1
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Zhang YL, Tang TT, Wang B, Wen Y, Feng Y, Yin Q, Jiang W, Zhang Y, Li ZL, Wu M, Wu QL, Song J, Crowley SD, Lan HY, Lv LL, Liu BC. Identification of a Novel ECM Remodeling Macrophage Subset in AKI to CKD Transition by Integrative Spatial and Single-Cell Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309752. [PMID: 39119903 DOI: 10.1002/advs.202309752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 06/14/2024] [Indexed: 08/10/2024]
Abstract
The transition from acute kidney injury (AKI) to chronic kidney disease (CKD) is a critical clinical issue. Although previous studies have suggested macrophages as a key player in promoting inflammation and fibrosis during this transition, the heterogeneity and dynamic characterization of macrophages are still poorly understood. Here, we used integrated single-cell RNA sequencing and spatial transcriptomic to characterize the spatiotemporal heterogeneity of macrophages in murine AKI-to-CKD model of unilateral ischemia-reperfusion injury. A marked increase in macrophage infiltration at day 1 was followed by a second peak at day 14 post AKI. Spatiotemporal profiling revealed that injured tubules and macrophages co-localized early after AKI, whereas in late chronic stages had spatial proximity to fibroblasts. Further pseudotime analysis revealed two distinct lineages of macrophages in this transition: renal resident macrophages differentiated into the pro-repair subsets, whereas infiltrating monocyte-derived macrophages contributed to chronic inflammation and fibrosis. A novel macrophage subset, extracellular matrix remodeling-associated macrophages (EAMs) originating from monocytes, linked to renal fibrogenesis and communicated with fibroblasts via insulin-like growth factors (IGF) signalling. In sum, our study identified the spatiotemporal dynamics of macrophage heterogeneity with a unique subset of EAMs in AKI-to-CKD transition, which could be a potential therapeutic target for preventing CKD development.
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Affiliation(s)
- Yi-Lin Zhang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Tao-Tao Tang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Yi Wen
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Ye Feng
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Qing Yin
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Wei Jiang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Yue Zhang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Min Wu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Qiu-Li Wu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Jing Song
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Steven D Crowley
- Division of Nephrology, Department of Medicine, Duke University and Durham VA Medical Centers, Durham, NC, 27705, USA
| | - Hui-Yao Lan
- Departments of Medicine & Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, 210009, China
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2
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Muto Y, Dixon EE, Yoshimura Y, Ledru N, Kirita Y, Wu H, Humphreys BD. Epigenetic reprogramming driving successful and failed repair in acute kidney injury. SCIENCE ADVANCES 2024; 10:eado2849. [PMID: 39110788 PMCID: PMC11305376 DOI: 10.1126/sciadv.ado2849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Acute kidney injury (AKI) causes epithelial damage followed by subsequent repair. While successful repair restores kidney function, this process is often incomplete and can lead to chronic kidney disease (CKD) in a process called failed repair. To better understand the epigenetic reprogramming driving this AKI-to-CKD transition, we generated a single-nucleus multiomic atlas for the full mouse AKI time course, consisting of ~280,000 single-nucleus transcriptomes and epigenomes. We reveal cell-specific dynamic alterations in gene regulatory landscapes reflecting, especially, activation of proinflammatory pathways. We further generated single-nucleus multiomic data from four human AKI samples including validation by genome-wide identification of nuclear factor κB binding sites. A regularized regression analysis identifies key regulators involved in both successful and failed repair cell fate, identifying the transcription factor CREB5 as a regulator of both successful and failed tubular repair that also drives proximal tubular cell proliferation after injury. Our interspecies multiomic approach provides a foundation to comprehensively understand cell states in AKI.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E. Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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3
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Yamamoto S, Yamamoto S, Takahashi M, Mii A, Okubo A, Toriu N, Nakagawa S, Abe T, Fukuma S, Imamura H, Yamamoto M, Yanagita M. Visualization of intracellular ATP dynamics in different nephron segments under pathophysiological conditions using the kidney slice culture system. Kidney Int 2024:S0085-2538(24)00409-5. [PMID: 38996810 DOI: 10.1016/j.kint.2024.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/11/2024] [Accepted: 05/24/2024] [Indexed: 07/14/2024]
Abstract
ATP depletion plays a central role in the pathogenesis of kidney diseases. Recently, we reported spatiotemporal intracellular ATP dynamics during ischemia reperfusion (IR) using GO-ATeam2 mice systemically expressing an ATP biosensor. However, observation from the kidney surface did not allow visualization of deeper nephrons or accurate evaluation of ATP synthesis pathways. Here, we established a novel ATP imaging system using slice culture of GO-ATeam2 mouse kidneys, evaluated the ATP synthesis pathway, and analyzed intracellular ATP dynamics using an ex vivo IR-mimicking model and a cisplatin nephropathy model. Proximal tubules (PTs) were found to be strongly dependent on oxidative phosphorylation (OXPHOS) using the inhibitor oligomycin A, whereas podocytes relied on both OXPHOS and glycolysis using phloretin an active transport inhibitor of glucose. We also confirmed that an ex vivo IR-mimicking model could recapitulate ATP dynamics in vivo; ATP recovery in PTs after reoxygenation varied depending on anoxic time length, whereas ATP in distal tubules (DTs) recovered well even after long-term anoxia. After cisplatin administration, ATP levels in PTs decreased first, followed by a decrease in DTs. An organic cation transporter 2 inhibitor, cimetidine, suppressed cisplatin uptake in kidney slices, leading to better ATP recovery in PTs, but not in DTs. Finally, we confirmed that a mitochondria protection reagent (Mitochonic Acid 5) delayed the cisplatin-induced ATP decrease in PTs. Thus, our novel system may provide new insights into the energy dynamics and pathogenesis of kidney disease.
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Affiliation(s)
- Shigenori Yamamoto
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shinya Yamamoto
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Takahashi
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akiko Mii
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihiro Okubo
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoya Toriu
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shunsaku Nakagawa
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Takaaki Abe
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shingo Fukuma
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromi Imamura
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masamichi Yamamoto
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
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4
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Schnell J, Miao Z, Achieng M, Fausto CC, Wang V, Kuyper FD, Thornton ME, Grubbs B, Kim J, Lindström NO. Stepwise developmental mimicry generates proximal-biased kidney organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601028. [PMID: 39005387 PMCID: PMC11244853 DOI: 10.1101/2024.06.28.601028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The kidney maintains body fluid homeostasis by reabsorbing essential compounds and excreting waste. Proximal tubule cells, crucial for renal reabsorption of a range of sugars, ions, and amino acids, are highly susceptible to damage, leading to pathologies necessitating dialysis and kidney transplants. While human pluripotent stem cell-derived kidney organoids are used for modeling renal development, disease, and injury, the formation of proximal nephron cells in these 3D structures is incomplete. Here, we describe how to drive the development of proximal tubule precursors in kidney organoids by following a blueprint of in vivo human nephrogenesis. Transient manipulation of the PI3K signaling pathway activates Notch signaling in the early nephron and drives nephrons toward a proximal precursor state. These "proximal-biased" (PB) organoid nephrons proceed to generate proximal nephron precursor cells. Single-cell transcriptional analyses across the organoid nephron differentiation, comparing control and PB types, confirm the requirement of transient Notch signaling for proximal development. Indicative of functional maturity, PB organoids demonstrate dextran and albumin uptake, akin to in vivo proximal tubules. Moreover, PB organoids are highly sensitive to nephrotoxic agents, display an injury response, and drive expression of HAVCR1 / KIM1 , an early proximal-specific marker of kidney injury. Injured PB organoids show evidence of collapsed tubules, DNA damage, and upregulate the injury-response marker SOX9 . The PB organoid model therefore has functional relevance and potential for modeling mechanisms underpinning nephron injury. These advances improve the use of iPSC-derived kidney organoids as tools to understand developmental nephrology, model disease, test novel therapeutics, and for understanding human renal physiology.
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5
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Faivre A, Bugarski M, Rinaldi A, Sakhi IB, Verissimo T, Legouis D, Rutkowski JM, Correia S, Kaminska M, Dalga D, Malpetti D, Cippa PE, de Seigneux S, Hall AM. Spatiotemporal Landscape of Kidney Tubular Responses to Glomerular Proteinuria. J Am Soc Nephrol 2024; 35:854-869. [PMID: 38652545 PMCID: PMC11230716 DOI: 10.1681/asn.0000000000000357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Key Points
Glomerular proteinuria induces large-scale changes in gene expression along the nephron.Increased protein uptake in the proximal tubule results in axial remodeling and injury.Increased protein delivery to the distal tubule causes dedifferentiation of the epithelium.
Background
Large increases in glomerular protein filtration induce major changes in body homeostasis and are associated with a higher risk of kidney functional decline and cardiovascular disease. We investigated how elevated protein exposure modifies the landscape of tubular function along the entire nephron, to understand the cellular changes that mediate these important clinical phenomena.
Methods
We conducted single-nucleus RNA sequencing, functional intravital imaging, and antibody staining to spatially map transport processes along the mouse kidney tubule. We then delineated how these were altered in a transgenic mouse model of inducible glomerular proteinuria (POD-ATTAC) at 7 and 28 days.
Results
Glomerular proteinuria activated large-scale and pleiotropic changes in gene expression in all major nephron sections. Extension of protein uptake from early (S1) to later (S2) parts of the proximal tubule initially triggered dramatic expansion of a hybrid S1/2 population, followed by injury and failed repair, with the cumulative effect of loss of canonical S2 functions. Proteinuria also induced acute injury in S3. Meanwhile, overflow of luminal proteins to the distal tubule caused transcriptional convergence between specialized regions and generalized dedifferentiation.
Conclusions
Proteinuria modulated cell signaling in tubular epithelia and caused distinct patterns of remodeling and injury in a segment-specific manner.
Podcast
This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/JASN/2024_05_01_ASN0000000000000357.mp3
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Affiliation(s)
- Anna Faivre
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Milica Bugarski
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Anna Rinaldi
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Imene B Sakhi
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Thomas Verissimo
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - David Legouis
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
- Division of Intensive Care, Department of Acute Medicine, University Hospital of Geneva, Geneva, Switzerland
| | | | - Sara Correia
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Monika Kaminska
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Delal Dalga
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Daniele Malpetti
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Pietro E Cippa
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Sophie de Seigneux
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
- Department of Medicine, Service of Nephrology, Geneva University Hospitals, Geneva, Switzerland
| | - Andrew M Hall
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Zurich Kidney Center, Zurich, Switzerland
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6
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Hinze C, Lovric S, Halloran PF, Barasch J, Schmidt-Ott KM. Epithelial cell states associated with kidney and allograft injury. Nat Rev Nephrol 2024; 20:447-459. [PMID: 38632381 DOI: 10.1038/s41581-024-00834-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
The kidney epithelium, with its intricate arrangement of highly specialized cell types, constitutes the functional core of the organ. Loss of kidney epithelium is linked to the loss of functional nephrons and a subsequent decline in kidney function. In kidney transplantation, epithelial injury signatures observed during post-transplantation surveillance are strong predictors of adverse kidney allograft outcomes. However, epithelial injury is currently neither monitored clinically nor addressed therapeutically after kidney transplantation. Several factors can contribute to allograft epithelial injury, including allograft rejection, drug toxicity, recurrent infections and postrenal obstruction. The injury mechanisms that underlie allograft injury overlap partially with those associated with acute kidney injury (AKI) and chronic kidney disease (CKD) in the native kidney. Studies using advanced transcriptomic analyses of single cells from kidney or urine have identified a role for kidney injury-induced epithelial cell states in exacerbating and sustaining damage in AKI and CKD. These epithelial cell states and their associated expression signatures are also observed in transplanted kidney allografts, suggesting that the identification and characterization of transcriptomic epithelial cell states in kidney allografts may have potential clinical implications for diagnosis and therapy.
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Affiliation(s)
- Christian Hinze
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Svjetlana Lovric
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, Alberta, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan Barasch
- Division of Nephrology, Columbia University, New York City, NY, USA
| | - Kai M Schmidt-Ott
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany.
