Identifying cell-enriched miRNAs in kidney injury and repair
Katie L. Connor, Oliver Teenan, Carolynn Cairns, Victoria Banwell, Rachel A.B. Thomas, Julie Rodor, Sarah Finnie, Riinu Pius, Gillian M. Tannahill, Vishal Sahni, Caroline O.S. Savage, Jeremy Hughes, Ewen M. Harrison, Robert B. Henderson, Lorna P. Marson, Bryan R. Conway, Stephen J. Wigmore, Laura Denby
Katie L. Connor, Oliver Teenan, Carolynn Cairns, Victoria Banwell, Rachel A.B. Thomas, Julie Rodor, Sarah Finnie, Riinu Pius, Gillian M. Tannahill, Vishal Sahni, Caroline O.S. Savage, Jeremy Hughes, Ewen M. Harrison, Robert B. Henderson, Lorna P. Marson, Bryan R. Conway, Stephen J. Wigmore, Laura Denby
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Research Article Nephrology

Identifying cell-enriched miRNAs in kidney injury and repair

Abstract

Small noncoding RNAs, miRNAs (miRNAs), are emerging as important modulators in the pathogenesis of kidney disease, with potential as biomarkers of kidney disease onset, progression, or therapeutic efficacy. Bulk tissue small RNA-sequencing (sRNA-Seq) and microarrays are widely used to identify dysregulated miRNA expression but are limited by the lack of precision regarding the cellular origin of the miRNA. In this study, we performed cell-specific sRNA-Seq on tubular cells, endothelial cells, PDGFR-β+ cells, and macrophages isolated from injured and repairing kidneys in the murine reversible unilateral ureteric obstruction model. We devised an unbiased bioinformatics pipeline to define the miRNA enrichment within these cell populations, constructing a miRNA catalog of injury and repair. Our analysis revealed that a significant proportion of cell-specific miRNAs in healthy animals were no longer specific following injury. We then applied this knowledge of the relative cell specificity of miRNAs to deconvolute bulk miRNA expression profiles in the renal cortex in murine models and human kidney disease. Finally, we used our data-driven approach to rationally select macrophage-enriched miR-16-5p and miR-18a-5p and demonstrate that they are promising urinary biomarkers of acute kidney injury in renal transplant recipients.

Authors

Katie L. Connor, Oliver Teenan, Carolynn Cairns, Victoria Banwell, Rachel A.B. Thomas, Julie Rodor, Sarah Finnie, Riinu Pius, Gillian M. Tannahill, Vishal Sahni, Caroline O.S. Savage, Jeremy Hughes, Ewen M. Harrison, Robert B. Henderson, Lorna P. Marson, Bryan R. Conway, Stephen J. Wigmore, Laura Denby

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Figure 4

Global expression changes of cell-enriched miRNAs in the bulk and single-population data sets with injury and repair.

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Global expression changes of cell-enriched miRNAs in the bulk and single...
(A) The cumulative distribution of the highly enriched miRNA expression changes (log fold change, LogFC) in the kidney tissue sRNA-Seq data set is shown. There is an increase in macrophage-enriched (Mac, green line) and PDGFR-β+ (red line) and decrease in proximal tubular cell–enriched (PT, blue line) miRNAs’ expression versus nonenriched miRNAs (purple line) in comparisons against sham (sham vs. UUO day 7 and sham vs. R-UUO) (ECs in pink). This is in keeping with the histology. (B) When comparing the macrophage-enriched miRNA expression in the bulk versus single-population Mac sRNA-Seq data sets, there was an upregulation of Mac enriched miRNAs within the bulk data set at UUO day 7 (vs. sham and UUO day 2) but not within the cells themselves. This suggests that the bulk changes may be due to changes in cellular proportions in the sample. (C) For PT cell–enriched miRNAs, there was a loss of expression both within the PT cells and to a greater extent the bulk tissue at UUO day 7 (vs. UUO day 2 and R–UUO). Upon reversal, PT cell–enriched miRNA expression increased within PT cells to a relatively greater extent than was evident in the bulk. empirical cumulative distribution function plots for all cell types and comparisons are shown in Supplemental Figures 7–9. Kolmogorov-Smirnov test was used to compare the distribution of the LogFC. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.