Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA205070 | ENA |
REPOSITORIES: ENA
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Project description:We study the global gene expression profiles of BKV viremia and nephropathy patients using microarrays in order to better understand the immunologic response to polyomavirus BK (BKV). BKV has become increasingly prevalent since the introduction of more potent immunosuppressive agents. It has been shown that as many as 30% of renal transplant recipients develop asymptomatic viral shedding in the urine shortly after transplant, 10-20% have viremia, and as many as 1-10% can go on to develop overt nephropathy (BKVN) that might lead to graft loss. To date, the genomics of BKV viremia and BKVN have not been investigated thoroughly by microarray. Patients who were enrolled in the IRB-approved Immune Monitoring Study had blood PAXGene samples taken at post-transplant visits and had clinically indicated biopsy samples were used for analysis. A total of 17 biopsy samples were used for gene expression profiling microarrays, three with histopathologic diagnosis of BKVN, 3 patients with evidence of BK viral replication in peripheral blood, but normal biopsy and 11 patients with normal biopsies or mild IFTA, and stable graft function. Blood PAXGene samples from 40 patients were used for gene expression profiling by microarrays, 14 patients with stable graft function and without BK viremia, 19 patients' blood samples at the time of BKV viremia, and 7 patients blood samples taken 1-2 months prior to development of BK viremia.
2013-05-23 | E-GEOD-47199 | biostudies-arrayexpress
Project description:We study the global gene expression profiles of BKV viremia and nephropathy patients using microarrays in order to better understand the immunologic response to polyomavirus BK (BKV). BKV has become increasingly prevalent since the introduction of more potent immunosuppressive agents. It has been shown that as many as 30% of renal transplant recipients develop asymptomatic viral shedding in the urine shortly after transplant, 10-20% have viremia, and as many as 1-10% can go on to develop overt nephropathy (BKVN) that might lead to graft loss. To date, the genomics of BKV viremia and BKVN have not been investigated thoroughly by microarray.
2013-05-23 | GSE47199 | GEO
Project description:Expression data from blood and biopsies of Donor-Specific Antibody positive patients
2025-01-24 | E-GEOD-50084 | ExpressionAtlas
Project description:Background: Although the clinical fingerprints of the BK virus (BKV) infection in kidney transplant recipients (KTRs) has been well documented, the systemic biological machinery involved in this complication is still poorly recognized. Proteomics analysis of urinary extracellular vesicles (EVs) can allow us to better address this knowledge gap. Methods: Twenty-nine adult KTRs with normal allograft function affected by BKV infection (15 with only viremia, 14 with viruria and viremia) and 15 controls (CTR) were enrolled and randomly divided in a training cohort (12 BKV and 6 CTR) used for the mass spectrometry analysis of the EVs protein content and a testing cohort(17 BKV and 9 CTR) used for the biological validation of the proteomic results by ELISA. Results: Mass spectrometry analysis revealed a large protein enrichment (more than 1500) in urinary EVs of BKV patients and controls. Pathway analysis by GSEA revealed that several biological gene ontologies (including immunity, complement activation, renal fibrosis, tubular diseases, epithelial to mesenchymal transition) were able to discriminate BKV versus CTR. Kinase was the only gene ontology annotation term negatively enriched in BKV (with SLK being the most down-regulated protein in BKV). Statistical analysis, then, identified a core panel of 70 proteins (including DNASE2, F12, AGT, CTSH, C4A, C7, FABP4 and BPNT1) able to discriminate the two study groups. Instead, although a set of proteins were able to differentiate patients with BKV viruria from those with both viremia-viruria, the urinary proteomic profile of these patients resulted quite similar between the two sub-groups. ELISA for SLK and ELISA for BPNT1 and DNASE2 validated proteomics results. Conclusions: Our study demonstrated that BK virus infection is able to significantly modify the urinary EVs proteomic profile of KTRs also in a very early stage of the disease (when patients still have normal allograft function and only BK viruria) suggesting, whether possible, to start an early preventive therapeutic approach to minimize the risk of the disease progression. Moreover, some 3 of our identified proteins could be employed in future as early urinary biomarkers and/or new therapeutic targets.
2022-12-13 | PXD035494 | Pride
Project description:Expression data from rejection and non-rejection kidney transplant patients
2020-09-03 | E-GEOD-46474 | ExpressionAtlas
Project description:Expression data from human renal allograft biopsies to investigate renal transplant rejection and failure
2025-01-24 | E-GEOD-21374 | ExpressionAtlas
Project description:Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes
2025-01-24 | E-GEOD-1563 | ExpressionAtlas
Project description:Gene expression data was analyzed to map with urine proteomics data gene expression data from kidney biopsies from kidney transplant patients with and without acute rejection, chronic allograft nephropathy and BK virus nephritis was used to study gene expression changes during acute rejection, chronic allograft nephropathy and bk virus nephropathy. Samples labeled STA16, STA22, STA14, and STA18 were included in the CAN vs no-CAN analysis as no-CAN samples as they also qualified as non-CAN samples.
2017-08-22 | GSE75693 | GEO
Project description:Kidney transplant injury processes are associated with molecular changes in renal tissue, primarily related to immune cell activation and infiltration. How these processes are reflected by molecular alterations in circulating immune cells is poorly understood. We performed RNA-sequencing on 384 biobanked blood samples from four transplant centers, taken at time of a kidney allograft biopsy, selected for their phenotype (acute T cell- and antibody-mediated rejection, polyomavirus-associated nephropathy, and control). We performed differential expression analysis and pathway analysis per phenotype. In peripheral blood, differentially expressed genes in rejection vs. no rejection samples demonstrated upregulation of glucocorticoid receptor and NOD-like receptor signaling pathways. Pathways enriched in antibody-mediated rejection were strongly immune-specific, whereas pathways enriched in T cell-mediated rejection were less immune related. Differentially expressed genes in polyoma viremia and polyomavirus-associated nephropathy were similar and demonstrated upregulation of mitochondrial dysfunction and interferon signaling pathways. Our results highlight the immune activation pathways in peripheral blood leukocytes at time of antibody-mediated rejection and polyomavirus nephropathy and provide a framework for future therapeutic interventions.
2022-05-06 | GSE175718 | GEO