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7
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Zhao Q, Zhang R, Wang Y, Li T, Xue J, Chen Z. FOXQ1, deubiquitinated by USP10, alleviates sepsis-induced acute kidney injury by targeting the CREB5/NF-κB signaling axis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167331. [PMID: 38960057 DOI: 10.1016/j.bbadis.2024.167331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Sepsis-induced acute kidney injury (S-AKI) is a severe and frequent complication that occurs during sepsis. This study aimed to understand the role of FOXQ1 in S-AKI and its potential upstream and downstream regulatory mechanisms. A cecal ligation and puncture induced S-AKI mouse model in vivo and an LPS-induced HK-2 cell model in vitro were used. FOXQ1 was significantly upregulated in CLP mice and downregulated in the LPS-induced HK-2 cells. Upregulation of FOXQ1 improved kidney injury and dysfunction in CLP mice. Overexpression of FOXQ1 remarkably suppressed the apoptosis and inflammatory response via down-regulating oxidative stress indicators and pro-inflammatory factors (IL-1β, IL-6, and TNF-α), both in vivo and in vitro. From online analysis, the CREB5/NF-κB axis was identified as the downstream target of FOXQ1. FOXQ1 transcriptionally activated CREB5, upregulating its expression. Overexpression of FOXQ1 suppressed the phosphorylation level and nucleus transport of p65. Rescue experiments showed that CREB5 mediates the protective role of FOXQ1 on S-AKI. Furthermore, FOXQ1 was identified as a substrate of USP10, a deubiquitinating enzyme. Ectopic expression of USP10 reduced the ubiquitination of FOXQ1, promoting its protein stability. USP10 upregulation alleviated LPS-induced cell apoptosis and inflammatory response, while suppression of FOXQ1 augmented these trends. Collectively, our results suggest that FOXQ1, deubiquitinated by USP10, plays a protective role in S-AKI induced inflammation and apoptosis by targeting CREB5/NF-κB axis.
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Affiliation(s)
- Qi Zhao
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ran Zhang
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Wang
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tiegang Li
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Jinqi Xue
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhiguang Chen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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8
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Yu P, Gu T, Rao Y, Liang W, Zhang X, Jiang H, Lu J, She J, Guo J, Yang W, Liu Y, Tu Y, Tang L, Zhou X. A novel marine-derived anti-acute kidney injury agent targeting peroxiredoxin 1 and its nanodelivery strategy based on ADME optimization. Acta Pharm Sin B 2024; 14:3232-3250. [PMID: 39027260 PMCID: PMC11252462 DOI: 10.1016/j.apsb.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/28/2024] [Accepted: 02/07/2024] [Indexed: 07/20/2024] Open
Abstract
Insufficient therapeutic strategies for acute kidney injury (AKI) necessitate precision therapy targeting its pathogenesis. This study reveals the new mechanism of the marine-derived anti-AKI agent, piericidin glycoside S14, targeting peroxiredoxin 1 (PRDX1). By binding to Cys83 of PRDX1 and augmenting its peroxidase activity, S14 alleviates kidney injury efficiently in Prdx1-overexpression (Prdx1-OE) mice. Besides, S14 also increases PRDX1 nuclear translocation and directly activates the Nrf2/HO-1/NQO1 pathway to inhibit ROS production. Due to the limited druggability of S14 with low bioavailability (2.6%) and poor renal distribution, a pH-sensitive kidney-targeting dodecanamine-chitosan nanoparticle system is constructed to load S14 for precise treatment of AKI. l-Serine conjugation to chitosan imparts specificity to kidney injury molecule-1 (Kim-1)-overexpressed cells. The developed S14-nanodrug exhibits higher therapeutic efficiency by improving the in vivo behavior of S14 significantly. By encapsulation with micelles, the AUC0‒t , half-life time, and renal distribution of S14 increase 2.5-, 1.8-, and 3.1-fold, respectively. The main factors contributing to the improved druggability of S14 nanodrugs include the lower metabolic elimination rate and UDP-glycosyltransferase (UGT)-mediated biotransformation. In summary, this study identifies a new therapeutic target for the marine-derived anti-AKI agent while enhancing its ADME properties and druggability through nanotechnology, thereby driving advancements in marine drug development for AKI.
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Affiliation(s)
- Ping Yu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tanwei Gu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yueyang Rao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weimin Liang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xi Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huanguo Jiang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jindi Lu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianglian She
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jianmin Guo
- Guangdong Lewwin Pharmaceutical Research Institute Co., Ltd., Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangdong Engineering Research Center for Innovative Drug Evaluation and Research, Guangzhou 510990, China
| | - Wei Yang
- Guangdong Lewwin Pharmaceutical Research Institute Co., Ltd., Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangdong Engineering Research Center for Innovative Drug Evaluation and Research, Guangzhou 510990, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yingfeng Tu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lan Tang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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9
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Gerhardt LMS. From the Beginning to the End: Effects of Proteinuria along the Renal Tubule. J Am Soc Nephrol 2024; 35:823-825. [PMID: 38814710 PMCID: PMC11230705 DOI: 10.1681/asn.0000000000000399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Affiliation(s)
- Louisa M S Gerhardt
- Fifth Department of Medicine, Faculty of Medicine Mannheim of the University of Heidelberg, University Medical Center Mannheim, Mannheim, Germany
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10
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Noonan ML, Muto Y, Yoshimura Y, Leckie-Harre A, Wu H, Kalinichenko VV, Humphreys BD, Chang-Panesso M. Injury-induced Foxm1 expression in the mouse kidney drives epithelial proliferation by a cyclin F-dependent mechanism. JCI Insight 2024; 9:e175416. [PMID: 38916959 DOI: 10.1172/jci.insight.175416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Acute kidney injury (AKI) strongly upregulates the transcription factor Foxm1 in the proximal tubule in vivo, and Foxm1 drives epithelial proliferation in vitro. Here, we report that deletion of Foxm1 either with a nephron-specific Cre driver or by inducible global deletion reduced proximal tubule proliferation after ischemic injury in vivo. Foxm1 deletion led to increased AKI to chronic kidney disease transition, with enhanced fibrosis and ongoing tubule injury 6 weeks after injury. We report ERK mediated FOXM1 induction downstream of the EGFR in primary proximal tubule cells. We defined FOXM1 genomic binding sites by cleavage under targets and release using nuclease (CUT&RUN) and compared the genes located near FOXM1 binding sites with genes downregulated in primary proximal tubule cells after FOXM1 knockdown. The aligned data sets revealed the cell cycle regulator cyclin F (CCNF) as a putative FOXM1 target. We identified 2 cis regulatory elements that bound FOXM1 and regulated CCNF expression, demonstrating that Ccnf is strongly induced after kidney injury and that Foxm1 deletion abrogates Ccnf expression in vivo and in vitro. Knockdown of CCNF also reduced proximal tubule proliferation in vitro. These studies identify an ERK/FOXM1/CCNF signaling pathway that regulates injury-induced proximal tubule cell proliferation.
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Affiliation(s)
- Megan L Noonan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Aidan Leckie-Harre
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Vladimir V Kalinichenko
- Phoenix Children's Health Research Institute, Department of Child Health, University of Arizona College of Medicine, Phoenix, Arizona, USA
- Division of Neonatology, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Monica Chang-Panesso
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
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11
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Muto Y, Yoshimura Y, Wu H, Chang-Panesso M, Ledru N, Woodward OM, Outeda P, Cheng T, Mahjoub MR, Watnick TJ, Humphreys BD. Multi-omics profiling of mouse polycystic kidney disease progression at a single cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.595830. [PMID: 38854144 PMCID: PMC11160654 DOI: 10.1101/2024.05.27.595830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease and causes significant morbidity, ultimately leading to end-stage kidney disease. PKD pathogenesis is characterized by complex and dynamic alterations in multiple cell types during disease progression, hampering a deeper understanding of disease mechanism and the development of therapeutic approaches. Here, we generate a single nucleus multimodal atlas of an orthologous mouse PKD model at early, mid and late timepoints, consisting of 125,434 single-nucleus transcriptomic and epigenetic multiomes. We catalogue differentially expressed genes and activated epigenetic regions in each cell type during PKD progression, characterizing cell-type-specific responses to Pkd1 deletion. We describe heterogeneous, atypical collecting duct cells as well as proximal tubular cells that constitute cyst epithelia in PKD. The transcriptional regulation of the cyst lining cell marker GPRC5A is conserved between mouse and human PKD cystic epithelia, suggesting shared gene regulatory pathways. Our single nucleus multiomic analysis of mouse PKD provides a foundation to understand the earliest changes molecular deregulation in a mouse model of PKD at a single-cell resolution.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Monica Chang-Panesso
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Owen M. Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patricia Outeda
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tao Cheng
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Moe R. Mahjoub
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Terry J. Watnick
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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12
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Cheng R, Wang X, Huang L, Lu Z, Wu A, Guo S, Li C, Mao W, Xie Y, Xu P, Tian R. Novel insights into the protective effects of leonurine against acute kidney injury: Inhibition of ER stress-associated ferroptosis via regulating ATF4/CHOP/ACSL4 pathway. Chem Biol Interact 2024; 395:111016. [PMID: 38670420 DOI: 10.1016/j.cbi.2024.111016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Acute kidney injury (AKI) is a common and serious global health problem with high risks of mortality and the development of chronic kidney diseases. Leonurine is a unique bioactive component from Leonurus japonicus Houtt. and exerts antioxidant, antiapoptotic or anti-inflammatory properties. This study aimed to explore the benefits of leonurine on AKI and the possible mechanisms involved, with a particular foc on the regulation of ferroptosis and endoplasmic reticulum (ER) stress. Our results showed that leonurine exhibited prominent protective effects against AKI, as evidenced by the amelioration of histopathological alterations and reduction of renal dysfunction. In addition, leonurine significantly suppressed ferroptosis in AKI both in vivo and in vitro by effectively restoring ultrastructural abnormalities in mitochondria, decreasing ASCL4 and 4-HNE levels, scavenging reactive oxygen species (ROS), as well as increasing GPX4 and GSH levels. In parallel, leonurine also markedly mitigated ER stress via down-regulating PERK, eIF-2α, ATF4, CHOP and CHAC1. Further studies suggested that ER stress was closely involved in erastin-induced ferroptosis, and leonurine protected tubular epithelial cells in vitro by inhibiting ER stress-associated ferroptosis via regulating ATF4/CHOP/ASCL4 signalling pathway. Mechanistically, ATF4 silencing in vitro regulated CHOP and ACSL4 expressions, ultimately weakening both ER stress and ferroptosis. Notably, analyses of single-cell RNA sequencing data revealed that ATF4, CHOP and ASCL4 in renal tubular cells were all abnormally upregulated in patients with AKI compared to healthy controls, suggesting their contributions to the pathogenesis of AKI. Altogether, these findings suggest that leonurine alleviates AKI by inhibiting ER stress-associated ferroptosis via regulating ATF4/CHOP/ASCL4 signalling pathway, thus providing novel mechanisms for AKI treatment.
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Affiliation(s)
- Ran Cheng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xiaowan Wang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Lihua Huang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Zhisheng Lu
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Aijun Wu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Shan Guo
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Chuang Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, 510120, China
| | - Wei Mao
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Ying Xie
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; State Key Laboratory of Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Peng Xu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, 510120, China.
| | - Ruimin Tian
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, Guangzhou, 510120, China; State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, 999078, China.
