Ontology highlight
ABSTRACT:
PROVIDER: PRJNA445233 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6884560_1.fastq.gz | Fastqsanger.gz | |||
| SRR6884560_2.fastq.gz | Fastqsanger.gz | |||
| SRR6884570_1.fastq.gz | Fastqsanger.gz | |||
| SRR6884570_2.fastq.gz | Fastqsanger.gz | |||
| SRR6884580_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Microbiota in fecal samples of non-IgE mediated cow´s milk protein allergy infants (CMPA)
| PRJNA487705 | ENA
Project description:Exclusively breast-fed infants can exhibit clear signs of IgE or non IgE-mediated cow’s milk allergy. The definite characterization of dietary cow’s milk proteins (CMP) that survive the maternal digestive tract to be absorbed into the bloodstream and secreted into breast milk remains missing. The aim of this study was to assess the occurrence of CMP-derived peptides in breast milk, using antibody-independent methods. Using high performance liquid chromatography-high resolution mass spectrometry in blinded assays, we identified 11 cow’s milk-derived peptides, including two β-lactoglobulin (2 out 6 samples) and one αs1-casein (1 out 6 samples) fragments, in breast milk from mothers receiving a cup of bovine milk daily. The β-lactoglobulin (β-Lg) fragments, namely f42-54 and f42-57, were absent in milk from mothers who observed a strict dairy-free diet (6 samples). In contrast, neither intact nor hydrolyzed β-Lg was detected by Western blot or competitive ELISA tests. CMP-derived peptides rather than intact CMP may sensitize or elicit allergic responses in the neonate through mother’s milk. Immunologically active peptides from the maternal diet could be involved in priming the newborn’s immune system to drive tolerogenic response in neonates and infants.
2016-07-19 | PXD003657 | Pride
Project description:Exclusively breast-fed infants can exhibit clear signs of IgE or non IgE-mediated cow’s milk allergy. The definite characterization of dietary cow’s milk proteins (CMP) that survive the maternal digestive tract to be absorbed into the bloodstream and secreted into breast milk remains missing. The aim of this study was to assess the occurrence of CMP-derived peptides in breast milk, using antibody-independent methods. Using high performance liquid chromatography-high resolution mass spectrometry in blinded assays, we identified 11 cow’s milk-derived peptides, including two ?-lactoglobulin (2 out 6 samples) and one ?s1-casein (1 out 6 samples) fragments, in breast milk from mothers receiving a cup of bovine milk daily. The ?-lactoglobulin (?-Lg) fragments, namely f42-54 and f42-57, were absent in milk from mothers who observed a strict dairy-free diet (6 samples). In contrast, neither intact nor hydrolyzed ?-Lg was detected by Western blot or competitive ELISA tests. CMP-derived peptides rather than intact CMP may sensitize or elicit allergic responses in the neonate through mother’s milk. Immunologically active peptides from the maternal diet could be involved in priming the newborn’s immune system to drive tolerogenic response in neonates and infants.
2017-04-02 | MSV000080880 | MassIVE
Project description:Background: Cow's milk allergy (CMA) is one of the most common food allergies (FA) in childhood. This condition can be IgE-mediated, non-IgE-mediated, or a combination of both. Diagnosis involves clinical history in conjunction with sensitization tests. However, these tests have limited predictive value, making the oral food challenge (OFC) the gold standard for diagnosis. Recent research has focused on identifying biomarkers, including DNA methylation patterns, for FA diagnosis. The aim of this study is to investigate the differences in DNA methylation associated with distinct patterns of CMA, to identify novel diagnostic biomarkers. Methods: Genome-wide DNA methylation profiling was performed on blood samples from infants with IgE-mediated CMA (CMAIE), non-IgE-mediated CMA (CMANIE), and non-allergic controls, at baseline and after 6 months of a exclusion diet in CMA groups. These results were then correlated with tolerance acquisition following the restrictive diet. Results: A total of 19 infants were enrolled (10 CMAIE, 6 CMANIE, and 3 controls). Significant differentially methylated regions (DMRs) annotated to both genes and promoters were identified in all groups, and a clear separation of the samples into their respective groups was observed. Furthermore, DMRs in promoters and genes were identified in tolerant CMAIE children after the exclusion diet, being associated to tolerance. Discussion: Differential DNA methylation in CMA children is a useful diagnostic biomarker, and it could also be valuable in predicting the resolution of such pathologies.
