Ontology highlight
ABSTRACT:
PROVIDER: PRJNA828554 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18838400_1.fastq.gz | Fastqsanger.gz | |||
| SRR18838400_2.fastq.gz | Fastqsanger.gz | |||
| SRR18838401_1.fastq.gz | Fastqsanger.gz | |||
| SRR18838401_2.fastq.gz | Fastqsanger.gz | |||
| SRR18838402_1.fastq.gz | Fastqsanger.gz |
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Project description:To uncover new molecular mechanisms involved in IgAN pathogenesis, we compared the genomic profiles of 12 IgAN patients with 8 healthy subjects, We included addiotional disease controls 3 FSGS(Focal Segmenal glomerulosclerosis) patients and 3 membrano proliferative glomerulonephritis type I (MPGN-I) controls in our study to evaluate if the WNT-β-catenin and PI3K/Akt pathways were specfic to IgAN. Gene expression profile comparison between 12IgAN patients and 8 Healthy Subjects. Gene Set Enrichment Analysis (GSEA) performed on the additional disease controls determined that the a priori defined set of genes and the pathways generated were specific to the IgAN
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Project description:We have performed a microRNA expression analysis in urine sediments from 18 IgAN patients, 6 healthy subjects and 8 disease controls(including 4 membranous nephropathy patients and 4 minimal change disease patients). Pathologic diagnosis of all IgAN patients was included in grades I–V by light microscopy according to the grading system of Lee et al. And we have identified a set of deregulated microRNAs with potential diagnostic value to identify patients with IgAN.
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Project description:In this study, we performed a comparative analysis of gut microbiota composition and gut microbiome-derived bacterial extracellular vesicles (bEVs) isolated from patients with solid tumours and healthy controls. After isolating bEVs from the faeces of solid tumour patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of faeces from patientsand controls using 16S rRNA sequencing. Machine learning was used to classify the samples into patients and controls based on their bEVs and faecal microbiomes.
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Project description:Immunoglobulin A nephropathy (IgAN) is the most common glomerulonephritis worldwide. However, biomarkers for predicting the progression or regression of IgAN remain a clinical challenge. In the present study, we aim to identify novel diagnostic and prognostic markers of IgAN. Using the cytokine antibody array, we detected serum and urinary levels of nine potential IgAN biomarkers in 32 IgAN patients and 16 healthy controls. The IgAN patients were grouped according to Lee’s grading system, with 16 patients with Grade I–II in the mild IgAN group and 16 with Grade III-V in the severe IgAN group. The associations between levels of these markers and IgAN were evaluated.
2022-07-13 | E-MTAB-11972 | biostudies-arrayexpress
Project description:To uncover new molecular mechanisms involved in IgAN pathogenesis, we compared the genomic profiles of 12 IgAN patients with 8 healthy subjects, We included addiotional disease controls 3 FSGS(Focal Segmenal glomerulosclerosis) patients and 3 membrano proliferative glomerulonephritis type I (MPGN-I) controls in our study to evaluate if the WNT-β-catenin and PI3K/Akt pathways were specfic to IgAN.
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Project description:The gut microbiome plays an important role in normal immune function and has been implicated in several autoimmune disorders. Here we use high-throughput 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=61) and healthy controls (n=43). Alterations in the gut microbiome in MS include increases in the genera Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signaling and NF-kB signaling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of the genera Prevotella and Sutterella, and decreased Sarcina, compared to untreated patients. MS patients of a second cohort show elevated breath methane compared to controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.
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Project description:The basic defect of IgA nephropathy (IgAN) lies within peripheral blood mononuclear cells rather than local kidney abnormalities. Previously we showed an altered gene expression in monocytes compared to B and T cells isolated from IgAN patients (Kidney Int, 2010), thus our aim here was to study this subset more closely at genome-wide level. total of 35 IgAN patients and 35 healthy blood donors (HBD) were included in this study. Illumina microarray technology was used to evaluate global differences in gene expression between monocytes isolated from IgAN patients and HBD. Bioinformatic analysis was performed with GenomeStudio and Genespring software. The connectivity between genes was evaluated using Ingenuity Pathway Analysis. Aberrantly expressed genes and pathways were then validated on an independent set of patients with RT-PCR western blot and flow cytometric analysis.
2015-03-30 | E-GEOD-58539 | biostudies-arrayexpress
Project description:Immunoglobulin A Nephropathy (IgAN) is a complex multifactorial disease whose genetic bases remain unknown. Distinct linkage and genome-wide association studies in both familial and sporadic IgAN suggest that there is a strong genetic component in IgAN. In this context, an intriguing role could be ascribed to copy number variants (CNVs) that have been recognized as an important source of genetic variation in humans. Here, we performed a whole-genome screening of CNVs in IgAN patients, their healthy relatives and healthy subjects (HS). A total of 217 individuals consisting of 51 IgAN cases and 166 healthy relatives were included in the initial screening. The high-throughput analysis of structural genetic variations, to find concordant aberrations across classes of samples, identified 178 IgAN-specific aberrations, specifically 114 loss and 64 gain. Several CNVs overlapped with regions evidenced by previous genome-wide genetic studies. Moreover, we found that IgAN patients characterized by deteriorated renal function carried low copy numbers of a CNV in chromosome 3 (chr3_loss:52031010-52260722). This CNV contained the TLR9 gene whose expression significantly correlated with the loss aberration in patients with progressive renal damage. Conversely, IgAN patients with normal renal function had no chr3_loss:52031010-52260722 and the TLR9 mRNA was expressed at the same level as in HS, still maintaining a strong correlation with the CNV. In conclusion, here we performed the first genome-wide CNV study in IgAN identifying some structural variants specific to IgAN patients and providing a collection of new candidate genes and loci that could help to dissect the complex genomic setting of the disease. Moreover, we identified a specific CNV, spanning the TLR9 gene, which could explain the disease severity in IgAN patients.
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