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Rudman-Melnick V, Adam M, Stowers K, Potter A, Ma Q, Chokshi SM, Vanhoutte D, Valiente-Alandi I, Lindquist DM, Nieman ML, Kofron JM, Chung E, Park JS, Potter SS, Devarajan P. Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney fibrosis. Sci Rep 2024; 14:439. [PMID: 38172172 PMCID: PMC10764314 DOI: 10.1038/s41598-023-50195-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/16/2023] [Indexed: 01/05/2024] Open
Abstract
Examining kidney fibrosis is crucial for mechanistic understanding and developing targeted strategies against chronic kidney disease (CKD). Persistent fibroblast activation and tubular epithelial cell (TEC) injury are key CKD contributors. However, cellular and transcriptional landscapes of CKD and specific activated kidney fibroblast clusters remain elusive. Here, we analyzed single cell transcriptomic profiles of two clinically relevant kidney fibrosis models which induced robust kidney parenchymal remodeling. We dissected the molecular and cellular landscapes of kidney stroma and newly identified three distinctive fibroblast clusters with "secretory", "contractile" and "vascular" transcriptional enrichments. Also, both injuries generated failed repair TECs (frTECs) characterized by decline of mature epithelial markers and elevation of stromal and injury markers. Notably, frTECs shared transcriptional identity with distal nephron segments of the embryonic kidney. Moreover, we identified that both models exhibited robust and previously unrecognized distal spatial pattern of TEC injury, outlined by persistent elevation of renal TEC injury markers including Krt8 and Vcam1, while the surviving proximal tubules (PTs) showed restored transcriptional signature. We also found that long-term kidney injuries activated a prominent nephrogenic signature, including Sox4 and Hox gene elevation, which prevailed in the distal tubular segments. Our findings might advance understanding of and targeted intervention in fibrotic kidney disease.
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Affiliation(s)
- Valeria Rudman-Melnick
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA
| | - Mike Adam
- Division Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kaitlynn Stowers
- Division Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Andrew Potter
- Division Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Qing Ma
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA
| | - Saagar M Chokshi
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA
| | - Davy Vanhoutte
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | - Diana M Lindquist
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Department of Radiology, University of Cincinnati, Cincinnati, OH, USA
- Department of Radiology and Medical Imaging, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michelle L Nieman
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH, USA
| | - J Matthew Kofron
- Division Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Eunah Chung
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA
| | - Joo-Seop Park
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Chicago, IL, USA
| | - S Steven Potter
- Division Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Prasad Devarajan
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229-3039, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
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Rudman-Melnick V, Adam M, Stowers K, Potter A, Ma Q, Chokshi SM, Vanhoutte D, Valiente-Alandi I, Lindquist DM, Nieman ML, Kofron JM, Potter SS, Devarajan P. Single-cell sequencing dissects the transcriptional identity of activated fibroblasts and identifies novel persistent distal tubular injury patterns in kidney fibrosis. Res Sq 2023:rs.3.rs-2880248. [PMID: 37293022 PMCID: PMC10246229 DOI: 10.21203/rs.3.rs-2880248/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Examining kidney fibrosis is crucial for mechanistic understanding and developing targeted strategies against chronic kidney disease (CKD). Persistent fibroblast activation and tubular epithelial cell (TEC) injury are key CKD contributors. However, cellular and transcriptional landscapes of CKD and specific activated kidney fibroblast clusters remain elusive. Here, we analyzed single cell transcriptomic profiles of two clinically relevant kidney fibrosis models which induced robust kidney parenchymal remodeling. We dissected the molecular and cellular landscapes of kidney stroma and newly identified three distinctive fibroblast clusters with "secretory", "contractile" and "vascular" transcriptional enrichments. Also, both injuries generated failed repair TECs (frTECs) characterized by decline of mature epithelial markers and elevation of stromal and injury markers. Notably, frTECs shared transcriptional identity with distal nephron segments of the embryonic kidney. Moreover, we identified that both models exhibited robust and previously unrecognized distal spatial pattern of TEC injury, outlined by persistent elevation of renal TEC injury markers including Krt8, while the surviving proximal tubules (PTs) showed restored transcriptional signature. Furthermore, we found that long-term kidney injuries activated a prominent nephrogenic signature, including Sox4 and Hox gene elevation, which prevailed in the distal tubular segments. Our findings might advance understanding of and targeted intervention in fibrotic kidney disease.
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Affiliation(s)
| | - Mike Adam
- Cincinnati Children's Hospital Medical Center
| | | | | | - Qing Ma
- Cincinnati Children's Hospital Medical Center
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