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13
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Pan W, Zhang W, Zheng B, Camellato BR, Stern J, Lin Z, Khodadadi-Jamayran A, Kim J, Sommer P, Khalil K, Weldon E, Bai J, Zhu Y, Meyn P, Heguy A, Mangiola M, Griesemer A, Keating BJ, Montgomery RA, Xia B, Boeke JD. Cellular dynamics in pig-to-human kidney xenotransplantation. MED 2024:S2666-6340(24)00207-1. [PMID: 38776915 DOI: 10.1016/j.medj.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/30/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Xenotransplantation of genetically engineered porcine organs has the potential to address the challenge of organ donor shortage. Two cases of porcine-to-human kidney xenotransplantation were performed, yet the physiological effects on the xenografts and the recipients' immune responses remain largely uncharacterized. METHODS We performed single-cell RNA sequencing (scRNA-seq) and longitudinal RNA-seq analyses of the porcine kidneys to dissect xenotransplantation-associated cellular dynamics and xenograft-recipient interactions. We additionally performed longitudinal scRNA-seq of the peripheral blood mononuclear cells (PBMCs) to detect recipient immune responses across time. FINDINGS Although no hyperacute rejection signals were detected, scRNA-seq analyses of the xenografts found evidence of endothelial cell and immune response activation, indicating early signs of antibody-mediated rejection. Tracing the cells' species origin, we found human immune cell infiltration in both xenografts. Human transcripts in the longitudinal bulk RNA-seq revealed that human immune cell infiltration and the activation of interferon-gamma-induced chemokine expression occurred by 12 and 48 h post-xenotransplantation, respectively. Concordantly, longitudinal scRNA-seq of PBMCs also revealed two phases of the recipients' immune responses at 12 and 48-53 h. Lastly, we observed global expression signatures of xenotransplantation-associated kidney tissue damage in the xenografts. Surprisingly, we detected a rapid increase of proliferative cells in both xenografts, indicating the activation of the porcine tissue repair program. CONCLUSIONS Longitudinal and single-cell transcriptomic analyses of porcine kidneys and the recipient's PBMCs revealed time-resolved cellular dynamics of xenograft-recipient interactions during xenotransplantation. These cues can be leveraged for designing gene edits and immunosuppression regimens to optimize xenotransplantation outcomes. FUNDING This work was supported by NIH RM1HG009491 and DP5OD033430.
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Affiliation(s)
- Wanqing Pan
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Binghan Zheng
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brendan R Camellato
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey Stern
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA; Department of Surgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ziyan Lin
- Applied Bioinformatics Laboratories (ABL), NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Jacqueline Kim
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA; Department of Surgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Philip Sommer
- Department of Anesthesiology, Perioperative Care & Pain Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Karen Khalil
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA
| | - Elaina Weldon
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA; Department of Surgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jiangshan Bai
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Peter Meyn
- Genome Technology Center, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Adriana Heguy
- Genome Technology Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Massimo Mangiola
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA
| | - Adam Griesemer
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA; Department of Surgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Brendan J Keating
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA; Department of Surgery, NYU Grossman School of Medicine, New York, NY 10016, USA; Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Robert A Montgomery
- NYU Langone Transplant Institute, NYU Langone Health, New York, NY 10016, USA; Department of Surgery, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Bo Xia
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Society of Fellows, Harvard University, Cambridge, MA 02138, USA.
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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14
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Li H, Li D, Ledru N, Xuanyuan Q, Wu H, Asthana A, Byers LN, Tullius SG, Orlando G, Waikar SS, Humphreys BD. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. Cell Metab 2024; 36:1105-1125.e10. [PMID: 38513647 PMCID: PMC11081846 DOI: 10.1016/j.cmet.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes. We find that the same cell type, including thin limb, thick ascending limb loop of Henle and principal cells, display distinct transcriptomic, chromatin accessibility, and metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene profiles revealed non-overlapping metabolic signatures between nephron segments and dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating multimodal omics with clinical data identified PLEKHA1 as a disease marker, and its in vitro knockdown increased gene expression in PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying the human kidney anatomy.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Lori N Byers
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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15
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Livingston MJ, Zhang M, Kwon SH, Chen JK, Li H, Manicassamy S, Dong Z. Autophagy activates EGR1 via MAPK/ERK to induce FGF2 in renal tubular cells for fibroblast activation and fibrosis during maladaptive kidney repair. Autophagy 2024; 20:1032-1053. [PMID: 37978868 PMCID: PMC11135847 DOI: 10.1080/15548627.2023.2281156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Macroautophagy/autophagy contributes to maladaptive kidney repair by inducing pro-fibrotic factors such as FGF2 (fibroblast growth factor 2), but the underlying mechanism remains elusive. Here, we show that EGR1 (early growth response 1) was induced in injured proximal tubules after ischemic acute kidney injury (AKI) and this induction was suppressed by autophagy deficiency in inducible, renal tubule-specific atg7 (autophagy related 7) knockout (iRT-atg7 KO) mice. In cultured proximal tubular cells, TGFB1 (transforming growth factor beta 1) induced EGR1 and this induction was also autophagy dependent. Egr1 knockdown in tubular cells reduced FGF2 expression during TGFB1 treatment, leading to less FGF2 secretion and decreased paracrine effects on fibroblasts. ChIP assay detected an increased binding of EGR1 to the Fgf2 gene promoter in TGFB1-treated tubular cells. Both Fgf2 and Egr1 transcription was inhibited by FGF2 neutralizing antibody, suggesting a positive feedback for EGR1-mediated FGF2 autoregulation. This feedback was confirmed using fgf2-deficient tubular cells and fgf2-deficient mice. Upstream of EGR1, autophagy deficiency in mice suppressed MAPK/ERK (mitogen-activated protein kinase) activation in post-ischemic renal tubules. This inhibition correlated with SQSTM1/p62 (sequestosome 1) aggregation and its sequestration of MAPK/ERK. SQSTM1/p62 interacted with MAPK/ERK and blocked its activation during TGFB1 treatment in autophagy-deficient tubular cells. Inhibition of MAPK/ERK suppressed EGR1 and FGF2 expression in maladaptive tubules, leading to the amelioration of renal fibrosis and improvement of renal function. These results suggest that autophagy activates MAPK/ERK in renal tubular cells, which induces EGR1 to transactivate FGF2. FGF2 is then secreted into the interstitium to stimulate fibroblasts for fibrogenesis.Abbreviation: 3-MA: 3-methyladenine; ACTA2/α-SMA: actin alpha 2, smooth muscle, aorta; ACTB/β-actin: actin, beta; AKI: acute kidney injury; aa: amino acid; ATG/Atg: autophagy related; BUN: blood urea nitrogen; ChIP: chromatin immunoprecipitation; CKD: chronic kidney disease; CM: conditioned medium; COL1A1: collagen, type I, alpha 1; COL4A1: collagen, type IV, alpha 1; CQ: chloroquine; DBA: dolichos biflorus agglutinin; EGR1: early growth response 1; ELK1: ELK1, member of ETS oncogene family; FGF2: fibroblast growth factor 2; FN1: fibronectin 1; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HAVCR1/KIM-1: hepatitis A virus cellular receptor 1; IP: immunoprecipitation; LIR: LC3-interacting region; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAP2K/MEK: mitogen-activated protein kinase kinase; MAPK: mitogen-activated protein kinase; NFKB: nuclear factor kappa B; PB1: Phox and Bem1; PFT: pifithrin α; PPIB/cyclophilin B: peptidylprolyl isomerase B; RT-qPCR: real time-quantitative PCR; SQSTM1/p62: sequestosome 1; TGFB1/TGF-β1: transforming growth factor beta 1; VIM: vimentin.
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Affiliation(s)
- Man J. Livingston
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Research Department, Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Ming Zhang
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Sang-Ho Kwon
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Jian-Kang Chen
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Santhakumar Manicassamy
- Department of Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Research Department, Charlie Norwood VA Medical Center, Augusta, GA, USA
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16
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Yang J, Zhuang H, Li J, Nunez-Nescolarde AB, Luo N, Chen H, Li A, Qu X, Wang Q, Fan J, Bai X, Ye Z, Gu B, Meng Y, Zhang X, Wu D, Sia Y, Jiang X, Chen W, Combes AN, Nikolic-Paterson DJ, Yu X. The secreted micropeptide C4orf48 enhances renal fibrosis via an RNA-binding mechanism. J Clin Invest 2024; 134:e178392. [PMID: 38625739 PMCID: PMC11093611 DOI: 10.1172/jci178392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
Renal interstitial fibrosis is an important mechanism in the progression of chronic kidney disease (CKD) to end-stage kidney disease. However, we lack specific treatments to slow or halt renal fibrosis. Ribosome profiling identified upregulation of a secreted micropeptide, C4orf48 (Cf48), in mouse diabetic nephropathy. Cf48 RNA and protein levels were upregulated in tubular epithelial cells in human and experimental CKD. Serum Cf48 levels were increased in human CKD and correlated with loss of kidney function, increasing CKD stage, and the degree of active interstitial fibrosis. Cf48 overexpression in mice accelerated renal fibrosis, while Cf48 gene deletion or knockdown by antisense oligonucleotides significantly reduced renal fibrosis in CKD models. In vitro, recombinant Cf48 (rCf48) enhanced TGF-β1-induced fibrotic responses in renal fibroblasts and epithelial cells independently of Smad3 phosphorylation. Cellular uptake of Cf48 and its profibrotic response in fibroblasts operated via the transferrin receptor. RNA immunoprecipitation-sequencing identified Cf48 binding to mRNA of genes involved in the fibrotic response, including Serpine1, Acta2, Ccn2, and Col4a1. rCf48 binds to the 3'UTR of Serpine1 and increases mRNA half-life. We identify the secreted Cf48 micropeptide as a potential enhancer of renal fibrosis that operates as an RNA-binding peptide to promote the production of extracellular matrix.
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Affiliation(s)
- Jiayi Yang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Hongjie Zhuang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinhua Li
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
- Department of Nephrology, Monash Health and Department of Medicine and
| | - Ana B. Nunez-Nescolarde
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ning Luo
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Huiting Chen
- The Second Clinical College, Guangdong Medical University, Dongguan, Guangdong, China
| | - Andy Li
- Department of Nephrology, Monash Health and Department of Medicine and
| | - Xinli Qu
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Qing Wang
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jinjin Fan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Xiaoyan Bai
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Bing Gu
- Department of Clinical Laboratory, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yue Meng
- Department of Clinical Laboratory, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xingyuan Zhang
- Department of Biostatistics, UNC Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Di Wu
- Department of Biostatistics, UNC Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Youyang Sia
- School of Life Science, Tsinghua University, Beijing, China
| | - Xiaoyun Jiang
- Department of Paediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Alexander N. Combes
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Xueqing Yu
- Department of Nephrology and
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
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17
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Li ZL, Huang MM, Yu MY, Nie DF, Fu SL, Di JJ, Lan T, Liu BC, Wu QL. Mitochondrial fumarate promotes ischemia/reperfusion-induced tubular injury. Acta Physiol (Oxf) 2024; 240:e14121. [PMID: 38409944 DOI: 10.1111/apha.14121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
AIM Mitochondrial dysfunction, a characteristic pathological feature of renal Ischemic/reperfusion injury (I/RI), predisposes tubular epithelial cells to maintain an inflammatory microenvironment, however, the exact mechanisms through which mitochondrial dysfunction modulates the induction of tubular injury remains incompletely understood. METHODS ESI-QTRAP-MS/MS approach was used to characterize the targeted metabolic profiling of kidney with I/RI. Tubule injury, mitochondrial dysfunction, and fumarate level were evaluated using qPCR, transmission electron microscopy, ELISA, and immunohistochemistry. RESULTS We demonstrated that tubule injury occurred at the phase of reperfusion in murine model of I/RI. Meanwhile, enhanced glycolysis and mitochondrial dysfunction were found to be associated with tubule injury. Further, we found that tubular fumarate, which resulted from fumarate hydratase deficiency and released from dysfunctional mitochondria, promoted tubular injury. Mechanistically, fumarate induced tubular injury by causing disturbance of glutathione (GSH) hemostasis. Suppression of GSH with buthionine sulphoximine administration could deteriorate the fumarate inhibition-mediated tubule injury recovery. Reactive oxygen species/NF-κB signaling activation played a vital role in fumarate-mediated tubule injury. CONCLUSION Our studies demonstrated that the mitochondrial-derived fumarate promotes tubular epithelial cell injury in renal I/RI. Blockade of fumarate-mediated ROS/NF-κB signaling activation may serve as a novel therapeutic approach to ameliorate hypoxic tubule injury.
