Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Anti-Glycan Reactivity in Humans is Driven by the Selection of B cells Utilizing Private Antibody Gene Rearrangements that are Affinity Maturated in Germinal Centers

ABSTRACT: The human antibody repertoire is broadly reactive with carbohydrate antigens represented in the universe of all living things, including both the host/self- as well as the commensal microflora-derived glycomes. Here we have used BCR receptor cloning and expression together with single-cell transcriptomics to analyze the B cell repertoire to the ubiquitous N-acetyl-D-glucosamine (GlcNAc) epitope in human cohorts and dissect the evolutionary history of this predominant class of antibodies. We find that circulating anti-GlcNAc B cells exhibiting canonical BMem phenotypes emerge rapidly after birth and couple this observation with evidence for germinal center-dependent affinity maturation of carbohydrate-specific B cell receptors in situ during early childhood. Direct analysis of individual B cell clonotypes reveals they exhibit strikingly distinct fine-specificity profiles for palettes of GlcNAc containing moieties. These results suggest that a generalized, exposure to complex environmental glycans drives the steady state anti-glycan repertoire.

ORGANISM(S): Homo sapiens

PROVIDER: GSE278639 | GEO | 2025/10/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression data from glucosamine-treated human synovial MH7A cells

Project description:Osteoarthritis (OA) is one of the major joint diseases. Glucosamine (GlcN) is widely used as a dietary supplement for OA. However, its precise mechanisms are not well understood. GlcN is utilized for the O-linked-N-acetylglucosamine (O-GlcNAc) modification of proteins, which participates in the regulation of cellular functions. In this study, we comprehensively analyzed the effect of GlcN and alloxan (O-GlcNAc transferase inhibitor, which prevented O-GlcNAc modification) on the gene expression using DNA microarray. GlcN downregulated or upregulated genes. Furthermore, among the GlcN-downregulated or upregulated genes, the expression of 62.7% of the genes was restored by alloxan.. Thus, it is suggested that GlcN regulates the gene expression by an O-GlcNAc modification-dependent or -independent mechanism.

2016-11-07 | GSE72575 | GEO

The Vibrio cholerae chitin utilization program

Project description:This SuperSeries is composed of the following subset Series: GSE3101: Chitin oligosaccharide induction GSE3102: Crab shell attachment GSE3103: Chitin sensor Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin. Refer to individual Series

2006-03-07 | E-GEOD-4388 | biostudies-arrayexpress

CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution

Project description:Recent studies have revealed that nucleotide-containing metabolites, including nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), 3′-dephospho-coenzyme A (dpCoA), uridine diphosphate glucose (UDP-Glc), and uridine diphosphate N-acetyl glucosamine (UDP-GlcNAc), can be incorporated into the RNA 5′-terminus as noncanonical initiating nucleotides (NCIN), resulting in NCIN-capped RNA (NCIN-RNA).

2025-05-12 | GSE253549 | GEO

N-acetyl-D-glucosamine is an oncometabolite modulating mast cell effector functions by chromatin remodeling

Project description:We investigated the metabolic regulation of mast cell (MC) functions to control them. MCs are sentinels of the immune system with functions involved not only in host defense but also, if not properly controlled, in MC disorders such as systemic mastocytosis (SM). We identified N-acetyl-D-glucosamine (GlcNAc or NAG) as both a circulating biomarker for SM severity and an oncometabolite that promotes uncontrolled degranulation and proliferation of MCs expressing the Kit kinase domain mutant allele, D816V, that is both an oncogene and characterizes patients with SM. Given the known role of GlcNAc-related protein glycosylation in modifying factors involved in epigenetic regulation of gene expression and the effects of GlcNAc on neoplastic MCs effector functions, we asked whether the increased susceptibility of KIT D816V MCs to GlcNAc was due to chromatin state changes.

