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Janosevic D, De Luca T, Eadon MT. The Kidney Precision Medicine Project and Single-Cell Biology of the Injured Proximal Tubule. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00361-4. [PMID: 39332674 DOI: 10.1016/j.ajpath.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/29/2024] [Accepted: 09/11/2024] [Indexed: 09/29/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has led to major advances in our understanding of proximal tubule subtypes in health and disease. The proximal tubule serves essential functions in overall homeostasis, but pathologic or physiologic perturbations can affect its transcriptomic signature and corresponding tasks. These alterations in proximal tubular cells are often described within a scRNA-seq atlas as cell states, which are pathophysiologic subclassifications based on molecular and morphological changes in a cell's response to that injury compared to its native state. This review describes the major cell states defined in the Kidney Precision Medicine Project's (KPMP) scRNA-seq atlas. The review then identifies the overlap between KPMP and other seminal works which may use different nomenclature or cluster proximal tubule cells at different resolutions to define cell state subtypes. The goal is for the reader to understand the key transcriptomic markers of important cellular injury and regeneration processes across this highly dynamic and evolving field.
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Affiliation(s)
- Danielle Janosevic
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Thomas De Luca
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Michael T Eadon
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202.
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2
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Rinaldi A, Cippà PE, Nemazanyy I, Anglicheau D, Pallet N. Taurine Deficiency Is a Hallmark of Injured Kidney Allografts. Transplantation 2024; 108:e218-e228. [PMID: 39167563 DOI: 10.1097/tp.0000000000004987] [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] [Indexed: 03/21/2024]
Abstract
BACKGROUND Taurine is one of the most abundant amino acids in humans. Low taurine levels are associated with cellular senescence, mitochondrial dysfunction, DNA damage, and inflammation in mouse, all of which can be reversed by supplementation. It is unknown whether taurine metabolism is associated with kidney allograft function and survival. METHODS We performed urine metabolomic profiling of kidney transplant recipients in the early and late phases after transplantation combined with transcriptomic analysis of human kidney allografts. Single-nucleus RNA sequencing data sets of mouse kidneys after ischemia-reperfusion injury were analyzed. We analyzed the association of urinary taurine levels and taurine metabolism genes with kidney function, histology, and graft survival. RESULTS Urine taurine concentrations were significantly lower in kidney transplant recipients who experienced delayed graft function. In a mouse model of ischemia-reperfusion injury, the taurine biosynthesis gene, CSAD , but not the taurine transporter SLC6A6 , was repressed. In the late stage of transplantation, low level of taurine in urine was associated with impaired kidney function and chronic structural changes. Urine taurine level in the lowest tertile was predictive of graft loss. Expression of the taurine transporter SLC6A6 in the upper median, but not CSAD , was associated with chronic kidney injury and was predictive of graft loss. CONCLUSIONS Low urine taurine level is a marker of injury in the kidney allograft, is associated with poor kidney function, is associated with chronic histological changes, and is predictive of graft survival. The differential expression of CSAD and SLC6A6 , depending on the time after transplantation and marks of injury, highlights different mechanisms affecting taurine metabolism.
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Affiliation(s)
- Anna Rinaldi
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Pietro E Cippà
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Ivan Nemazanyy
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, Institut National de la Santé et de la Recherche Médicale (INSERM) US24/CNRS UMS3633, Paris, France
| | - Dany Anglicheau
- INSERM U1151, Université Paris Cité, Paris, France
- Service de Néphrologie et Transplantation, Assistance Publique Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Nicolas Pallet
- Service de Biochimie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
- Université de Paris, INSERM UMRS1138, Centre de Recherche des Cordeliers, Paris, France
- Service de Néphrologie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
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3
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Beamish JA, Watts JA, Dressler GR. Gene regulation in regeneration after acute kidney injury. J Biol Chem 2024; 300:107520. [PMID: 38950862 PMCID: PMC11325799 DOI: 10.1016/j.jbc.2024.107520] [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: 06/03/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/03/2024] Open
Abstract
Acute kidney injury (AKI) is a common condition associated with significant morbidity, mortality, and cost. Injured kidney tissue can regenerate after many forms of AKI. However, there are no treatments in routine clinical practice to encourage recovery. In part, this shortcoming is due to an incomplete understanding of the genetic mechanisms that orchestrate kidney recovery. The advent of high-throughput sequencing technologies and genetic mouse models has opened an unprecedented window into the transcriptional dynamics that accompany both successful and maladaptive repair. AKI recovery shares similar cell-state transformations with kidney development, which can suggest common mechanisms of gene regulation. Several powerful bioinformatic strategies have been developed to infer the activity of gene regulatory networks by combining multiple forms of sequencing data at single-cell resolution. These studies highlight not only shared stress responses but also key changes in gene regulatory networks controlling metabolism. Furthermore, chromatin immunoprecipitation studies in injured kidneys have revealed dynamic epigenetic modifications at enhancer elements near target genes. This review will highlight how these studies have enhanced our understanding of gene regulation in injury response and regeneration.
