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High resolution spatial trancrioptomics combined with deep learning-based image segmentation enables single-cell spatial profiling of archival FFPE kidney tissue from patients with idiopathic nephrotic syndrome

ABSTRACT: We have perfomed Visium HD spatial transcriptomics on archival FFPE kidney biopsies from patients with different manifistations of nephrotic syndrome, i.e., steriod sensitive, frequent relapsing and/or steroid dependent, and focal segmental glomerulosclerosis. Using a pre-trained deep learning model from StarDist to segment nuclei, we reconstructed single-nucleus level spatial trancriptomic datasets through custom binning of subcellular capture areas. We integrated the datasets from the different patients and indentified conserved cell types. Moreover, we identified patient specific transcriptomic differences in the podocyte cell population. This article demonstrates the usefullness of this approach to future studies of pathophysilogical mechanisms in idiopathic nephrotic syndrome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE300895 | GEO | 2025/12/08

REPOSITORIES: GEO

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Project description:Background: Minimal change nephrotic syndrome (MCNS) is considered to be associated with T cell dysfunction, via unknown mechanisms. Experimental observations suggest that some humoral factors alter the permeability of glomerular filtration barrier. However, the nature of such factors remains still uncertain. Methods: Using cDNA microarrays, we performed gene expression profiling of peripheral blood mononuclear cells (PBMC) from three patients with MCNS during nephrosis and remission phases. To confirm the cDNA microarray results, we performed quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) analyses in nephrosis and remission samples from 20 MCNS patients and six patients with nephrotic syndrome due to membranous nephropathy. Results: Out of 24,446 genes screened, 33 genes were up-regulated (at least 1.5-fold) in PBMC from these MCNS patients during the nephrosis phase. Up-regulated genes mainly encoded proteins involved in signal transduction and cytokine response. For further examination, we selected two genes encoding provable secretary proteins, chemokine (C-C) ligand 13 (also known as monocyte chemotactic protein-4) (CCL13) and a novel galectin-related protein (HSPC159). The results of RT-PCR showed that expressions of CCL13 and HSPC159 mRNA in nephrosis PBMC samples are higher than those in remission PBMC samples from all 20 MCNS patients examined. On the other hand, these mRNA expression patterns were variable among six patients with membranous nephropathy. Conclusions: We conclude that CCL13 and HSPC159 mRNA expressions in PBMC is up-regulated in MCNS patients during the nephrosis phase. These expression changes in PBMC might be involved in the pathophysiologic processes of MCNS. Using cDNA microarrays, we performed gene expression profiling of peripheral blood mononuclear cells (PBMC) from three patients with MCNS during nephrosis and remission phases. To confirm the cDNA microarray results, we performed quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) analyses in nephrosis and remission samples from 20 MCNS patients and six patients with nephrotic syndrome due to membranous nephropathy.

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High resolution spatial trancrioptomics combined with deep learning-based image segmentation enables single-cell spatial profiling of archival FFPE kidney tissue from patients with idiopathic nephrotic syndrome

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