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Affiliation(s)
- Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Ming-Min Huang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Meng-Yao Yu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Di-Fei Nie
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Sha-Li Fu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Jing-Jing Di
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Ting Lan
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
| | - Qiu-Li Wu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, Jiangsu, China
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18
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Buse M, Cheng M, Jankowski V, Lellig M, Sterzer V, Strieder T, Leuchtle K, Martin IV, Seikrit C, Brinkkoettter P, Crispatzu G, Floege J, Boor P, Speer T, Kramann R, Ostendorf T, Moeller MJ, Costa IG, Stamellou E. Lineage tracing reveals transient phenotypic adaptation of tubular cells during acute kidney injury. iScience 2024; 27:109255. [PMID: 38444605 PMCID: PMC10914483 DOI: 10.1016/j.isci.2024.109255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Tubular injury is the hallmark of acute kidney injury (AKI) with a tremendous impact on patients and health-care systems. During injury, any differentiated proximal tubular cell (PT) may transition into a specific injured phenotype, so-called "scattered tubular cell" (STC)-phenotype. To understand the fate of this specific phenotype, we generated transgenic mice allowing inducible, reversible, and irreversible tagging of these cells in a murine AKI model, the unilateral ischemia-reperfusion injury (IRI). For lineage tracing, we analyzed the kidneys using single-cell profiling during disease development at various time points. Labeled cells, which we defined by established endogenous markers, already appeared 8 h after injury and showed a distinct expression set of genes. We show that STCs re-differentiate back into fully differentiated PTs upon the resolution of the injury. In summary, we show the dynamics of the phenotypic transition of PTs during injury, revealing a reversible transcriptional program as an adaptive response during disease.
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Affiliation(s)
- Marc Buse
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany
| | - Michaela Lellig
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany
| | - Viktor Sterzer
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Thiago Strieder
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Katja Leuchtle
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Ina V. Martin
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Claudia Seikrit
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Paul Brinkkoettter
- Department II of Internal Medicine and Centre for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Giuliano Crispatzu
- Department II of Internal Medicine and Centre for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Peter Boor
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Timotheus Speer
- Medical Clinic 4, Nephrology, University of Frankfurt und Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Rafael Kramann
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Tammo Ostendorf
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Marcus J. Moeller
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Ivan G. Costa
- Institute for Computational Genomics, RWTH Aachen University Hospital, Aachen, Germany
| | - Eleni Stamellou
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
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19
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Legouis D, Rinaldi A, Malpetti D, Arnoux G, Verissimo T, Faivre A, Mangili F, Rinaldi A, Ruinelli L, Pugin J, Moll S, Clivio L, Bolis M, de Seigneux S, Azzimonti L, Cippà PE. A transfer learning framework to elucidate the clinical relevance of altered proximal tubule cell states in kidney disease. iScience 2024; 27:109271. [PMID: 38487013 PMCID: PMC10937833 DOI: 10.1016/j.isci.2024.109271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/26/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
The application of single-cell technologies in clinical nephrology remains elusive. We generated an atlas of transcriptionally defined cell types and cell states of human kidney disease by integrating single-cell signatures reported in the literature with newly generated signatures obtained from 5 patients with acute kidney injury. We used this information to develop kidney-specific cell-level information ExtractoR (K-CLIER), a transfer learning approach specifically tailored to evaluate the role of cell types/states on bulk RNAseq data. We validated the K-CLIER as a reliable computational framework to obtain a dimensionality reduction and to link clinical data with single-cell signatures. By applying K-CLIER on cohorts of patients with different kidney diseases, we identified the most relevant cell types associated with fibrosis and disease progression. This analysis highlighted the central role of altered proximal tubule cells in chronic kidney disease. Our study introduces a new strategy to exploit the power of single-cell technologies toward clinical applications.
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Affiliation(s)
- David Legouis
- Division of Intensive Care, Department of Acute Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
| | - Anna Rinaldi
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
| | - Daniele Malpetti
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Gregoire Arnoux
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
| | - Thomas Verissimo
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
| | - Anna Faivre
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
- Division of Nephrology, Department of Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Francesca Mangili
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Andrea Rinaldi
- Institute of Oncological Research, 6500 Bellinzona, Switzerland
| | | | - Jerome Pugin
- Division of Intensive Care, Department of Acute Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Solange Moll
- Division of Pathology, Department of Diagnostic, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Luca Clivio
- Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
| | - Marco Bolis
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- Laboratory of Computational Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Sophie de Seigneux
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
- Division of Nephrology, Department of Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Laura Azzimonti
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Pietro E. Cippà
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
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20
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Rao SN, Zahm M, Casemayou A, Buleon M, Faguer S, Feuillet G, Iacovoni JS, Joffre OP, Gonzalez-Fuentes I, Lhuillier E, Martins F, Riant E, Zakaroff-Girard A, Schanstra JP, Saulnier-Blache JS, Belliere J. Single-cell RNA sequencing identifies senescence as therapeutic target in rhabdomyolysis-induced acute kidney injury. Nephrol Dial Transplant 2024; 39:496-509. [PMID: 37697719 DOI: 10.1093/ndt/gfad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND The role of macrophages in the development of rhabdomyolysis-induced acute kidney injury (RM-AKI) has been established, but an in-depth understanding of the changes in the immune landscape could help to improve targeted strategies. Whereas senescence is usually associated with chronic kidney processes, we also wished to explore whether senescence could also occur in AKI and whether senolytics could act on immune cells. METHODS Single-cell RNA sequencing was used in the murine glycerol-induced RM-AKI model to dissect the transcriptomic characteristics of CD45+ live cells sorted from kidneys 2 days after injury. Public datasets from murine AKI models were reanalysed to explore cellular senescence signature in tubular epithelial cells (TECs). A combination of senolytics (dasatinib and quercetin, DQ) was administered to mice exposed or not to RM-AKI. RESULTS Unsupervised clustering of nearly 17 000 single-cell transcriptomes identified seven known immune cell clusters. Sub-clustering of the mononuclear phagocyte cells revealed nine distinct cell sub-populations differently modified with RM. One macrophage cluster was particularly interesting since it behaved as a critical node in a trajectory connecting one major histocompatibility complex class IIhigh (MHCIIhigh) cluster only present in Control to two MHCIIlow clusters only present in RM-AKI. This critical cluster expressed a senescence gene signature, that was very different from that of the TECs. Senolytic DQ treatment blocked the switch from a F4/80highCD11blow to F4/80lowCD11bhigh phenotype, which correlated with prolonged nephroprotection in RM-AKI. CONCLUSIONS Single-cell RNA sequencing unmasked novel transitional macrophage subpopulation associated with RM-AKI characterized by the activation of cellular senescence processes. This work provides a proof-of-concept that senolytics nephroprotective effects may rely, at least in part, on subtle immune modulation.
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Affiliation(s)
- Snigdha N Rao
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Margot Zahm
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
| | - Audrey Casemayou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Marie Buleon
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Stanislas Faguer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
- Department of Nephrology and Organ Transplantation, Referral Centre for Rare Kidney Diseases, French Intensive Care Renal Network, University Hospital of Toulouse, Toulouse, France
| | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jason S Iacovoni
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Olivier P Joffre
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
| | - Ignacio Gonzalez-Fuentes
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Emeline Lhuillier
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Frédéric Martins
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Elodie Riant
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Alexia Zakaroff-Girard
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jean Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Julie Belliere
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
- Department of Nephrology and Organ Transplantation, Referral Centre for Rare Kidney Diseases, French Intensive Care Renal Network, University Hospital of Toulouse, Toulouse, France
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21
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Jin J, Yang YR, Gong Q, Wang JN, Ni WJ, Wen JG, Meng XM. Role of epigenetically regulated inflammation in renal diseases. Semin Cell Dev Biol 2024; 154:295-304. [PMID: 36328897 DOI: 10.1016/j.semcdb.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/01/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
Abstract
In recent decades, renal disease research has witnessed remarkable advances. Experimental evidence in this field has highlighted the role of inflammation in kidney disease. Epigenetic dynamics and immunometabolic reprogramming underlie the alterations in cellular responses to intrinsic and extrinsic stimuli; these factors determine cell identity and cell fate decisions and represent current research hotspots. This review focuses on recent findings and emerging concepts in epigenetics and inflammatory regulation and their effect on renal diseases. This review aims to summarize the role and mechanisms of different epigenetic modifications in renal inflammation and injury and provide new avenues for future research on inflammation-related renal disease and drug development.
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Affiliation(s)
- Juan Jin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Ya-Ru Yang
- Department of Clinical Pharmacology, Second Hospital of Anhui Medical University, Hefei, China
| | - Qian Gong
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Jia-Nan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China.
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22
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Ledru N, Wilson PC, Muto Y, Yoshimura Y, Wu H, Li D, Asthana A, Tullius SG, Waikar SS, Orlando G, Humphreys BD. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing. Nat Commun 2024; 15:1291. [PMID: 38347009 PMCID: PMC10861555 DOI: 10.1038/s41467-024-45706-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype that may promote fibrosis and chronic kidney disease. The healthy to failed repair change is marked by cell state-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq sequencing offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We develop a regularized regression approach to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generate a single nucleus multiomic dataset from seven adult human kidney samples and apply our method to study drivers of a failed injury response associated with kidney disease. We demonstrate that our approach is a highly effective tool for predicting key cis- and trans-regulatory elements underpinning the healthy to failed repair transition and use it to identify NFAT5 as a driver of the maladaptive proximal tubule state.
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Affiliation(s)
- Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Parker C Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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23
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Chen J, Zhang H, Yi X, Dou Q, Yang X, He Y, Chen J, Chen K. Cellular senescence of renal tubular epithelial cells in acute kidney injury. Cell Death Discov 2024; 10:62. [PMID: 38316761 PMCID: PMC10844256 DOI: 10.1038/s41420-024-01831-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/14/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024] Open
Abstract
Cellular senescence represents an irreversible state of cell-cycle arrest during which cells secrete senescence-associated secretory phenotypes, including inflammatory factors and chemokines. Additionally, these cells exhibit an apoptotic resistance phenotype. Cellular senescence serves a pivotal role not only in embryonic development, tissue regeneration, and tumor suppression but also in the pathogenesis of age-related degenerative diseases, malignancies, metabolic diseases, and kidney diseases. The senescence of renal tubular epithelial cells (RTEC) constitutes a critical cellular event in the progression of acute kidney injury (AKI). RTEC senescence inhibits renal regeneration and repair processes and, concurrently, promotes the transition of AKI to chronic kidney disease via the senescence-associated secretory phenotype. The mechanisms underlying cellular senescence are multifaceted and include telomere shortening or damage, DNA damage, mitochondrial autophagy deficiency, cellular metabolic disorders, endoplasmic reticulum stress, and epigenetic regulation. Strategies aimed at inhibiting RTEC senescence, targeting the clearance of senescent RTEC, or promoting the apoptosis of senescent RTEC hold promise for enhancing the renal prognosis of AKI. This review primarily focuses on the characteristics and mechanisms of RTEC senescence, and the impact of intervening RTEC senescence on the prognosis of AKI, aiming to provide a foundation for understanding the pathogenesis and providing potentially effective approaches for AKI treatment.
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Affiliation(s)
- Juan Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Huhai Zhang
- Department of Nephrology, Southwest Hospital, Army Medical University, 400042, Chongqing, China
| | - Xiangling Yi
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Qian Dou
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Xin Yang
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Yani He
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China
| | - Jia Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China.
| | - Kehong Chen
- Department of Nephrology, Daping Hospital, Army Medical University, 400042, Chongqing, China.
- State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, China.
