The spatially resolved transcriptome signatures of glomeruli in chronic kidney disease
Geremy Clair, Hasmik Soloyan, Paolo Cravedi, Andrea Angeletti, Fadi Salem, Laith Al-Rabadi, Roger E. De Filippo, Stefano Da Sacco, Kevin V. Lemley, Sargis Sedrakyan, Laura Perin
Geremy Clair, Hasmik Soloyan, Paolo Cravedi, Andrea Angeletti, Fadi Salem, Laith Al-Rabadi, Roger E. De Filippo, Stefano Da Sacco, Kevin V. Lemley, Sargis Sedrakyan, Laura Perin
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Research Article Nephrology

The spatially resolved transcriptome signatures of glomeruli in chronic kidney disease

Abstract

Here, we used digital spatial profiling (DSP) to describe the glomerular transcriptomic signatures that may characterize the complex molecular mechanisms underlying progressive kidney disease in Alport syndrome, focal segmental glomerulosclerosis, and membranous nephropathy. Our results revealed significant transcriptional heterogeneity among diseased glomeruli, and this analysis showed that histologically similar glomeruli manifested different transcriptional profiles. Using glomerular pathology scores to establish an axis of progression, we identified molecular pathways with progressively decreased expression in response to increasing pathology scores, including signal recognition particle–dependent cotranslational protein targeting to membrane and selenocysteine synthesis pathways. We also identified a distinct signature of upregulated and downregulated genes common to all the diseases investigated when compared with nondiseased tissue from nephrectomies. These analyses using DSP at the single-glomerulus level could help to increase insight into the pathophysiology of kidney disease and possibly the identification of biomarkers of disease progression in glomerulopathies.

Authors

Geremy Clair, Hasmik Soloyan, Paolo Cravedi, Andrea Angeletti, Fadi Salem, Laith Al-Rabadi, Roger E. De Filippo, Stefano Da Sacco, Kevin V. Lemley, Sargis Sedrakyan, Laura Perin

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Figure 4

Comparison of transcriptional programs among AS, FSGS, and MN glomeruli.

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Comparison of transcriptional programs among AS, FSGS, and MN glomeruli....
(A) Unsupervised principal component analysis (PCA) based on label-free quantification of the transcripts expressed in all glomeruli, based on PC1, PC2, and PC3. Percentage of total variance is indicated on each PC axis. Significantly enriched GO terms and KEGG and REACTOME pathways (EASE-modified Fisher’s exact P < 0.05) are listed for the top 10% of transcripts contributing the most to each principal component. (B) Unsupervised PCA based on label-free quantification of the transcripts expressed in adult glomeruli, based on principal components (PC1, PC2, PC3). Percentage of total variance is indicated after each principal component. A list of significantly enriched GO terms and KEGG and REACTOME pathways (EASE-modified Fisher’s exact P < 0.05) is provided for the top 10% of transcripts contributing the most to each principal component. (C) Venn diagrams showing the total number of differentially upregulated and downregulated genes (Student’s t test and binomial GLM test BH-adjusted P < 0.05) in AS (no. 3), FSGS (no. 4 and 5), and MN (no. 6 and 7) glomeruli as well as nondiseased glomeruli (no. 9 and10). Significantly enriched GO terms and KEGG and REACTOME pathways (EASE-modified Fisher’s exact P < 0.05) for the genes commonly upregulated (n = 42 genes) and commonly downregulated (n = 128 genes) in all the samples are depicted next to the Venn diagrams. (D) Box plots depicting the Z-scores for CCND1, GJA5, and ADAMTS13, commonly upregulated or downregulated, in all diseased glomeruli versus nondiseased (no. 9 and 10) control glomeruli (Student’s t test). **P < 0.01; ***P < 0.001; ****P < 0.0001. Data are shown as the mean ± SD. (E) Representative immunofluorescence images of CCND1 (yellow), GJA5 (green), and ADAMTS13 (red) on kidney sections derived from AS, FSGS, and MN and nondiseased kidney tissue. Nuclei are stained blue with DAPI. Dotted lines indicate the glomerular ROIs to distinguish staining in the glomerulus versus tubules. Scale bars: 50 mm.