2025-12-17 | GSE289021 | GEO
Project description:Cow milk (CM) allergy is the most prevalent food allergy in young children in the US and Great Britain. Current diagnostic tests are either unreliable (IgE, skin prick test), or resource-intensive with risks (food challenges). Here we set out to determine if allergen-specific T cells in cow milk allergic (CMA) patients have a distinct quality and/or quantity that could potentially be used as a diagnostic marker. Starting from cow milk extract, we mapped T cell responses to a set of reactive epitopes that we compiled in a peptide pool. This pool induced cytokine responses in in vitro cultured cells distinguishing allergic from non-allergic subjects. Using single-cell RNA and paired TCR sequencing we detected significant changes in the transcriptional program and clonality of cow milk antigen-specific (CM+) T cells elicited by the pool in allergic vs. non-allergic subjects ex vivo. CM+ T cells from allergic subjects had increased percentages of FOXP3+ over FOXP3- cells. FOXP3+ cells are often equated with regulatory T cells (Tregs) that have suppressive activity, but CM+ FOXP3+ cells from allergic subjects showed significant expression of interferon-responsive genes and dysregulated chemokine receptor expression compared to non-allergic subjects, suggesting that these are not conventional Tregs. The CM+ FOXP3+ cells were also more clonally expanded than the FOXP3- population. We were further able to utilize surface markers (CD25, CD127, CCR7) in combination with our peptide pool stimulation to quantify these CM+ FOXP3+ cells by a simple flow cytometry assay. We show increased percentages of CM+ CD127-CD25+ cells from CMA subjects in an independent cohort, which could be used for diagnostic purposes. Looking specifically for Th2 cells normally associated with allergic diseases, we found a small population of clonally expanded CM+ cells that were significantly increased in CMA subjects and that had high expression of Th2 cytokines and pathogenic Th2/Tfh markers. Overall, these findings suggest that there are several differences in the phenotype of CM+ T cells with CM allergy and that the increase in CM+ FOXP3+ cells is a potential diagnostic marker of an allergic state. Such markers have promising applications in monitoring natural disease outgrowth and/or the efficacy of immunotherapy that will need to be validated in future studies.
2023-08-10 | GSE231590 | GEO
Project description:Immunotherapy strategies have been studied for IgE-mediated food allergies but have not been studied for non-IgE mediated food allergy disorders, including eosinophilic esophagitis. We interrogated the transcriptional signatures of peripheral CD4+ cells isolated from pediatric eosinophilic esophagitis patients enrolled in a phase IIa clinical trial of milk-antigen epicutaneous immunotherapy. We analyzed differential expression in peripheral CD4+ cells before therapy in patients before and after milk-exclusion diet. RNA-sequencing analysis revealed that there were 244 differentially expressed genes in peripheral blood CD4+ cells of EoE patients consuming milk versus those eliminating it, and 129 DEGs in CD4+ cells isolated after EPIT versus after placebo (FDR<0.05). Gene set enrichment analysis identifies enrichment of hallmark interferon-a and -g response signatures in peripheral CD4+ T cells from EoE patients during active disease on a milk-containing diet. In post-EPIT therapy samples, our analysis identifies enrichment in T-cell receptor signaling, antigen presentation, costimulation, and cytokine signaling pathways. These data suggest a unique peripheral CD4+ T cell gene signature is present in EoE patients during active disease. We observe a distinct transcriptional profile post-EPIT therapy in EoE patients, suggesting that EPIT alters CD4+ responses in EoE patients.
2021-08-03 | GSE173895 | GEO
Project description:<p><strong>SCOPE:</strong> Cow's milk allergy (CMA) is one of the most prevalent food allergies in early childhood, often treated via elimination diets including standard amino acid-based formula or amino acid-based formula supplemented with synbiotics (AAF or AAF-S). This work aimed to assess the effect of cow's milk (CM) tolerance acquisition and synbiotic (inulin, oligofructose, Bifidobacterium breve M-16 V) supplementation on the fecal metabolome in infants with IgE-mediated CMA.</p><p><strong>METHODS AND RESULTS: </strong>The CMA-allergic infants received AAF or AAF-S for a year during which fecal samples were collected. The samples were subjected to metabolomics analyses covering gut microbial metabolites including SCFAs, tryptophan metabolites and bile acids (BAs). Longitudinal data analysis suggested amino acids, BAs and branched SCFAs alterations in infants who outgrew CMA during the intervention. Synbiotic supplementation significantly modified the fecal metabolome after 6 months of intervention, including altered purine, BA and unsaturated fatty acid levels, and increased metabolites of infant-type Bifidobacterium species: indolelactic acid and 4-hydroxyphenyllactic acid.</p><p><strong>CONCLUSION: </strong>This study offers no clear conclusion on the impact of CM-tolerance acquisition on the fecal metabolome. However, our results show that 6 months of synbiotic supplementation successfully altered fecal metabolome and suggest induced bifidobacteria activity, which subsequently declined after 12 months of intervention.</p>
2024-09-02 | MTBLS8954 | MetaboLights
Project description:Milk and soy are reported to contain bioactive molecules with antibacterial and immunomodulatory actions, which may be beneficial to people with IBD. The aim of this study was to determine whether diets containing ruminant milk or soy solids reduce intestinal inflammation in Il10-/- mice. Male Il10-/- mice and C57BL/6J mice were fed diets containing 40% (w/w) sheep, goat, or cow whole milk powder, 40% (w/w) soy solids (NOW® Foods Soy Milk Powder, Instant), or one of two control diets (casein-free modified-AIN76A or standard AIN76A) from 4 to 11 weeks of age. Diets were based on AIN76A, which was included as an inter-experimental control for inflammation. For all diets except AIN76A, total protein, fat, carbohydrate and energy were kept as similar as possible. Weight and food intake were measured throughout the experiment (three times weekly), and intestinal tissue was taken for histopathology evaluation of inflammation and analysis of gene expression. Analysis of mouse weight and feed intake both showed a significant strain-diet interaction: Il10-/- mice fed the cow and goat milk diets ate less and gained less weight than all the other diet groups. This diet effect was not evident for the C57BL/6J mice. Il10-/- mice on the cow and goat milk diets had reduced colon histological injury scores relative to those on the other diets. Il10-/- mice on the cow and goat milk diets also had reduced expression of many immune/inflammatory-related genes and pathways.