2023-04-20 | GSE149106 | GEO

Long primed germinal centers with enduring affinity maturation and clonal migration

Project description:Germinal centers (GCs) are the engines of antibody evolution. Using HIV Env protein immunogen priming in rhesus monkeys (RM) followed by a long period without further immunization, we demonstrate GC B cells (BGC) lasted at least 6 months. A 186-fold BGC cell increase was present by week 10 compared to a conventional immunization. Single cell transcriptional profiling revealed both light and dark zone GC states were sustained. Antibody somatic hypermutation (SHM) of BGC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding BGC cells were still 49-fold above baseline at 29 weeks, suggesting they could be active for even longer periods of time. High HIV neutralizing antibody titers were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing significant immunodominance challenges for B cells. Memory B cells (BMem) generated under these long priming conditions had higher levels of SHM, and both BMem cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning the >6-month GC period were identified, demonstrating continuous GC activity and selection for at least 191 days with no additional antigen exposure. A long prime, slow delivery (12-day) immunization approach holds promise for difficult vaccine targets, and suggests that patience can have great value for tuning GCs to maximize antibody responses.

2022-09-15 | GSE209904 | GEO

The Vibrio cholerae chitin utilization program

Project description:Abstract: Chitin, an insoluble polymer of GlcNAc, is an abundant source of carbon, nitrogen, and energy for marine microorganisms. Microarray expression profiling and mutational studies of Vibrio cholerae growing on a natural chitin surface, or with the soluble chitin oligosaccharides (GlcNAc)(2-6), GlcNAc, or the glucosamine dimer (GlcN)2 identified three sets of differentially regulated genes. We show that (i) ChiS, a sensor histidine kinase, regulates expression of the (GlcNAc)(2-6) gene set, including a (GlcNAc)2 catabolic operon, two extracellular chitinases, a chitoporin, and a PilA-containing type IV pilus, designated ChiRP (chitin-regulated pilus) that confers a significant growth advantage to V. cholerae on a chitin surface; (ii) GlcNAc causes the coordinate expression of genes involved with chitin chemotaxis and adherence and with the transport and assimilation of GlcNAc; (iii) (GlcN)2 induces genes required for the transport and catabolism of nonacetylated chitin residues; and (iv) the constitutively expressed MSHA pilus facilitates adhesion to the chitin surface independent of surface chemistry. Collectively, these results provide a global portrait of a complex, multistage V. cholerae program for the efficient utilization of chitin. This SuperSeries is composed of the SubSeries listed below.

2006-03-08 | GSE4388 | GEO

Bulk RNA-seq of lung-resident memory B cells and comparison to splenic memory and naive B cells

Project description:The aim was to utilise bulk RNAseq to compare the transcriptional profiles of memory B cells (Bmem) from the lung tissue to circulatory Bmem derived from spleen, in the context of X31 influenza-induced immune memory. In this study we utilise AID-Cre Rosa-Stop-YFP reporter mice to track previously activated B cell populations, and combine this with an X31-influenza-specific HA probe to isolate flu-specific Bmem. We find that lung Bmem express a number of tissue retention-associated genes (Cd44, Cd69) and downregulate circulatory genes (Sell, S1pr1), in comparison to splenic Bmem. We also identify a number of chemotactic factors (Cxcr3, Ccr1, Ccr5) that are expressed at higher levels in lung Bmem than splenic Bmem.

2022-03-28 | GSE183135 | GEO

Mucus-derived glycans are inhibitory signals for Salmonella Typhimurium SPI-1-mediated invasion

Project description:Mucus forms a critical barrier against enteric pathogens like Salmonella enterica serovar Typhimurium. While in vivo studies indicate that secreted, gel-forming mucins and specifically Core 3 glycosylation are protective against S. Typhimurium, the molecular mechanisms involved remain unclear. Here, we measure gene expression changes in Salmonella enterica serovar Typhimurium LT2 following growth in SPI-1 inducing medium (LB + 0.3M NaCl) with or without purified MUC2 (0.1%, w/v), MUC2 glycans (0.1%, w/v), a pool of monosaccharide components comprised of D-galactose, D-GalNAc, D-GlcNAc, D-fuc, and Neu5Ac (0.1%, w/v), or specific individual mucin sugars, namely N-acetyl galactosamine (GalNAc) (0.2%, w/v) and N-acetyl glucosamine (GlcNAc) (0.2%, w/v). Notably, we find MUC2, MUC2 glycans, and to a lesser extent,D-GalNAc and D-GlcNAc downregulate SPI-1 gene expression.

