Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12342830_1.fastq.gz | Fastqsanger.gz | |||
| SRR12342830_2.fastq.gz | Fastqsanger.gz |
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Project description:Denys-Drash syndrom is a rare disease. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of kidney tissue cells in an infant with Denys-Drash syndrom.
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Project description:Alport syndrome is a progressive kidney disease caused by pathogenic variants in genes encoding type IV collagen, a major structural component of the glomerular basement membrane (GBM). Abnormal GBM architecture impairs filtration and triggers inflammation, fibrosis, and eventual kidney failure. Because disease progression is irreversible, identifying early molecular changes is essential for understanding disease onset. We performed glomerular single-cell RNA sequencing (scRNA-seq) in a Col4a5 G5X Alport mouse model at 5 weeks of age, prior to detectable proteinuria or GBM/podocyte abnormalities (pre-onset), and at 8 weeks, when mild proteinuria and structural defects emerged. Despite the early stage, scRNA-seq revealed widespread transcriptional alterations, most prominently in podocytes. Among genes upregulated at both time points, we identified Tumor Necrosis Factor Superfamily Member 15 (Tnfsf15), previously associated with kidney disease susceptibility but with unclear function. To determine its role in Alport syndrome, we generated Tnfsf15-deficient Alport mice. Tnfsf15 homozygous knockout mice exhibited increased proteinuria and exacerbated glomerular injury compared with Tnfsf15(+/+) Alport mice during early disease. These findings support a protective role for Tnfsf15 in the early stages of Alport syndrome, mitigating proteinuria and limiting glomerular injury.
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Project description:Proteomic analysis of plasma extracellular vesicles from primary Sjögren syndrom patients, compared to systemic lupus erythematosus patients and helathy donors
2023-06-13 | PXD041452 | Pride
Project description:COL4A3/A4/A5 mutations have been identified as critical causes of Alport syndrome and other genetic chronic kidney diseases. However, the underlying pathogenesis remains unclear, and specific treatments are lacking. Here, we constructed a transgenic Alport syndrome mouse model by generating a mutation (Col4a3 p.G799R) identified previously from one large Alport syndrome family into mice. We observed that the mutation caused a pathological decrease in intracellular and secreted collagen IV α3α4α5 heterotrimers. The mutant collagen IV α3 chains abnormally accumulated in the endoplasmic reticulum and exhibited defective secretion, leading to persistent endoplasmic reticulum stress in vivo and in vitro. RNA-seq analysis revealed that the MyD88/p38 MAPK pathway plays key roles in mediating subsequent inflammation and apoptosis signaling activation. Treatment with tauroursodeoxycholic acid, a chemical chaperone drug that functions as an endoplasmic reticulum stress inhibitor, effectively suppressed endoplasmic reticulum stress, promoted secretion of the α3 chains, and inhibited the activation of the MyD88/p38 MAPK pathway. Tauroursodeoxycholic acid treatment significantly improved renal function in vivo. These results partly clarified the pathogenesis of renal injuries associated with Alport syndrome, especially in glomeruli, and suggested that tauroursodeoxycholic acid might be useful for the early clinical treatment of Alport syndrome.
2024-08-28 | GSE261588 | GEO
Project description:Human velocardiofacial syndrom/DiGeorg (VCFS/DGS) syndrom is a complex developmental disease with various expression of a large number of phenotypes. Craniofacial, cardiac, behavioural and endocrinological phenotypes are cardinal symptoms liked to the 22Q11.2 deletion occuring in 1/4.000 births. Several genes located within the 1.5 to 3 Mb deletion resemble a number of phenotypes demonstrated in mouse models for these genes including the endothelin receptor A (Ednra) gene. This is the first report on gene dosage effects observed in a dominant mouse model carrying an EdnraY129F point-mutation. EdnraY129F/+ mice are viable despite a strong cardiac phenotype alike to Fallot's tetralogy concomitant with cardiofacial, otolaryngeal phenotypes and deafness.