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Affiliation(s)
- Jeffrey A Beamish
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason A Watts
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Gregory R Dressler
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
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4
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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] [Grants] [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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5
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Guo S, Dong Y, Du R, Liu YX, Liu S, Wang Q, Liu JS, Xu H, Jiang YJ, Hao H, Fan LL, Xiang R. Single-cell transcriptomic profiling reveals decreased ER protein Reticulon3 drives the progression of renal fibrosis. MOLECULAR BIOMEDICINE 2024; 5:24. [PMID: 38937317 PMCID: PMC11211315 DOI: 10.1186/s43556-024-00187-x] [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: 03/13/2024] [Accepted: 05/17/2024] [Indexed: 06/29/2024] Open
Abstract
Chronic kidney disease (CKD) poses a significant global health dilemma, emerging from complex causes. Although our prior research has indicated that a deficiency in Reticulon-3 (RTN3) accelerates renal disease progression, a thorough examination of RTN3 on kidney function and pathology remains underexplored. To address this critical need, we generated Rtn3-null mice to study the consequences of RTN3 protein deficiency on CKD. Single-cell transcriptomic analyses were performed on 47,885 cells from the renal cortex of both healthy and Rtn3-null mice, enabling us to compare spatial architectures and expression profiles across 14 distinct cell types. Our analysis revealed that RTN3 deficiency leads to significant alterations in the spatial organization and gene expression profiles of renal cells, reflecting CKD pathology. Specifically, RTN3 deficiency was associated with Lars2 overexpression, which in turn caused mitochondrial dysfunction and increased reactive oxygen species levels. This shift induced a transition in renal epithelial cells from a functional state to a fibrogenic state, thus promoting renal fibrosis. Additionally, RTN3 deficiency was found to drive the endothelial-to-mesenchymal transition process and disrupt cell-cell communication, further exacerbating renal fibrosis. Immunohistochemistry and Western-Blot techniques were used to validate these observations, reinforcing the critical role of RTN3 in CKD pathogenesis. The deficiency of RTN3 protein in CKD leads to profound changes in cellular architecture and molecular profiles. Our work seeks to elevate the understanding of RTN3's role in CKD's narrative and position it as a promising therapeutic contender.
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Affiliation(s)
- Shuai Guo
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Cell Biology, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yi Dong
- Department of Cell Biology, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ran Du
- Department of Cell Biology, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yu-Xing Liu
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Shu Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Qin Wang
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ji-Shi Liu
- Department of Nephrology, The third Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center For Critical Kidney Disease In Hunan Province, Changsha, China
| | - Hui Xu
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yu-Jie Jiang
- Department of Cell Biology, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, USA
| | - Huang Hao
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.
| | - Liang-Liang Fan
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- Department of Cell Biology, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
| | - Rong Xiang
- Department of Nephrology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
- Department of Cell Biology, Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.
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6
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Yaffe HC, von Ahrens D, Urioste A, Mas VR, Akalin E. Impact of Deceased-donor Acute Kidney Injury on Kidney Transplantation. Transplantation 2024; 108:1283-1295. [PMID: 37990359 DOI: 10.1097/tp.0000000000004848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Even as record numbers of deceased donors are undergoing organ recovery, the global transplant community continues to struggle with a shortage of donor organs and a high organ discard rate. Acute kidney injury (AKI) occurs in many hospitalized patients, including up to 25% of patients in critical condition. Registry studies have shown a significant increase in nonrecovery or organ discard rates in AKI donors, despite most studies reporting similar clinical outcomes compared with non-AKI donors. This review aims to capture the salient information learned from these studies and to summarize the efforts that have been made to gain a more granular understanding of how kidneys from donors with AKI behave posttransplant. In particular, we reviewed the studies that analyzed the clinical outcomes in different stages of AKI and AKI in marginal donors, such as kidney donor profile index of >85%, older donors, and donation after circulatory death donors. We summarized studies investigating molecular biomarkers, transcriptomics, and possible future therapeutic targets for postdonation AKI.
