degradation pathway in yeast

Project description:In eukaryotic cells, unconjugated oligosaccharides structurally related to N-glycans (FNGs) are generated either from misfolded N-glycoproteins destined for endoplasmic reticulum (ER)-associated degradation (ERAD), or from lipid-linked oligosaccharides, donor substrates for N-glycosylation of proteins. The mechanism responsible for the generation of FNGs is now well understood, but whether there are other type of free glycans remain unclarified. Here, we report on the accumulation of O-mannosylated free glycans in budding yeast that were cultured in media containing mannose as a carbon source. A structural analysis of these glycans revealed that their structures are identical to those of O-mannosyl glycans that are attached to glycoproteins. Deletion of the cyc8 gene, encoding a general transcription repressor, resulted in the accumulation of excessive amounts of the free O-glycans, concomitant with a severe growth defect, a reduction in the level of cellular O-mannosylated proteins, and compromised cell wall integrity. Our findings provide evidence for a regulated pathway for O-glycoprotein degradation in yeast and offer critical insights into the catabolic mechanisms that control the fate of O-glycosylated proteins.

2019-07-24 | GSE130332 | GEO

Serum protein N-glycosylation changes in multiple myeloma

Project description:<h4><strong>BACKGROUND:</strong> Multiple myeloma is characterized by clonal proliferation of malignant plasma cells in the bone marrow that produce monoclonal immunoglobulins. N-glycosylation changes of these monoclonal immunoglobulins have been reported in multiple myeloma, but previous studies only detected limited serum N-glycan features.</h4><h4><strong>METHODS:</strong> Here, a more detailed study of the human serum N-glycome of 91 multiple myeloma patients and 51 controls was performed. We additionally analyzed sequential samples from patients (n = 7) which were obtained at different time points during disease development as well as 16 paired blood serum and bone marrow plasma samples. N-glycans were enzymatically released and measured by mass spectrometry after linkage specific derivatization of sialic acids.</h4><h4><strong>RESULTS:</strong> A decrease in both α2,3- and α2,6-sialylation, galactosylation and an increase in fucosylation within complex-type N-glycans were found in multiple myeloma patients compared to controls, as well as a decrease in difucosylation of diantennary glycans. The observed glycosylation changes were present in all ISS stages, including the 'low-risk' ISS I. In individual patients, difucosylation of diantennary glycans decreased with development of the disease. Protein N-glycosylation features from blood and bone marrow showed strong correlation. Moreover, associations of monoclonal immunoglobulin (M-protein) and albumin levels with glycan traits were discovered in multiple myeloma patients.</h4><h4><strong>CONCLUSIONS & GENERAL SIGNIFICANCE: </strong>In conclusion, serum protein N-glycosylation analysis could successfully distinguish multiple myeloma from healthy controls. Further studies are needed to assess the potential roles of glycan trait changes and the associations of glycans with clinical parameters in multiple myeloma early detection and prognosis.</h4>

2022-04-27 | MTBLS676 | MetaboLights

core fucosylation as well as their modified glycoproteins associated with diseases

Project description:Core fucosylation is a form of fucose attached to the initial N-acetylglucosamine (GlcNAc) of N-linked glycans catalyzed by alpha-1,6 fucosyltransferase (Fut8).1 Corefucosylated N-glycans are widely mapped on cell surfaces, body fluids, and secreted proteins.

2024-01-17 | PXD048588 | JPOST Repository

Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts.

Project description:The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA degradation and processing events. While much of our current understanding of RNA exosome function has been elucidated using genetics and cell biology based studies of protein functions, in particular in S. cerevisiae, many important contributions in the field have been enabled through use of in vitro reconstituted complexes. Here, we present an overview of our approach to purify exosome components from recombinant sources and reconstitute them into functional complexes. Three chapters following this overview provide detailed protocols for reconstituting exosome complexes from S. cerevisiae, S. pombe, and H. sapiens. We additionally provide insight on some of the drawbacks of these methods and highlight several important discoveries that have been achieved using reconstituted complexes.

| S-EPMC8565498 | biostudies-literature

Black Carbon Impacts on Paraburkholderia xenovorans Strain LB400 Cell Enrichment and Activity: Implications toward Lower-Chlorinated Polychlorinated Biphenyls Biodegradation

Project description:Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. Biphenyl dioxygenase gene (bphA) abundance on four BC types demonstrated corn kernel biochar hosted at least four orders of magnitude more attached cells per gram than other feedstocks, and microscopic imaging revealed the attached live cell fraction was >1.5X more on corn kernel biochar than GAC. BC characteristics (i.e., sorption potential, surface area, pH) drove cell attachment differences. Reverse transcription qPCR indicated BC feedstocks significantly influenced bphA expression in attached cells. The bphA transcript-per-gene ratio of attached cells was >10-fold more than suspended cells, confirmed by transcriptomics. RNA-seq also demonstrated significant upregulation of biphenyl and benzoate degradation pathways on attached cells, revealing biofilm formation potential and cell-cell communication pathway connections. These novel findings demonstrate aerobic PCB-degrading cell abundance and activity could be tuned by adjusting BC feedstocks/ attributes to improve LC-PCBs biodegradation.

2023-11-03 | GSE246487 | GEO

The role of glycans and glycosylation in cell-type specific effects on viral infectivity

Project description:Our lab has previously used the Glyco v3 gene-chip to analyze RNA from human macrophages and T-cells, as part of a project examining the effect of cellular origin on the viral infectivity of HIV/SIV. Our experiments have led us to hypothesize that the different glycosylation pathways present in macrophages and T-cells result in the production of virions with differently glycosylated viral proteins and different glycans present on the virion surface. Furthermore, studies with glycosidases using the Glyco v3 gene-chip have indicated that these differences in the glycosylation profiles of virions derived from different cell types may influence viral infectivity. Here we used glyco v3 chips for identifying the enzymes active in the glycosylation pathways of 174xCEM and 293 cells, which are cell types commonly used in HIV and SIV research. These analyses will allow us a better understanding of the role of glycans and glycosylation in cell-type specific effects on viral infectivity because there is a much larger amount of data on virus derived from these cell types and we will be able to relate our studies more directly to previous work in our lab and other labs. RNA from 174xCEM and HEK293 cells, cell types commonly used in HIV and SIV research, was isolated and sent to Microarray Core (E). RNA was prepared in duplicate, totaling 4 samples. Samples were labeled and hybridized to the GLYCOv3 array and gene expression patterns were used to identify enzymes active in glycosylation pathways.

2011-06-14 | E-GEOD-29924 | biostudies-arrayexpress

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