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 6

Expression of selected enriched miRNAs in IRI.

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Expression of selected enriched miRNAs in IRI. For the IRI model C57BL/6...
For the IRI model C57BL/6 mice underwent unilateral renal artery occlusion, resulting in warm ischemia for 18 minutes, followed by reperfusion and recovery for 2–21 days. (A) IRI mice demonstrated significant acute tubular necrosis on H&E staining at 2 and 7 days after injury. Scale bar: 50 μm. Data are expressed as median ± min and max value. One-way ANOVA with Tukey’s multiple-comparison test, ****P < 0.0001. (B) The normal renal architecture was progressively disrupted with significant fibrosis formation (semiquantified using picrosirius red staining) evident after 2 weeks. Scale bar: 50 μm. Data are expressed as median ± min and max value. ANOVA test with Tukey’s multiple-comparison test, *P < 0.05, **P < 0.01, ****P < 0.0001. (C) This injury was accompanied by increased macrophage number (F4/80 staining) as compared with sham animals. Scale bar: 50 μm. Data are expressed as median ± min and max value. ANOVA test with Tukey’s multiple-comparison test, *P < 0.05, **P < 0.01. (D) Within the kidney, we noted an upregulation of macrophage-enriched miR-16-5p and miR-18a-5p and downregulation of PT cell–enriched miR-194-5p with injury. Data expressed as mean ± SEM. ANOVA test with Tukey’s multiple-comparison test. *P < 0.05, **P < 0.01, ***P < 0.001, *****P < 0.00001.