Swiss infant cohort 0-2y
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ABSTRACT:
PROVIDER: PRJEB53381 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Infant gut colonization study conducted on a Swiss cohort
| PRJEB53435 | ENA
Project description:Prophages in the Infant Gut from a Large Danish Cohort Study
| PRJEB46693 | ENA
Project description:Microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent and related functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. Thus, we employed shotgun proteomics via nano-2D-LC-MS/MS to simultaneously monitor microbial and human proteins in fecal samples from a healthy preterm infant during early development. ). All MS/MS spectra were searched against a predicted protein database containing 25 microbial species along with the Human RefSeq2011 genome using the SEQUEST algorithm (Eng et al, 1994), and filtered with DTASelect version 1.9 (Tabb et al, 2002) at the peptide level with standard filters [SEQUEST Xcorrs of at least 1.8 (+1), 2.5 (+2) 3.5 (+3)] organizing identified peptides to their corresponding protein sequences. This study provides the first elucidation of coordinated human and microbial proteins in the infant gut during early development.
2014-12-16 | PXD000114 | Pride
Project description:Extensive molecular and prognostic characterization of wild-type MLL infant ALL. Background: Approximately 20% of all infant ALL cases carry wild-type (or germline) MLL genes. To date, wild-type MLL infant ALL patients are generally regarded as young pediatric precursor B-ALL patients, but extensive characterization of this specific patient group largely remains unacknowledged. Methods: We here studied a relatively large cohort of 78 wild-type MLL infant ALL samples, using clinical parameters, array-comparative genomic hybridization analysis, gene expression profiling, multiplex ligation-dependent probe amplification, and conventional sequencing. Findings: Wild-type MLL infant ALL patients are generally characterized by a lower incidence of favourable prognostic factors than pediatric (non-infant) B-ALL patients, and patients at high risk of therapy failure typically display an immature pro-B immunophenotype or respond poorly to prednisone. Using gene expression profiling, we found MEIS1 expression to additionally be highly predictive for clinical outcome in wild-type MLL infant ALL with a favourable prognosis in the wild-type MLL infants with low MEIS1 expression (DFS 88%% versus 50%, p=0•01). Overall the incidence of DNA copy number variations and genetic abnormalities in genes involved in B-cell differentiation is lower in wild-type MLL infant ALL patients as compared with pediatric precursor B-ALL patients. Interpretation: Wild-type MLL infant ALL represents a highly heterogeneous patient group, which cannot be unified by one or a few known recurrent genomic aberrations. High-level MEIS1 expression and an immature pro-B immunophenotype in high-risk wild-type MLL infant ALL patients shows parallel with the unfavourable prognosis of MLL-rearranged infant ALL patients. In contrast, wild-type MLL infant ALL patients expressing lower levels of MEIS1 and displaying more differentiated (pre-B or common) phenotypes may well be more related to pediatric precursor B-ALL patients older than 1 year of age. We advocate that a treatment strategy in wild-type MLL infant ALL based on MEIS1 expression could be beneficial for improving survival. Gene expression profiling of wild-type MLL infant ALL. Additional wild-type MLL infant ALL patient samples (n=17) to the earlier samples published under GSE19475 (GSM485309 to GSM485322).
2014-10-01 | E-GEOD-58565 | biostudies-arrayexpress
Project description:Human breast milk (BM) plays a critical role in infant development and health, particularly in cognitive, immune, and cardiometabolic functions. BM contains extracellular vesicles (EVs) that can transport biologically relevant cargo from mother to infant, including microRNAs (miRNAs). However, to date, most studies on BMEVs have been limited in sample size. We aimed to investigate BMEV-miRNA profiles in a human population cohort, characterize BMEV-miRNAs patterns, and assess potential pathways and ontology. We thus conducted the first study to describe the EV miRNA profile of BM in 364 mothers from a population-based mother-infant cohort in the Faroe Islands using small RNA sequencing. We detected 1,523 miRNAs with ≥ one read in 70% of samples, and 447 miRNAs with ≥ one read in 100% of samples. Using hierarchical clustering, we determined five BMEV-miRNA clusters, the top three consisting of 15, 27 and 67 miRNAs. Correlation coefficients indicated that the expression of many miRNAs within the top three clusters was highly correlated. Top-cluster BMEV-miRNAs were involved in pathways enriched for the endocrine system, cellular community, neurodevelopment, and cancers. Future studies investigating determinants of BMEV-miRNAs and associated health outcomes are needed to elucidate the role of BMEV-miRNAs in health and disease.
2021-03-12 | GSE146880 | GEO
Project description:Extensive molecular and prognostic characterization of wild-type MLL infant ALL. Background: Approximately 20% of all infant ALL cases carry wild-type (or germline) MLL genes. To date, wild-type MLL infant ALL patients are generally regarded as young pediatric precursor B-ALL patients, but extensive characterization of this specific patient group largely remains unacknowledged. Methods: We here studied a relatively large cohort of 78 wild-type MLL infant ALL samples, using clinical parameters, array-comparative genomic hybridization analysis, gene expression profiling, multiplex ligation-dependent probe amplification, and conventional sequencing. Findings: Wild-type MLL infant ALL patients are generally characterized by a lower incidence of favourable prognostic factors than pediatric (non-infant) B-ALL patients, and patients at high risk of therapy failure typically display an immature pro-B immunophenotype or respond poorly to prednisone. Using gene expression profiling, we found MEIS1 expression to additionally be highly predictive for clinical outcome in wild-type MLL infant ALL with a favourable prognosis in the wild-type MLL infants with low MEIS1 expression (DFS 88%% versus 50%, p=0•01). Overall the incidence of DNA copy number variations and genetic abnormalities in genes involved in B-cell differentiation is lower in wild-type MLL infant ALL patients as compared with pediatric precursor B-ALL patients. Interpretation: Wild-type MLL infant ALL represents a highly heterogeneous patient group, which cannot be unified by one or a few known recurrent genomic aberrations. High-level MEIS1 expression and an immature pro-B immunophenotype in high-risk wild-type MLL infant ALL patients shows parallel with the unfavourable prognosis of MLL-rearranged infant ALL patients. In contrast, wild-type MLL infant ALL patients expressing lower levels of MEIS1 and displaying more differentiated (pre-B or common) phenotypes may well be more related to pediatric precursor B-ALL patients older than 1 year of age. We advocate that a treatment strategy in wild-type MLL infant ALL based on MEIS1 expression could be beneficial for improving survival.
2014-10-01 | GSE58565 | GEO
Project description:The aggressive MLL-rearranged leukemias are well-known for their unique gene-expression profiles. The goal of this study was to characterize the MLL-specific DNA methylation profiles in infant acute lymphoblastic leukemia (ALL). Genome-wide DNA methylation profiling was performed on primary infant ALL samples. The majority of infant ALL samples demonstrated severe DNA hypermethylation compared with normal pediatric bone marrows, which implies that targeting of DNA methylation may be an interesting option for future therapeutic strategies in MLL-rearranged infant ALL. Using ALL cell lines carrying the MLL translocation t(4;11) (SEMK2 and RS4;11) as a model for the patient cells, we demonstrated that the hypermethylated genes are sensitive to demethylation.
2009-11-23 | GSE18400 | GEO
Project description:Prospective cohort carriage study
| PRJEB53187 | ENA