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24
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Muto Y, Dixon EE, Yoshimura Y, Ledru N, Kirita Y, Wu H, Humphreys BD. Epigenetic reprogramming driving successful and failed repair in acute kidney injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576421. [PMID: 38328130 PMCID: PMC10849487 DOI: 10.1101/2024.01.20.576421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Acute kidney injury (AKI) causes epithelial damage followed by subsequent repair. While successful repair restores kidney function, this process is often incomplete and can lead to chronic kidney disease (CKD) in a process called failed repair. To better understand the epigenetic reprogramming driving this AKI-to-CKD transition we generated a single nucleus multiomic atlas for the full mouse AKI time course, consisting of ~280,000 single nucleus transcriptomes and epigenomes. We reveal cell-specific dynamic alterations in gene regulatory landscapes reflecting especially activation of proinflammatory pathways. We further generated single nucleus multiomic data from four human AKI samples including validation by genome-wide identification of NF-kB binding sites. A regularized regression analysis identifies key regulators involved in both successful and failed repair cell fate, identifying the transcription factor CREB5 as a regulator of both successful and failed tubular repair that also drives proximal tubule cell proliferation after injury. Our interspecies multiomic approach provides a foundation to comprehensively understand cell states in AKI.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E. Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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25
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Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Fong SL, Kim N, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nat Commun 2024; 15:12. [PMID: 38195585 PMCID: PMC10776631 DOI: 10.1038/s41467-023-44186-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 12/03/2023] [Indexed: 01/11/2024] Open
Abstract
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq and scATAC-seq) on insectivorous (Eptesicus fuscus; big brown bat) and frugivorous (Artibeus jamaicensis; Jamaican fruit bat) bat kidneys and pancreases and identify key cell population, gene expression and regulatory differences associated with the Jamaican fruit bat that also relate to human disease, particularly diabetes. We find a decrease in loop of Henle and an increase in collecting duct cells, and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the Jamaican fruit bat kidney. The Jamaican fruit bat pancreas shows an increase in endocrine and a decrease in exocrine cells, and differences in genes and regulatory elements involved in insulin regulation. We also find that these frugivorous bats share several molecular characteristics with human diabetes. Combined, our work provides insights from a frugivorous mammal that could be leveraged for therapeutic purposes.
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Affiliation(s)
- Wei E Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Biology, Menlo College, 1000 El Camino Real, Atherton, CA, 94027, USA
| | - Seungbyn Baek
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hai P Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Yien-Ming Kuo
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Rachael Bradley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sarah L Fong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Alex Galazyuk
- Hearing Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology, Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lisa Noelle Cooper
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Martin Hemberg
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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26
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Li Y, Liu Z, Han X, Liang F, Zhang Q, Huang X, Shi X, Huo H, Han M, Liu X, Zhu H, He L, Shen L, Hu X, Wang J, Wang QD, Smart N, Zhou B, He B. Dynamics of Endothelial Cell Generation and Turnover in Arteries During Homeostasis and Diseases. Circulation 2024; 149:135-154. [PMID: 38084582 DOI: 10.1161/circulationaha.123.064301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/06/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Endothelial cell (EC) generation and turnover by self-proliferation contributes to vascular repair and regeneration. The ability to accurately measure the dynamics of EC generation would advance our understanding of cellular mechanisms of vascular homeostasis and diseases. However, it is currently challenging to evaluate the dynamics of EC generation in large vessels such as arteries because of their infrequent proliferation. METHODS By using dual recombination systems based on Cre-loxP and Dre-rox, we developed a genetic system for temporally seamless recording of EC proliferation in vivo. We combined genetic recording of EC proliferation with single-cell RNA sequencing and gene knockout to uncover cellular and molecular mechanisms underlying EC generation in arteries during homeostasis and disease. RESULTS Genetic proliferation tracing reveals that ≈3% of aortic ECs undergo proliferation per month in adult mice during homeostasis. The orientation of aortic EC division is generally parallel to blood flow in the aorta, which is regulated by the mechanosensing protein Piezo1. Single-cell RNA sequencing analysis reveals 4 heterogeneous aortic EC subpopulations with distinct proliferative activity. EC cluster 1 exhibits transit-amplifying cell features with preferential proliferative capacity and enriched expression of stem cell markers such as Sca1 and Sox18. EC proliferation increases in hypertension but decreases in type 2 diabetes, coinciding with changes in the extent of EC cluster 1 proliferation. Combined gene knockout and proliferation tracing reveals that Hippo/vascular endothelial growth factor receptor 2 signaling pathways regulate EC proliferation in large vessels. CONCLUSIONS Genetic proliferation tracing quantitatively delineates the dynamics of EC generation and turnover, as well as EC division orientation, in large vessels during homeostasis and disease. An EC subpopulation in the aorta exhibits more robust cell proliferation during homeostasis and type 2 diabetes, identifying it as a potential therapeutic target for vascular repair and regeneration.
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Affiliation(s)
- Yi Li
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
| | - Zixin Liu
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
| | - Ximeng Han
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
| | - Feng Liang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
| | - Qianyu Zhang
- School of Life Science and Technology, ShanghaiTech University, China (Q.Z., M.H., B.Z.)
| | - Xiuzhen Huang
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
| | - Huanhuan Huo
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
| | - Maoying Han
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
- School of Life Science and Technology, ShanghaiTech University, China (Q.Z., M.H., B.Z.)
| | - Xiuxiu Liu
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
| | - Huan Zhu
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
| | - Lingjuan He
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China (L.H.)
| | - Linghong Shen
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
| | - Xinyang Hu
- Department of Cardiology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China (X.H., J.W.)
| | - Jian'an Wang
- Department of Cardiology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China (X.H., J.W.)
| | - Qing-Dong Wang
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (Q.D.W.)
| | - Nicola Smart
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, UK (N.S.)
| | - Bin Zhou
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
- New Cornerstone Investigator Institute, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China (Y.L., Z.L., X. Han, X. Huang, M.H., X.L., H.Z., B.Z.)
- School of Life Science and Technology, ShanghaiTech University, China (Q.Z., M.H., B.Z.)
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, China (B.Z.)
| | - Ben He
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, China (Y.L., X. Han, F.L., X.S., H.H., L.S., B.Z., B.H.)
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27
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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] [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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28
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Yamashita N, Kramann R. Mechanisms of kidney fibrosis and routes towards therapy. Trends Endocrinol Metab 2024; 35:31-48. [PMID: 37775469 DOI: 10.1016/j.tem.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]
Abstract
Kidney fibrosis is the final common pathway of virtually all chronic kidney diseases (CKDs) and is therefore considered to be a promising therapeutic target for these conditions. However, despite great progress in recent years, no targeted antifibrotic therapies for the kidney have been approved, likely because the complex mechanisms that initiate and drive fibrosis are not yet completely understood. Recent single-cell genomic approaches have allowed novel insights into kidney fibrosis mechanisms in mouse and human, particularly the heterogeneity and differentiation processes of myofibroblasts, the role of injured epithelial cells and immune cells, and their crosstalk mechanisms. In this review we summarize the key mechanisms that drive kidney fibrosis, including recent advances in understanding the mechanisms, as well as potential routes for developing novel targeted antifibrotic therapeutics.
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Affiliation(s)
- Noriyuki Yamashita
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology, and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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29
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Rex N, Melk A, Schmitt R. Cellular senescence and kidney aging. Clin Sci (Lond) 2023; 137:1805-1821. [PMID: 38126209 PMCID: PMC10739085 DOI: 10.1042/cs20230140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Life expectancy is increasing worldwide, and by 2050 the proportion of the world's population over 65 years of age is estimated to surpass 1.5 billion. Kidney aging is associated with molecular and physiological changes that cause a loss of renal function and of regenerative potential. As the aging population grows, it is crucial to understand the mechanisms underlying these changes, as they increase the susceptibility to developing acute kidney injury (AKI) and chronic kidney disease (CKD). Various cellular processes and molecular pathways take part in the complex process of kidney aging. In this review, we will focus on the phenomenon of cellular senescence as one of the involved mechanisms at the crossroad of kidney aging, age-related disease, and CKD. We will highlight experimental and clinical findings about the role of cellular senescence in kidney aging and CKD. In addition, we will review challenges in senescence research and emerging therapeutic aspects. We will highlight the great potential of senolytic strategies for the elimination of harmful senescent cells to promote healthy kidney aging and to avoid age-related disease and CKD. This review aims to give insight into recent discoveries and future developments, providing a comprehensive overview of current knowledge on cellular senescence and anti-senescent therapies in the kidney field.
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Affiliation(s)
- Nikolai Rex
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
| | - Anette Melk
- Department of Pediatric Kidney, Liver and Metabolic Diseases, Medical School Hannover, Germany
| | - Roland Schmitt
- Department of Nephrology and Hypertension, Medical School Hannover, Germany
- Department of Nephrology and Hypertension, University Hospital Schleswig-Holstein, Kiel, Germany
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30
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Polonsky M, Gerhardt LMS, Yun J, Koppitch K, Colón KL, Amrhein H, Zheng S, Yuan GC, Thomson M, Cai L, McMahon AP. Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568217. [PMID: 38045285 PMCID: PMC10690238 DOI: 10.1101/2023.11.22.568217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, and injury-invoked inflammation and fibrosis. Deciphering molecular pathways and cellular interactions driving these processes is challenging due to the complex renal architecture. Here, we applied single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics revealed injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicted Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis revealed cellular microenvironments resembling early tertiary lymphoid structures and identified associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease. One-Sentence Summary: Spatial transcriptomics predicted a molecular interplay amongst neighboring cell-types in the injured mammalian kidney Main Text.
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31
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Cao S, Pan Y, Terker AS, Arroyo Ornelas JP, Wang Y, Tang J, Niu A, Kar SA, Jiang M, Luo W, Dong X, Fan X, Wang S, Wilson MH, Fogo A, Zhang MZ, Harris RC. Epidermal growth factor receptor activation is essential for kidney fibrosis development. Nat Commun 2023; 14:7357. [PMID: 37963889 PMCID: PMC10645887 DOI: 10.1038/s41467-023-43226-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Fibrosis is the progressive accumulation of excess extracellular matrix and can cause organ failure. Fibrosis can affect nearly every organ including kidney and there is no specific treatment currently. Although Epidermal Growth Factor Receptor (EGFR) signaling pathway has been implicated in development of kidney fibrosis, underlying mechanisms by which EGFR itself mediates kidney fibrosis have not been elucidated. We find that EGFR expression increases in interstitial myofibroblasts in human and mouse fibrotic kidneys. Selective EGFR deletion in the fibroblast/pericyte population inhibits interstitial fibrosis in response to unilateral ureteral obstruction, ischemia or nephrotoxins. In vivo and in vitro studies and single-nucleus RNA sequencing analysis demonstrate that EGFR activation does not induce myofibroblast transformation but is necessary for the initial pericyte/fibroblast migration and proliferation prior to subsequent myofibroblast transformation by TGF-ß or other profibrotic factors. These findings may also provide insight into development of fibrosis in other organs and in other conditions.
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Affiliation(s)
- Shirong Cao
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Yu Pan
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
- Division of Nephrology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Andrew S Terker
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Juan Pablo Arroyo Ornelas
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Yinqiu Wang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Jiaqi Tang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Aolei Niu
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Sarah Abu Kar
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Mengdi Jiang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Wentian Luo
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Xinyu Dong
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Xiaofeng Fan
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Suwan Wang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
| | - Matthew H Wilson
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA
- Veterans Affairs, Nashville, TN, USA
| | - Agnes Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ming-Zhi Zhang
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA.
| | - Raymond C Harris
- Division of Nephrology and Hypertension, Department of Medicine, Nashville, TN, USA.
- Vanderbilt Center for Kidney Disease, Nashville, TN, USA.
- Veterans Affairs, Nashville, TN, USA.
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Miao Z, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney. Dev Cell 2023; 58:2338-2358.e5. [PMID: 37673062 PMCID: PMC10873092 DOI: 10.1016/j.devcel.2023.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility, and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA sequencing (RNA-seq) data demonstrated that sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR)-mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation, whereas analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, disease, and metabolic linkage of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhen Miao
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ingileif B Hallgrimsdottir
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA.