2019-12-01 | GSE39830 | GEO
Project description:This study investigated the impact of a high cellulose diet (HCD) on intestinal homeostasis and food allergy development in BALB/c mice. While soluble fibers are known to mitigate FA via short-chain fatty acid (SCFA) production, the role of insoluble fibers like cellulose remains unclear. Mice fed HCD exhibited gut dysbiosis, characterized by increased Proteobacteria, decreased tight junction protein expression, and intestinal barrier impairment, despite unchanged SCFA levels. RNA sequencing revealed HCD-induced upregulation of immune pathways, including the positive regulation of B and T cells differentiation and antigen receptor-mediated signaling pathway. Following ovalbumin (OVA) sensitization, HCD-fed mice displayed exacerbated allergic symptoms, including elevated OVA-specific IgE, IgG, histamine, and mMCP-1 levels. Gut microbiota analysis highlighted enrichment of potentially pathogenic taxa in HCD+OVA groups. Fecal microbiota transplantation (FMT) from HCD donors to antibiotic-treated recipients showed severe food allergy responses, confirming microbiota-mediated effects. These findings demonstrate that HCD exacerbates food allergy through gut microbial dysbiosis, intestinal barrier disruption, and intestinal immune disorder.
2025-06-17 | GSE299687 | GEO
Project description:Milk-derived extracellular vesicles (mEVs) have been proved to play a critical role in intercellular communication, mainly through the microRNAs (miRNAs) that they carry, to regulate biological functions of the target cells. Given miRNAs are evolutionarily conserved, EVs present in commercial milk may play a role in the physiology and health consumers. It is therefore essential to know the effects of technological treatments such as skimming and spray drying on the EV content of milk powders and on the cargo of bioactive molecules, in particular miRNAs, that they convey. Since goat’s milk or goat milk based formulas are considered as a healthy alternative for infants with cow’s milk sensitivities, including allergy, we undertook to analyze the EV content of skimmed and unskimmed goat's milk powders and to characterize their RNA content, in particular their miRNomes. mEVs were isolated using an optimized protocol based on Size Exclusion Chromatography (SEC) and compared regarding morphology, number and size by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Their RNA and protein content were determined and their miRNomes established, using RNA sequencing. In this study we demonstrated that goat milk powders, skimmed or not upstream the spray drying treatment, contained many mEVs, ranging from 5.4 1011 to 2.5 1012 particles per mL of reconstituted milk, with an average size between 136.8 and 160.6 nm. We also demonstrated that mEVs carried significant amounts of RNA, including miRNAs. Using RT-qPCR, mRNAs encoding five of the major milk proteins were detected, suggesting that mEVs originated from mammary epithelial cells. We established the goat milk powder miRNome by identifying 351 miRNAs of which 233 are common to the 262 miRNAs previously profiled in raw goat milk. The 20 most abundant miRNAs (TOP 20) account for 80% of the total reads and the hierarchy of this TOP 20 miRNAs is somewhat overturned when comparing goat milk powder and raw goat milk. Surprisingly, whereas the comparison of raw from cow and goat milk confirmed the prevalence of miR-148a, miR-21-5p and miR-26a/miR-30a-5p, let-7a-5p and let-7f, which occupied ranks 1 and 2, respectively, in powders, were relegated to ranks 6 and 10 and 5 and 11 in raw goat and cow milk, respectively. Conversely to what was previously reported, we provide evidence that: i) EVs of typical morphology are present in goat milk powders; ii) mEVs survived the technological processes used to produce the powders; iii) their miRNA cargo is protected from degradation even though their miRNomes are not an exact mirror of miRNomes of EVs derived from fluid raw milk.
2025-01-01 | GSE254484 | GEO