2025-09-25 | GSE278090 | GEO

AMINO SUGARS RESHAPE INTERACTIONS BETWEEN STREPTOCOCCUS MUTANS AND STREPTOCOCCUS GORDONII

Project description:Amino sugars, particularly glucosamine (GlcN) and N-acetylglucosamine (GlcNAc) are abundant carbon and nitrogen sources that are continually supplied in host secretions and the diet to biofilms colonizing the human mouth. Evidence is emerging that these amino sugars may provide an ecological advantage to beneficial commensals over oral pathobionts. Here we performed transcriptome analysis on Streptococcus mutans and Streptococcus gordonii growing in single-species or dual-species cultures with glucose, GlcN or GlcNAc as the primary carbohydrate source. Compared to glucose, GlcN caused drastic transcriptomic shifts in each bacterium when they were cultured alone. Likewise, co-cultivation in the presence of GlcN yielded transcriptomic profiles that were dramatically different than the single-species results from GlcN-grown cells. In contrast, GlcNAc elicited only minor changes in the transcriptome of either organism, in both single- and dual-species cultures. Interestingly, genes involved in pyruvate metabolism were among the most significantly affected by GlcN in both species, and these changes were consistent with measurements of pyruvate in culture supernates. Differing a previous report, growth of S. mutans alone with GlcN inhibited expression of multiple operons required for mutacin production. Co-cultivation with S. gordonii consistently increased the expression by S. mutans of two manganese transporter operons (slo and mntH) and decreased expression of mutacin genes. Conversely, S. gordonii appeared to be less affected by the presence of S. mutans, but did show increases in genes for biosynthetic processes in the co-cultures. In conclusion, amino sugars profoundly altered the interactions between the pathogen and the commensal, likely by reprogramming their central metabolism.

2020-06-09 | GSE152021 | GEO

Antibiotic abuse during endodontic treatment in private dental centers.

Project description:We evaluated antibiotic prescription practices during root canal treatments among general dentists in private dental clinics in Al-Madinah Al Munawarah, Saudi Arabia. Methods: A self-administered, questionnaire about antibiotic used during root canal treatment was distributed to 75 randomly selected general dental practitioners working in private dental clinics in Al-Madinah Al-Munawarah, Saudi Arabia, between March and April 2016. The questionnaires were collected one week later. To compare results of the collected data, Chi-square test was used. Results: The results revealed that 60% of the dentists prescribed amoxicillin with clavulanic acid as the first choice treatment for endodontic pathosis. Clindamycin (51.6%) was the first choice for patients who were allergic to penicillin. Forty-five percent of the general practitioners prescribed antibiotics for 5 days. Approximately 83.3% of general practitioners prescribed antibiotics for acute apical abscesses. Prophylactic antibiotics were prescribed for cases with a history of infective endocarditis (65.5%), non-controlled diabetes (60.3%), placement of a prosthetic joint in the previous 2 years (46.6%), congenital heart disease (36.2%), and kidney dialysis shunts (34.5%). Conclusion: This study reveals antibiotic abuse in endodontic treatment practice in private dental clinics in Al-Madinah Al Munawarah, Saudi Arabia. General dental practitioners are lacking knowledge regarding the prescription of antibiotics in endodontic treatment and situations requiring prophylactic antibiotics.

| S-EPMC5556303 | biostudies-other

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