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Beamish JA, Telang AC, McElliott MC, Al-Suraimi A, Chowdhury M, Ference-Salo JT, Otto EA, Menon R, Soofi A, Weinberg JM, Patel SR, Dressler GR. Pax Protein Depletion in Proximal Tubules Triggers Conserved Mechanisms of Resistance to Acute Ischemic Kidney Injury and Prevents Transition to Chronic Kidney Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.559511. [PMID: 37873377 PMCID: PMC10592940 DOI: 10.1101/2023.10.03.559511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Acute kidney injury (AKI) is a common condition that lacks effective treatments. In part this shortcoming is due to an incomplete understanding of the genetic mechanisms that control pathogenesis and recovery. Pax2 and Pax8 are homologous transcription factors with overlapping functions that are critical for kidney development and are re-activated in AKI. In this report, we examined the role of Pax2 and Pax8 in recovery from ischemic AKI. We found that Pax2 and Pax8 are upregulated after severe AKI and correlate with chronic injury. Surprisingly, we then discovered that proximal-tubule-selective deletion of Pax2 and Pax8 resulted in a less severe chronic injury phenotype. This effect was mediated by protection against the acute insult, similar to preconditioning. Prior to injury, Pax2 and Pax8 mutant mice develop a unique subpopulation of S3 proximal tubule cells that display features usually seen only in acute or chronic injury. The expression signature of these cells was strongly enriched with genes associated with other mechanisms of protection against ischemic AKI including caloric restriction, hypoxic preconditioning, and female sex. Taken together, our results identify a novel role for Pax2 and Pax8 in mature proximal tubules that regulates critical genes and pathways involved in both injury response and protection from ischemic AKI. TRANSLATIONAL STATEMENT Identifying the molecular and genetic regulators unique to the nephron that dictate vulnerability to injury and regenerative potential could lead to new therapeutic targets to treat ischemic kidney injury. Pax2 and Pax8 are two homologous nephron-specific transcription factors that are critical for kidney development and physiology. Here we report that proximal-tubule-selective depletion of Pax2 and Pax8 protects against both acute and chronic injury and induces an expression profile in the S3 proximal tubule with common features shared among diverse conditions that protect against ischemia. These findings highlight a new role for Pax proteins as potential therapeutic targets to treat AKI.
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Lu Z, Xu S, Liao H, Zhang Y, Lu Z, Li Z, Chen Y, Guo F, Tang F, He Z. Identification of signature genes for renal ischemia‒reperfusion injury based on machine learning and WGCNA. Heliyon 2023; 9:e21151. [PMID: 37928383 PMCID: PMC10622618 DOI: 10.1016/j.heliyon.2023.e21151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/04/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Background As an inevitable event after kidney transplantation, ischemia‒reperfusion injury (IRI) can lead to a decrease in kidney transplant success. The search for signature genes of renal ischemia‒reperfusion injury (RIRI) is helpful in improving the diagnosis and guiding clinical treatment. Methods We first downloaded 3 datasets from the GEO database. Then, differentially expressed genes (DEGs) were identified and applied for functional enrichment analysis. After that, we performed three machine learning methods, including random forest (RF), Lasso regression analysis, and support vector machine recursive feature elimination (SVM-RFE), to further predict candidate genes. WGCNA was also executed to screen candidate genes from DEGs. Then, we took the intersection of candidate genes to obtain the signature genes of RIRI. Receiver operating characteristic (ROC) analysis was conducted to measure the predictive ability of the signature genes. Kaplan‒Meier analysis was used for association analysis between signature genes and graft survival. Verifying the expression of signature genes in the ischemia cell model. Results A total of 117 DEGs were screened out. Subsequently, RF, Lasso regression analysis, SVM-RFE and WGCNA identified 17, 25, 18 and 74 candidate genes, respectively. Finally, 3 signature genes (DUSP1, FOS, JUN) were screened out through the intersection of candidate genes. ROC analysis suggested that the 3 signature genes could well diagnose and predict RIRI. Kaplan‒Meier analysis indicated that patients with low FOS or JUN expression had a longer OS than those with high FOS or JUN expression. Finally, we validated using the ischemia cell model that compared to the control group, the expression level of JUN increased under hypoxic conditions. Conclusions Three signature genes (DUSP1, FOS, JUN) offer a good prediction for RIRI outcome and may serve as potential therapeutic targets for RIRI intervention, especially JUN. The prediction of graft survival by FOS and JUN may improve graft survival in patients with RIRI.
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Affiliation(s)
- Zechao Lu
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Senkai Xu
- The Sixth Clinical College of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Haiqin Liao
- The Second Clinical College of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Yixin Zhang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Clinical Research Center for Urological Diseases, Guangzhou, Guangdong, China
| | - Zeguang Lu
- The Second Clinical College of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Zhibiao Li
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Yushu Chen
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Feng Guo
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Fucai Tang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Zhaohui He
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
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Yoshikawa T, Oguchi A, Toriu N, Sato Y, Kobayashi T, Ogawa O, Haga H, Sakurai S, Yamamoto T, Murakawa Y, Yanagita M. Tertiary Lymphoid Tissues Are Microenvironments with Intensive Interactions between Immune Cells and Proinflammatory Parenchymal Cells in Aged Kidneys. J Am Soc Nephrol 2023; 34:1687-1708. [PMID: 37548710 PMCID: PMC10561819 DOI: 10.1681/asn.0000000000000202] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023] Open
Abstract
SIGNIFICANCE STATEMENT Ectopic lymphoid structures called tertiary lymphoid tissues (TLTs) develop in several kidney diseases and are associated with poor renal prognosis. However, the mechanisms underlying TLT expansion and their effect on renal regeneration remain unclear. The authors report that single-nucleus RNA sequencing and validation experiments demonstrate that TLTs potentially amplify inflammation in aged injured kidneys. Lymphocytes within TLTs promote proinflammatory phenotypes of the surrounding proximal tubules and fibroblasts within the TLTs via proinflammatory cytokine production. These proinflammatory parenchymal cells then interact with immune cells by chemokine or cytokine production. Such cell-cell interactions potentially increase inflammation, expand TLTs, and exacerbate kidney injury. These findings help illuminate renal TLT pathology and suggest potential therapeutic targets. BACKGROUND Ectopic lymphoid structures called tertiary lymphoid tissues (TLTs) develop in several kidney diseases and are associated with poor renal prognosis. However, the mechanisms that expand TLTs and underlie exacerbation of kidney injury remain unclear. METHODS We performed single-nucleus RNA sequencing (snRNA-seq) on aged mouse kidneys with TLTs after ischemia-reperfusion injury. The results were validated using immunostaining, in situ hybridization of murine and human kidneys, and in vitro experiments. RESULTS Using snRNA-seq, we identified proinflammatory and profibrotic Vcam1+ injured proximal tubules (PTs) with NF κ B and IFN-inducible transcription factor activation. VCAM1 + PTs were preferentially localized around TLTs and drove inflammation and fibrosis via the production of multiple chemokines or cytokines. Lymphocytes within TLTs expressed Tnf and Ifng at high levels, which synergistically upregulated VCAM1 and chemokine expression in cultured PT cells. In addition, snRNA-seq also identified proinflammatory and profibrotic fibroblasts, which resided within and outside TLTs, respectively. Proinflammatory fibroblasts exhibited STAT1 activation and various chemokine or cytokine production, including CXCL9/CXCL10 and B cell-activating factor, contributing to lymphocyte recruitment and survival. IFN γ upregulated the expression of these molecules in cultured fibroblasts in a STAT1-dependent manner, indicating potential bidirectional interactions between IFN γ -producing CXCR3 + T cells and proinflammatory fibroblasts within TLTs. The cellular and molecular components described in this study were confirmed in human kidneys with TLTs. CONCLUSIONS These findings suggest that TLTs potentially amplify inflammation by providing a microenvironment that allows intense interactions between renal parenchymal and immune cells. These interactions may serve as novel therapeutic targets in kidney diseases involving TLT formation.
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Affiliation(s)
- Takahisa Yoshikawa
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akiko Oguchi
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Naoya Toriu
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yuki Sato
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Kobayashi
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Ogawa
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoko Sakurai
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- IFOM-ETS, Milan, Italy
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
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De Chiara L, Semeraro R, Mazzinghi B, Landini S, Molli A, Antonelli G, Angelotti ML, Melica ME, Maggi L, Conte C, Peired AJ, Cirillo L, Raglianti V, Magi A, Annunziato F, Romagnani P, Lazzeri E. Polyploid tubular cells initiate a TGF-β1 controlled loop that sustains polyploidization and fibrosis after acute kidney injury. Am J Physiol Cell Physiol 2023; 325:C849-C861. [PMID: 37642236 PMCID: PMC10635654 DOI: 10.1152/ajpcell.00081.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Polyploidization of tubular cells (TC) is triggered by acute kidney injury (AKI) to allow survival in the early phase after AKI, but in the long run promotes fibrosis and AKI-chronic kidney disease (CKD) transition. The molecular mechanism governing the link between polyploid TC and kidney fibrosis remains to be clarified. In this study, we demonstrate that immediately after AKI, expression of cell cycle markers mostly identifies a population of DNA-damaged polyploid TC. Using transgenic mouse models and single-cell RNA sequencing we show that, unlike diploid TC, polyploid TC accumulate DNA damage and survive, eventually resting in the G1 phase of the cell cycle. In vivo and in vitro single-cell RNA sequencing along with sorting of polyploid TC shows that these cells acquire a profibrotic phenotype culminating in transforming growth factor (TGF)-β1 expression and that TGF-β1 directly promotes polyploidization. This demonstrates that TC polyploidization is a self-sustained mechanism. Interactome analysis by single-cell RNA sequencing revealed that TGF-β1 signaling fosters a reciprocal activation loop among polyploid TC, macrophages, and fibroblasts to sustain kidney fibrosis and promote CKD progression. Collectively, this study contributes to the ongoing revision of the paradigm of kidney tubule response to AKI, supporting the existence of a tubulointerstitial cross talk mediated by TGF-β1 signaling produced by polyploid TC following DNA damage.NEW & NOTEWORTHY Polyploidization in tubular epithelial cells has been neglected until recently. Here, we showed that polyploidization is a self-sustained mechanism that plays an important role during chronic kidney disease development, proving the existence of a cross talk between infiltrating cells and polyploid tubular cells. This study contributes to the ongoing revision of kidney adaptation to injury, posing polyploid tubular cells at the center of the process.
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Affiliation(s)
- Letizia De Chiara
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Roberto Semeraro
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Benedetta Mazzinghi
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Samuela Landini
- Medical Genetics Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Alice Molli
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Giulia Antonelli
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Maria Lucia Angelotti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Maria Elena Melica
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Carolina Conte
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Anna Julie Peired
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Luigi Cirillo
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Valentina Raglianti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Flow Cytometry Diagnostic Center and Immunotherapy (CDCI), Careggi University Hospital, Florence, Italy
| | - Paola Romagnani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, IRCCS, Florence, Italy
| | - Elena Lazzeri
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
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Yoshimura Y, Muto Y, Omachi K, Miner JH, Humphreys BD. Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids. J Am Soc Nephrol 2023; 34:1672-1686. [PMID: 37488681 PMCID: PMC10561821 DOI: 10.1681/asn.0000000000000197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023] Open
Abstract
SIGNIFICANCE STATEMENT HNF4 genes promote proximal tubule differentiation in mice, but their function in human nephrogenesis is not fully defined. This study uses human pluripotent stem cell (PSC)-derived kidney organoids as a model to investigate HNF4A and HNF4G functions. The loss of HNF4A , but not HNF4G , impaired reabsorption-related molecule expression and microvilli formation in human proximal tubules. Cleavage under targets and release using nuclease (CUT&RUN) sequencing and CRISPR-mediated transcriptional activation (CRISPRa) further confirm that HNF4A directly regulates its target genes. Human kidney organoids provide a good model for studying transcriptional regulation in human kidney development. BACKGROUND The proximal tubule plays a major role in electrolyte homeostasis. Previous studies have shown that HNF4A regulates reabsorption-related genes and promotes proximal tubule differentiation during murine kidney development. However, the functions and gene regulatory mechanisms of HNF4 family genes in human nephrogenesis have not yet been investigated. METHODS We generated HNF4A -knock out (KO), HNF4G -KO, and HNF4A/4G -double KO human pluripotent stem cell lines, differentiated each into kidney organoids, and used immunofluorescence analysis, electron microscopy, and RNA-seq to analyze them. We probed HNF4A-binding sites genome-wide by cleavage under targets and release using nuclease sequencing in both human adult kidneys and kidney organoid-derived proximal tubular cells. Clustered Regularly Interspaced Short Palindromic Repeats-mediated transcriptional activation validated HNF4A and HNF4G function in proximal tubules during kidney organoid differentiation. RESULTS Organoids lacking HNF4A , but not HNF4G , showed reduced expression of transport-related, endocytosis-related, and brush border-related genes, as well as disorganized brush border structure in the apical lumen of the organoid proximal tubule. Cleavage under targets and release using nuclease revealed that HNF4A primarily bound promoters and enhancers of genes that were downregulated in HNF4A -KO, suggesting direct regulation. Induced expression of HNF4A or HNF4G by CRISPR-mediated transcriptional activation drove increased expression of selected target genes during kidney organoid differentiation. CONCLUSIONS This study reveals regulatory mechanisms of HNF4A and HNF4G during human proximal tubule differentiation. The experimental strategy can be applied more broadly to investigate transcriptional regulation in human kidney development.
