Dataset Information

CosMx 6175 human gene for human kidney delayed graft function (DGF) and immediate graft function (IGF)

ABSTRACT: This dataset includes CosMx spatial transcriptomic data from human kidney biopsies collected one hour post-transplantation. Patients were then monitored and categorized into two groups: those with immediate graft function (IGF) and those with delayed graft function (DGF). DGF refers to cases where patients required dialysis for one or more weeks before kidney function was restored. The biopsies were formalin-fixed, paraffin-embedded, and sectioned using a microtome. Sample processing followed NanoString's standard protocol, utilizing a pre-made 6175-gene panel to detect the spatial location and expression levels of each gene, without any additional custom probes.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE282193 | GEO | 2025/02/15

REPOSITORIES: GEO

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Project description:Delayed graft function (DGF) is associated with a reduced long-term graft survival. Ischemia-reperfusion damage and donors' features have been always considered as key pathogenic factors in this setting. The aim of our study was to evaluate the role of recipients' characteristics in the development of DGF to discover early genomics biomarkers in peripheral blood mononuclear cells (PBMC) in order to identify patients at risk. We prospectively enrolled 932 kidney graft recipients from 466 donors for both kidneys. A total of 226 recipients experienced DGF. Among the 466 donors, 290 couples of recipients both patients presented with early graft function (EGF, group A), 50 couples experienced DGF (group B) and 126 couples of recipients were discordant as one presented DGF and the other promptly recovered graft function (group C). In group C we randomly selected 10 couples of DGF/EGF recipients. Peripheral blood mononuclear cells (PBMC) were harvested before transplantation; their transcriptomic profile was investigated by a microarray approach and microarray results were validated by qPCR in an independent group (DGF n=25; EGF n=25). In the whole study group, DGF was independently associated with both donors’ and recipient’s features. Moreover, group A, B and C presented significant differences in both donors’ and recipients’ characteristics. In group C of patients, DGF was significantly associated with body mass index, dialysis modality and number of mismatches. Two-hundred and seventy-three genes were differentially expressed before transplantation in discordant EGF/DGF patients of group C. Their main biological functions were immune dysfunction and inflammation. Among the differentially expressed genes, we observed a significant increase in the expression of CCR2, the MCP-1 receptor, in DGF patients. CCR-2 and MCP-1 up-regulation was confirmed in an independent cohort of patients. Our results suggest that recipients' clinical and immunological features, potentially modulated by dialysis modality, are associated with the development of DGF independently of donors' features.

Dataset Information

CosMx 6175 human gene for human kidney delayed graft function (DGF) and immediate graft function (IGF)

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