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Project description:Alport syndrome is a glomerular disease. To understand the disease progression of alport syndrome and potential therapeutical effects of hEV derived from AFSCs, we performed spatial transcriptomics to profile the heterogeniety of cell populations in kidneys of mouse of AS through disease progression and hEV treated AS mice as well. Our analysis sheds light on key functional parts of the kidney responsible in disease progression as well as potential targets of hEV therapy.
2024-11-30 | GSE245039 | GEO
Project description:Human velocardiofacial syndrom/DiGeorg (VCFS/DGS) syndrom is a complex developmental disease with various expression of a large number of phenotypes. Craniofacial, cardiac, behavioural and endocrinological phenotypes are cardinal symptoms liked to the 22Q11.2 deletion occuring in 1/4.000 births. Several genes located within the 1.5 to 3 Mb deletion resemble a number of phenotypes demonstrated in mouse models for these genes including the endothelin receptor A (Ednra) gene. This is the first report on gene dosage effects observed in a dominant mouse model carrying an EdnraY129F point-mutation. EdnraY129F/+ mice are viable despite a strong cardiac phenotype alike to Fallot's tetralogy concomitant with cardiofacial, otolaryngeal phenotypes and deafness. Total RNA obtained from 4 male heterzygote and 4 male wildtype mice
2014-05-02 | E-GEOD-47781 | biostudies-arrayexpress
Project description:Chronic kidney disease (CKD) is characterised by kidney fibrosis and represents a major public health concern. Alport syndrome, a common monogenic cause of kidney failure caused by genetic variants in the type IV collagen genes COL4A3, COL4A4 or COL4A5, leads to abnormal basement membrane remodelling and kidney fibrosis. Understanding the dynamics and mechanisms of kidney matrix remodelling is crucial for directing emerging gene therapies and developing non-invasive biomarkers to detect and stage kidney fibrosis earlier, ultimately enabling risk stratification and timely intervention. To define the temporal and spatial dynamics of kidney matrix remodelling, we applied a multi-omics strategy in a Col4a5-/- mouse model of X-linked Alport syndrome, integrating stable isotope metabolic labelling, deep proteomic profiling, bulk RNA sequencing, super-resolution imaging, and bioinformatic prediction. Transcriptomic profiling identified enrichment of extracellular matrix degradation pathways and upregulation of matrix proteases. 13C-Lysine labelling coupled with mass spectrometry revealed altered abundance and accelerated turnover of basement membrane components in Alport kidneys. Super-resolution imaging confirmed spatial disorganisation of matrix proteins, supporting a loss of structural integrity. Using peptide location fingerprinting, we mapped damage modifications and predicted fragmentation in ~40 kidney matrix proteins, including collagens, laminins and nidogens. Targeted assays validated the presence of these predicted matrix fragments in serum from children with COL4A3–5 variants, demonstrating detectable alterations in circulating basement membrane peptides compared to healthy controls. These data define an uncoupling of matrix synthesis and degradation as a hallmark of Alport-associated kidney fibrosis. Our integrative approach establishes a framework for linking matrix proteolysis and basement membrane fragmentation with clinically accessible biomarkers of kidney matrix remodelling. The detection of circulating matrix fragments offers a promising non-invasive strategy to monitor basement membrane integrity and stage kidney fibrosis, with potential utility in both diagnosis and therapeutic response assessment in Alport syndrome and broader CKD contexts.
2026-05-21 | PXD067091 | Pride
Project description:Microarrays were used to identify the differentially expressed genes in the hippocampus of control and Noonan syndrom mice at basal state and in response to 4AP-Bic stimulation (10 min). Functional analysis was performed to determine the biological significance of the data.
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Project description:RNAseq of mouse kidney RNA from Col4a5 muntant mice crossed with diversity ourbred mice to find modifier genes of Alport disease.
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