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Affiliation(s)
- Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Kohei Omachi
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Jeffrey H. Miner
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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Naas S, Schiffer M, Schödel J. Hypoxia and renal fibrosis. Am J Physiol Cell Physiol 2023; 325:C999-C1016. [PMID: 37661918 DOI: 10.1152/ajpcell.00201.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Renal fibrosis is the final stage of most progressive kidney diseases. Chronic kidney disease (CKD) is associated with high comorbidity and mortality. Thus, preventing fibrosis and thereby preserving kidney function increases the quality of life and prolongs the survival of patients with CKD. Many processes such as inflammation or metabolic stress modulate the progression of kidney fibrosis. Hypoxia has also been implicated in the pathogenesis of renal fibrosis, and oxygen sensing in the kidney is of outstanding importance for the body. The dysregulation of oxygen sensing in the diseased kidney is best exemplified by the loss of stimulation of erythropoietin production from interstitial cells in the fibrotic kidney despite anemia. Furthermore, hypoxia is present in acute or chronic kidney diseases and may affect all cell types present in the kidney including tubular and glomerular cells as well as resident immune cells. Pro- and antifibrotic effects of the transcription factors hypoxia-inducible factors 1 and 2 have been described in a plethora of animal models of acute and chronic kidney diseases, but recent advances in sequencing technologies now allow for novel and deeper insights into the role of hypoxia and its cell type-specific effects on the progression of renal fibrosis, especially in humans. Here, we review existing literature on how hypoxia impacts the development and progression of renal fibrosis.
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Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Dai Y, Chen Y, Mo D, Jin R, Huang Y, Zhang L, Zhang C, Gao H, Yan Q. Inhibition of ACSL4 ameliorates tubular ferroptotic cell death and protects against fibrotic kidney disease. Commun Biol 2023; 6:907. [PMID: 37670055 PMCID: PMC10480178 DOI: 10.1038/s42003-023-05272-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Ferroptosis is a recently recognized form of regulated cell death, characterized by iron-dependent accumulation of lipid peroxidation. Ample evidence has depicted that ferroptosis plays an essential role in the cause or consequence of human diseases, including cancer, neurodegenerative disease and acute kidney injury. However, the exact role and underlying mechanism of ferroptosis in fibrotic kidney remain unknown. Acyl-CoA synthetase long-chain family member 4 (ACSL4) has been demonstrated as an essential component in ferroptosis execution by shaping lipid composition. In this study, we aim to discuss the potential role and underlying mechanism of ACSL4-mediated ferroptosis of tubular epithelial cells (TECs) during renal fibrosis. The unbiased gene expression studies showed that ACSL4 expression was tightly associated with decreased renal function and the progression of renal fibrosis. To explore the role of ACSL4 in fibrotic kidney, ACSL4 specific inhibitor rosiglitazone (ROSI) was used to disturb the high expression of ACSL4 in TECs induced by TGF-β, unilateral ureteral obstruction (UUO) and fatty acid (FA)-modeled mice in vivo, and ACSL4 siRNA was used to knockdown ACSL4 in TGF-β-induced HK2 cells in vitro. The results demonstrated that inhibition and knockdown of ACSL4 effectively attenuated the occurrence of ferroptosis in TECs and alleviated the interstitial fibrotic response. In addition, the expression of various profibrotic cytokines all decreased after ROSI-treated in vivo and in vitro. Further investigation showed that inhibition of ACSL4 obviously attenuates the progression of renal fibrosis by reducing the proferroptotic precursors arachidonic acid- and adrenic acid- containing phosphatidylethanolamine (AA-PE and AdA-PE). In conclusion, these results suggest ACSL4 is essential for tubular ferroptotic death during kidney fibrosis development and ACSL4 inhibition is a viable therapeutic approach to preventing fibrotic kidney diseases.
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Affiliation(s)
- Yue Dai
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuting Chen
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dexiameng Mo
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Jin
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Huang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Le Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongyu Gao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Qi Yan
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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40
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Canela VH, Bowen WS, Ferreira RM, Syed F, Lingeman JE, Sabo AR, Barwinska D, Winfree S, Lake BB, Cheng YH, Gaut JP, Ferkowicz M, LaFavers KA, Zhang K, Coe FL, Worcester E, Jain S, Eadon MT, Williams JC, El-Achkar TM. A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. Nat Commun 2023; 14:4140. [PMID: 37468493 PMCID: PMC10356953 DOI: 10.1038/s41467-023-38975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/24/2023] [Indexed: 07/21/2023] Open
Abstract
Kidney stone disease causes significant morbidity and increases health care utilization. In this work, we decipher the cellular and molecular niche of the human renal papilla in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.
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Affiliation(s)
- Victor Hugo Canela
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - William S Bowen
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ricardo Melo Ferreira
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Farooq Syed
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James E Lingeman
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Angela R Sabo
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Daria Barwinska
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Seth Winfree
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Blue B Lake
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Ying-Hua Cheng
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University, St. Louis, MO, USA
| | - Michael Ferkowicz
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kaice A LaFavers
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kun Zhang
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Fredric L Coe
- Department of Medicine, Division of Nephrology, University of Chicago, Chicago, IL, USA
| | - Elaine Worcester
- Department of Medicine, Division of Nephrology, University of Chicago, Chicago, IL, USA
| | - Sanjay Jain
- Department of Medicine, Division of Nephrology, Washington University, St. Louis, MO, USA.
| | - Michael T Eadon
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - James C Williams
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Tarek M El-Achkar
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Indianapolis VA Medical Center, Indianapolis, IN, USA.
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41
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Bhatia D, Choi ME. Autophagy and mitophagy: physiological implications in kidney inflammation and diseases. Am J Physiol Renal Physiol 2023; 325:F1-F21. [PMID: 37167272 PMCID: PMC10292977 DOI: 10.1152/ajprenal.00012.2023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023] Open
Abstract
Autophagy is a ubiquitous intracellular cytoprotective quality control program that maintains cellular homeostasis by recycling superfluous cytoplasmic components (lipid droplets, protein, or glycogen aggregates) and invading pathogens. Mitophagy is a selective form of autophagy that by recycling damaged mitochondrial material, which can extracellularly act as damage-associated molecular patterns, prevents their release. Autophagy and mitophagy are indispensable for the maintenance of kidney homeostasis and exert crucial functions during both physiological and disease conditions. Impaired autophagy and mitophagy can negatively impact the pathophysiological state and promote its progression. Autophagy helps in maintaining structural integrity of the kidney. Mitophagy-mediated mitochondrial quality control is explicitly critical for regulating cellular homeostasis in the kidney. Both autophagy and mitophagy attenuate inflammatory responses in the kidney. An accumulating body of evidence highlights that persistent kidney injury-induced oxidative stress can contribute to dysregulated autophagic and mitophagic responses and cell death. Autophagy and mitophagy also communicate with programmed cell death pathways (apoptosis and necroptosis) and play important roles in cell survival by preventing nutrient deprivation and regulating oxidative stress. Autophagy and mitophagy are activated in the kidney after acute injury. However, their aberrant hyperactivation can be deleterious and cause tissue damage. The findings on the functions of autophagy and mitophagy in various models of chronic kidney disease are heterogeneous and cell type- and context-specific dependent. In this review, we discuss the roles of autophagy and mitophagy in the kidney in regulating inflammatory responses and during various pathological manifestations.
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Affiliation(s)
- Divya Bhatia
- Division of Nephrology and Hypertension, Joan and Sanford I. Weill Department of Medicine, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, New York, United States
| | - Mary E Choi
- Division of Nephrology and Hypertension, Joan and Sanford I. Weill Department of Medicine, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, New York, United States
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42
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Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB, Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S. An atlas of healthy and injured cell states and niches in the human kidney. Nature 2023; 619:585-594. [PMID: 37468583 PMCID: PMC10356613 DOI: 10.1038/s41586-023-05769-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/30/2023] [Indexed: 07/21/2023]
Abstract
Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
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Affiliation(s)
- Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Seth Winfree
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ricardo Melo Ferreira
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kian Kalhor
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Daria Barwinska
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edgar A Otto
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Michael Ferkowicz
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sarah Urata
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit S Naik
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Bo Zhang
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Yan Wu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Diane Salamon
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James C Williams
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xin Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Paul J Hoover
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Teia Noel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anitha Vijayan
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Sylvia E Rosas
- Kidney and Hypertension Unit, Joslin Diabetes Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Francis P Wilson
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Paul M Palevsky
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - John R Sedor
- Lerner Research and Glickman Urology and Kidney Institutes, Cleveland Clinic, Cleveland, OH, USA
| | - Robert D Toto
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eric H Kim
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | | | - Anna Greka
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael T Eadon
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Pierre C Dagher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Tarek M El-Achkar
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA.
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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43
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Cippà PE, McMahon AP. Proximal tubule responses to injury: interrogation by single-cell transcriptomics. Curr Opin Nephrol Hypertens 2023; 32:352-358. [PMID: 37074682 PMCID: PMC10330172 DOI: 10.1097/mnh.0000000000000893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
PURPOSE OF REVIEW Acute kidney injury (AKI) occurs in approximately 10-15% of patients admitted to hospital and is associated with adverse clinical outcomes. Despite recent advances, management of patients with AKI is still mainly supportive, including the avoidance of nephrotoxins, volume and haemodynamic management and renal replacement therapy. A better understanding of the renal response to injury is the prerequisite to overcome current limitations in AKI diagnostics and therapy. RECENT FINDINGS Single-cell technologies provided new opportunities to study the complexity of the kidney and have been instrumental for rapid advancements in the understanding of the cellular and molecular mechanisms of AKI. SUMMARY We provide an update on single-cell technologies and we summarize the recent discoveries on the cellular response to injury in proximal tubule cells from the early response in AKI, to the mechanisms of tubule repair and the relevance of maladaptive tubule repair in the transition to chronic kidney disease.
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Affiliation(s)
- Pietro E Cippà
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculity of Biomedical Sciences, Università della Svizzera Italiana, Lugano Switzerland
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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44
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McDaniels JM, Shetty AC, Kuscu C, Kuscu C, Bardhi E, Rousselle T, Drachenberg C, Talwar M, Eason JD, Muthukumar T, Maluf DG, Mas VR. Single nuclei transcriptomics delineates complex immune and kidney cell interactions contributing to kidney allograft fibrosis. Kidney Int 2023; 103:1077-1092. [PMID: 36863444 PMCID: PMC10200746 DOI: 10.1016/j.kint.2023.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 03/04/2023]
Abstract
Chronic allograft dysfunction (CAD), characterized histologically by interstitial fibrosis and tubular atrophy, is the major cause of kidney allograft loss. Here, using single nuclei RNA sequencing and transcriptome analysis, we identified the origin, functional heterogeneity, and regulation of fibrosis-forming cells in kidney allografts with CAD. A robust technique was used to isolate individual nuclei from kidney allograft biopsies and successfully profiled 23,980 nuclei from five kidney transplant recipients with CAD and 17,913 nuclei from three patients with normal allograft function. Our analysis revealed two distinct states of fibrosis in CAD; low and high extracellular matrix (ECM) with distinct kidney cell subclusters, immune cell types, and transcriptional profiles. Imaging mass cytometry analysis confirmed increased ECM deposition at the protein level. Proximal tubular cells transitioned to an injured mixed tubular (MT1) phenotype comprised of activated fibroblasts and myofibroblast markers, generated provisional ECM which recruited inflammatory cells, and served as the main driver of fibrosis. MT1 cells in the high ECM state achieved replicative repair evidenced by dedifferentiation and nephrogenic transcriptional signatures. MT1 in the low ECM state showed decreased apoptosis, decreased cycling tubular cells, and severe metabolic dysfunction, limiting the potential for repair. Activated B, T and plasma cells were increased in the high ECM state, while macrophage subtypes were increased in the low ECM state. Intercellular communication between kidney parenchymal cells and donor-derived macrophages, detected several years post-transplantation, played a key role in injury propagation. Thus, our study identified novel molecular targets for interventions aimed to ameliorate or prevent allograft fibrogenesis in kidney transplant recipients.
