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Resource and Technical AdvanceIn-Press PreviewNephrology Open Access | 10.1172/jci.insight.146374

Snapshots of nascent RNA reveal cell- and stimulus- specific responses to acute kidney injury

Tian Huai Shen,1 Jacob Stauber,1 Katherine Xu,1 Alexandra Jacunski,2 Neal Paragas,3 Miriam Callahan,1 Run Banlengchit,1 Abraham D. Levitman,1 Beatriz Desanti de Oliveira,1 Andrew Beenken,1 Madeleine S. Grau,1 Edwin Mathieu,1 Qingyin Zhang,1 Yuanji Li,1 Tejashree Gopal,1 Nathaniel Askanase,1 Siddarth Arumugam,4 Sumit Mohan,1 Pamela I. Good,5 Jacob S. Stevens,1 Fangming Lin,5 Samuel K. Sia,4 Chyuan-Sheng Lin,6 Vivette D'Agati,7 Krzysztof Kiryluk,1 Nicholas P. Tatonetti,2 and Jonathan Barasch1

1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

Find articles by Shen, T. in: PubMed | Google Scholar

1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

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6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

2Department of Biomedical Informatics, Columbia University Medical Center, New York, United States of America

3Department of Medicine, Division of Nephrology, University of Washington, Seattle, United States of America

4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

5Department of Pediatrics, Columbia University Medical Center, New York, United States of America

6Department of Pathology and Cell Biology, Columbia University Medical Center, New York, United States of America

7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

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4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

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7Department of Pathology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

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1Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, United States of America

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7Department of Pathology, Columbia University Medical Center, New York, United States of America

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4Department of Biomedical Engineering, Columbia University Medical Center, New York, United States of America

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7Department of Pathology, Columbia University Medical Center, New York, United States of America

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Published March 1, 2022 - More info

JCI Insight. https://doi.org/10.1172/jci.insight.146374.
Copyright © 2022, Shen et al. This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Published March 1, 2022 - Version history
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Abstract

The current strategy to detect acute injury of kidney tubular cells relies on changes in serum levels of creatinine. Yet serum creatinine (sCr) is a marker of both functional and pathological processes and does not specifically assay tubular injury. In addition, sCr may require days to reach diagnostic thresholds, yet tubular cells respond with programs of damage and repair within minutes or hours. To detect acute responses to clinically relevant stimuli, we created Rosa26-floxed-stop uracil phosphoribosyl-transferase (Uprt) expressing mice and inoculated 4-thiouracil (TU) to tag nascent RNA at selected time points. Cre-driven TU-tagged RNA was isolated from whole kidneys and demonstrated that volume depletion and ischemia induced different genetic programs. Even lineage related cell types expressed different genes in response to the two stressors. TU-tagging also demonstrated the transient nature of the responses. Because we placed Uprt in the ubiquitously active Rosa-26 locus, RNAs from many cell types can be tagged in vivo and their roles interrogated under various conditions. In short, TU labeling identifies stimulus-specific, cell-specific, and time-dependent acute responses that are otherwise difficult to detect with other technologies and are entirely obscured when sCr is the sole metric of kidney damage.

Graphical Abstract
graphical abstract
Supplemental material

View Supplemental Table 1. Hoxb7Cre pulldown vs Total RNA values from male and female controls; p<0.05; n=21 mice

View Supplemental Table 2. Atp6v1b1Cre pulldown vs Total RNA values from male and female controls; p<0.05; n=21 mice.

View Supplemental Table 3. Hoxb7Cre pulldown ischemia vs Hoxb7Cre pulldown from control kidneys; p<0.05; male mice; n=7.

View Supplemental Table 4. Hoxb7Cre pulldown volume depleted vs Hoxb7Cre pulldown from control kidneys; p<0.05; male mice; n=7.

View Supplemental Table 5. Hoxb7Cre pulldown from ischemic vs volume depleted kidneys; p<0.05; log2 fold >1

View Supplemental Table 6. Atp6v1b1Cre pulldown ischemia vs Atp6v1b1Cre pulldown from control kidneys; male; p<0.05; n=7.

View Supplemental Table 7. Atp6v1b1Cre pulldown volume depletion vs Atp6v1b1Cre pulldown from control kidneys; p<0.05; male; n=8.

View Supplemental Table 8. Atp6v1b1Cre pulldown from ischemic vs volume depleted kidneys; p<0.05; log2 fold >1

View Supplemental Table 9. Atp6v1b1Cre vs Hoxb7Cre pulldowns from ischemia kidneys; p<0.05; log2 fold >1

View Supplemental Table 10. Atp6v1b1Cre vs Hoxb7Cre pulldowns from volume depleted kidneys. p<0.05; log2 fold >1

View Supplemental Table 11. Genes coding for secreted proteins comparing volume depletion and ischemic kidneys; p<0.05; log2 difference >1.

View Supplemental Table 12. Primers

View Supplemental Table 13. Probes and Antibodies

View

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  • Version 1 (March 1, 2022): In-Press Preview
  • Version 2 (March 22, 2022): Electronic publication

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