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Affiliation(s)
- Jennifer M McDaniels
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Elissa Bardhi
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Thomas Rousselle
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cinthia Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Manish Talwar
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - James D Eason
- Transplant Research Institute, James D. Eason Transplant Institute, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Daniel G Maluf
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA; Program in Transplantation, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Valeria R Mas
- Division of Surgical Sciences, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.
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45
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An P, Sáenz Robles MT, Cantalupo PG, Naik AS, Sealfon R, Imperiale MJ, Pipas JM. Cultured Renal Proximal Tubular Epithelial Cells Resemble a Stressed/Damaged Kidney While Supporting BK Virus Infection. J Virol 2023; 97:e0034323. [PMID: 37166336 PMCID: PMC10231206 DOI: 10.1128/jvi.00343-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/22/2023] [Indexed: 05/12/2023] Open
Abstract
BK virus (BKV; human polyomavirus 1) infections are asymptomatic in most individuals, and the virus persists throughout life without harm. However, BKV is a threat to transplant patients and those with immunosuppressive disorders. Under these circumstances, the virus can replicate robustly in proximal tubule epithelial cells (PT). Cultured renal proximal tubule epithelial cells (RPTE) are permissive to BKV and have been used extensively to characterize different aspects of BKV infection. Recently, lines of hTERT-immortalized RPTE have become available, and preliminary studies indicate they support BKV infection as well. Our results indicate that BKV infection leads to a similar response in primary and immortalized RPTE. In addition, we examined the patterns of global gene expression of primary and immortalized RPTE and compared them with uncultured PT freshly dissociated from human kidney. As expected, PT isolated from the healthy kidney express a number of differentiation-specific genes that are associated with kidney function. However, the expression of most of these genes is absent or repressed in cultured RPTE. Rather, cultured RPTE exhibit a gene expression profile indicative of a stressed or injured kidney. Inoculation of cultured RPTE with BKV results in the suppression of many genes associated with kidney stress. In summary, this study demonstrated similar global gene expression patterns and responses to BKV infection between primary and immortalized RPTE. Moreover, results from bulk transcriptome sequencing (RNA-seq) and SCT experiments revealed distinct transcriptomic signatures representing cell injury and stress in primary RPTE in contrast to the uncultured, freshly dissociated PT from human kidney. IMPORTANCE Cultured primary human cells provide powerful tools for the study of viral infectious cycles and host virus interactions. In the case of BKV-associated nephropathy, viral replication occurs primarily in the proximal tubule epithelia in the kidney. Consequently, cultured primary and immortalized renal proximal tubule epithelial cells (RPTE) are widely used to study BKV infection. In this work, using bulk and single-cell transcriptomics, we found that primary and immortalized RPTE responded similarly to BKV infection. However, both uninfected primary and immortalized RPTE have gene expression profiles that are markedly different from healthy proximal tubule epithelia isolated directly from human kidney without culture. Cultured RPTE are in a gene expression state indicative of an injured or stressed kidney. These results raise the possibility that BKV replicates preferentially in injured or stressed kidney epithelial cells during nephropathy.
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Affiliation(s)
- Ping An
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Paul G. Cantalupo
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Abhijit S. Naik
- Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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46
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O'Sullivan ED, Mylonas KJ, Xin C, Baird DP, Carvalho C, Docherty MH, Campbell R, Matchett KP, Waddell SH, Walker AD, Gallagher KM, Jia S, Leung S, Laird A, Wilflingseder J, Willi M, Reck M, Finnie S, Pisco A, Gordon-Keylock S, Medvinsky A, Boulter L, Henderson NC, Kirschner K, Chandra T, Conway BR, Hughes J, Denby L, Bonventre JV, Ferenbach DA. Indian Hedgehog release from TNF-activated renal epithelia drives local and remote organ fibrosis. Sci Transl Med 2023; 15:eabn0736. [PMID: 37256934 DOI: 10.1126/scitranslmed.abn0736] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Progressive fibrosis is a feature of aging and chronic tissue injury in multiple organs, including the kidney and heart. Glioma-associated oncogene 1 expressing (Gli1+) cells are a major source of activated fibroblasts in multiple organs, but the links between injury, inflammation, and Gli1+ cell expansion and tissue fibrosis remain incompletely understood. We demonstrated that leukocyte-derived tumor necrosis factor (TNF) promoted Gli1+ cell proliferation and cardiorenal fibrosis through induction and release of Indian Hedgehog (IHH) from renal epithelial cells. Using single-cell-resolution transcriptomic analysis, we identified an "inflammatory" proximal tubular epithelial (iPT) population contributing to TNF- and nuclear factor κB (NF-κB)-induced IHH production in vivo. TNF-induced Ubiquitin D (Ubd) expression was observed in human proximal tubular cells in vitro and during murine and human renal disease and aging. Studies using pharmacological and conditional genetic ablation of TNF-induced IHH signaling revealed that IHH activated canonical Hedgehog signaling in Gli1+ cells, which led to their activation, proliferation, and fibrosis within the injured and aging kidney and heart. These changes were inhibited in mice by Ihh deletion in Pax8-expressing cells or by pharmacological blockade of TNF, NF-κB, or Gli1 signaling. Increased amounts of circulating IHH were associated with loss of renal function and higher rates of cardiovascular disease in patients with chronic kidney disease. Thus, IHH connects leukocyte activation to Gli1+ cell expansion and represents a potential target for therapies to inhibit inflammation-induced fibrosis.
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Affiliation(s)
- Eoin D O'Sullivan
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia
| | - Katie J Mylonas
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Cuiyan Xin
- Renal Division and Division of Engineering in Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David P Baird
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Cyril Carvalho
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Marie-Helena Docherty
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Ross Campbell
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Kylie P Matchett
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Scott H Waddell
- Cancer Research UK Scotland Centre and MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alexander D Walker
- Cancer Research UK Scotland Centre and MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Kevin M Gallagher
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Department of Urology, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Siyang Jia
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Steve Leung
- Department of Urology, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Alexander Laird
- Department of Urology, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Julia Wilflingseder
- Renal Division and Division of Engineering in Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Physiology and Pathophysiology, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Michaela Willi
- Laboratory of Genetics and Physiology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Maximilian Reck
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Sarah Finnie
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Angela Pisco
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Alexander Medvinsky
- Centre for Regenerative Medicine. University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Luke Boulter
- Cancer Research UK Scotland Centre and MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neil C Henderson
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Cancer Research UK Scotland Centre and MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Kristina Kirschner
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Tamir Chandra
- Cancer Research UK Scotland Centre and MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bryan R Conway
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Jeremy Hughes
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Laura Denby
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Joseph V Bonventre
- Renal Division and Division of Engineering in Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David A Ferenbach
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Renal Division and Division of Engineering in Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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47
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Nakai K, Umehara M, Minamida A, Yamauchi-Sawada H, Sunahara Y, Matoba Y, Okuno-Ozeki N, Nakamura I, Nakata T, Yagi-Tomita A, Uehara-Watanabe N, Ida T, Yamashita N, Kamezaki M, Kirita Y, Konishi E, Yasuda H, Matoba S, Tamagaki K, Kusaba T. Streptozotocin induces renal proximal tubular injury through p53 signaling activation. Sci Rep 2023; 13:8705. [PMID: 37248327 DOI: 10.1038/s41598-023-35850-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/24/2023] [Indexed: 05/31/2023] Open
Abstract
Streptozotocin (STZ), an anti-cancer drug that is primarily used to treat neuroendocrine tumors (NETs) in clinical settings, is incorporated into pancreatic β-cells or proximal tubular epithelial cells through the glucose transporter, GLUT2. However, its cytotoxic effects on kidney cells have been underestimated and the underlying mechanisms remain unclear. We herein demonstrated that DNA damage and subsequent p53 signaling were responsible for the development of STZ-induced tubular epithelial injury. We detected tubular epithelial DNA damage in NET patients treated with STZ. Unbiased transcriptomics of STZ-treated tubular epithelial cells in vitro showed the activation of the p53 signaling pathway. STZ induced DNA damage and activated p53 signaling in vivo in a dose-dependent manner, resulting in reduced membrane transporters. The pharmacological inhibition of p53 and sodium-glucose transporter 2 (SGLT2) mitigated STZ-induced epithelial injury. However, the cytotoxic effects of STZ on pancreatic β-cells were preserved in SGLT2 inhibitor-treated mice. The present results demonstrate the proximal tubular-specific cytotoxicity of STZ and the underlying mechanisms in vivo. Since the cytotoxic effects of STZ against β-cells were not impaired by dapagliflozin, pretreatment with an SGLT2 inhibitor has potential as a preventative remedy for kidney injury in NET patients treated with STZ.
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Affiliation(s)
- Kunihiro Nakai
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Minato Umehara
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Atsushi Minamida
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hiroko Yamauchi-Sawada
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yasuto Sunahara
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yayoi Matoba
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Natsuko Okuno-Ozeki
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Itaru Nakamura
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomohiro Nakata
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Aya Yagi-Tomita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Noriko Uehara-Watanabe
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomoharu Ida
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Noriyuki Yamashita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Michitsugu Kamezaki
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Eiichi Konishi
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroaki Yasuda
- Department of Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Keiichi Tamagaki
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tetsuro Kusaba
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan.
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48
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539585. [PMID: 37205355 PMCID: PMC10187285 DOI: 10.1101/2023.05.06.539585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA-seq data demonstrated sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR) mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation while analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, and disease and metabolic linkage, of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Lead Contact
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49
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Zhang Y, Yang Y, Yang F, Liu X, Zhan P, Wu J, Wang X, Wang Z, Tang W, Sun Y, Zhang Y, Xu Q, Shang J, Zhen J, Liu M, Yi F. HDAC9-mediated epithelial cell cycle arrest in G2/M contributes to kidney fibrosis in male mice. Nat Commun 2023; 14:3007. [PMID: 37230975 DOI: 10.1038/s41467-023-38771-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Renal tubular epithelial cells (TECs) play a key role in kidney fibrosis by mediating cycle arrest at G2/M. However, the key HDAC isoforms and the underlying mechanism that are involved in G2/M arrest of TECs remain unclear. Here, we find that Hdac9 expression is significantly induced in the mouse fibrotic kidneys, especially in proximal tubules, induced by aristolochic acid nephropathy (AAN) or unilateral ureter obstruction (UUO). Tubule-specific deletion of HDAC9 or pharmacological inhibition by TMP195 attenuates epithelial cell cycle arrest in G2/M, then reduces production of profibrotic cytokine and alleviates tubulointerstitial fibrosis in male mice. In vitro, knockdown or inhibition of HDAC9 alleviates the loss of epithelial phenotype in TECs and attenuates fibroblasts activation through inhibiting epithelial cell cycle arrest in G2/M. Mechanistically, HDAC9 deacetylates STAT1 and promotes its reactivation, followed by inducing G2/M arrest of TECs, finally leading to tubulointerstitial fibrosis. Collectively, our studies indicate that HDAC9 may be an attractive therapeutic target for kidney fibrosis.
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Affiliation(s)
- Yang Zhang
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Yujie Yang
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Fan Yang
- Department of Neurosurgery, Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Xiaohan Liu
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Ping Zhan
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Jichao Wu
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Xiaojie Wang
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Ziying Wang
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Wei Tang
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Yu Sun
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Yan Zhang
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Qianqian Xu
- Department of Organ Transplantation, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jin Shang
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Junhui Zhen
- Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Min Liu
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China.
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China.
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50
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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. RESEARCH SQUARE 2023:rs.3.rs-2880248. [PMID: 37293022 PMCID: PMC10246229 DOI: 10.21203/rs.3.rs-2880248/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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