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Affiliation(s)
- Hillary C Yaffe
- Montefiore Einstein Center for Transplantation, Department of Surgery, Montefiore Medical Center, Bronx, NY
- Albert Einstein College of Medicine, Bronx, NY
| | - Dagny von Ahrens
- Montefiore Einstein Center for Transplantation, Department of Surgery, Montefiore Medical Center, Bronx, NY
- Albert Einstein College of Medicine, Bronx, NY
| | - Alejandra Urioste
- Surgical Sciences Division, University of Maryland School of Medicine, Baltimore, MD
| | - Valeria R Mas
- Surgical Sciences Division, University of Maryland School of Medicine, Baltimore, MD
| | - Enver Akalin
- Albert Einstein College of Medicine, Bronx, NY
- Montefiore Einstein Center for Transplantation, Department of Medicine, Montefiore Medical Center, Bronx, NY
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7
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Liu Y, Wang Y, Xu C, Zhang Y, Wang Y, Qin J, Lan HY, Wang L, Huang Y, Mak KK, Zheng Z, Xia Y. Activation of the YAP/KLF5 transcriptional cascade in renal tubular cells aggravates kidney injury. Mol Ther 2024; 32:1526-1539. [PMID: 38414248 PMCID: PMC11081877 DOI: 10.1016/j.ymthe.2024.02.031] [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: 09/13/2023] [Revised: 01/11/2024] [Accepted: 02/24/2024] [Indexed: 02/29/2024] Open
Abstract
The Hippo/YAP pathway plays a critical role in tissue homeostasis. Our previous work demonstrated that renal tubular YAP activation induced by double knockout (dKO) of the upstream Hippo kinases Mst1 and Mst2 promotes tubular injury and renal inflammation under basal conditions. However, the importance of tubular YAP activation remains to be established in injured kidneys in which many other injurious pathways are simultaneously activated. Here, we show that tubular YAP was already activated 6 h after unilateral ureteral obstruction (UUO). Tubular YAP deficiency greatly attenuated tubular cell overproliferation, tubular injury, and renal inflammation induced by UUO or cisplatin. YAP promoted the transcription of the transcription factor KLF5. Consistent with this, the elevated expression of KLF5 and its target genes in Mst1/2 dKO or UUO kidneys was blocked by ablation of Yap in tubular cells. Inhibition of KLF5 prevented tubular cell overproliferation, tubular injury, and renal inflammation in Mst1/2 dKO kidneys. Therefore, our results demonstrate that tubular YAP is a key player in kidney injury. YAP and KLF5 form a transcriptional cascade, where tubular YAP activation induced by kidney injury promotes KLF5 transcription. Activation of this cascade induces tubular cell overproliferation, tubular injury, and renal inflammation.
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Affiliation(s)
- Yang Liu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Department of Nephrology, Center of Nephrology and Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yu Wang
- Department of Endocrinology and Metabolism, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Chunhua Xu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yu Zhang
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yang Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jinzhong Qin
- The Key Laboratory of Model Animal for Disease Study of the Ministry of Education, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China; Guangdong-Hong Kong Joint Laboratory for Immune and Genetic Kidney Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Kingston Kinglun Mak
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
| | - Zhihua Zheng
- Department of Nephrology, Center of Nephrology and Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.
| | - Yin Xia
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Guangdong-Hong Kong Joint Laboratory for Immune and Genetic Kidney Disease, The Chinese University of Hong Kong, Hong Kong, China; Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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8
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Heeger PS, Haro MC, Jordan S. Translating B cell immunology to the treatment of antibody-mediated allograft rejection. Nat Rev Nephrol 2024; 20:218-232. [PMID: 38168662 DOI: 10.1038/s41581-023-00791-0] [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] [Accepted: 11/10/2023] [Indexed: 01/05/2024]
Abstract
Antibody-mediated rejection (AMR), including chronic AMR (cAMR), causes ~50% of kidney allograft losses each year. Despite attempts to develop well-tolerated and effective therapeutics for the management of AMR, to date, none has obtained FDA approval, thereby highlighting an urgent unmet medical need. Discoveries over the past decade from basic, translational and clinical studies of transplant recipients have provided a foundation for developing novel therapeutic approaches to preventing and treating AMR and cAMR. These interventions are aimed at reducing donor-specific antibody levels, decreasing graft injury and fibrosis, and preserving kidney function. Innovative approaches emerging from basic science findings include targeting interactions between alloreactive T cells and B cells, and depleting alloreactive memory B cells, as well as donor-specific antibody-producing plasmablasts and plasma cells. Therapies aimed at reducing the cytotoxic antibody effector functions mediated by natural killer cells and the complement system, and their associated pro-inflammatory cytokines, are also undergoing evaluation. The complexity of the pathogenesis of AMR and cAMR suggest that multiple approaches will probably be required to treat these disease processes effectively. Definitive answers await results from large, double-blind, multicentre, randomized controlled clinical trials.
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Affiliation(s)
- Peter S Heeger
- Comprehensive Transplant Center, Department of Medicine, Division of Nephrology Cedars-Sinai Medical Center Los Angeles, Los Angeles, CA, USA
| | - Maria Carrera Haro
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA
| | - Stanley Jordan
- Comprehensive Transplant Center, Department of Medicine, Division of Nephrology Cedars-Sinai Medical Center Los Angeles, Los Angeles, CA, USA.
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9
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Lundy DJ, Szomolay B, Liao CT. Systems Approaches to Cell Culture-Derived Extracellular Vesicles for Acute Kidney Injury Therapy: Prospects and Challenges. FUNCTION 2024; 5:zqae012. [PMID: 38706963 PMCID: PMC11065115 DOI: 10.1093/function/zqae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 05/07/2024] Open
Abstract
Acute kidney injury (AKI) is a heterogeneous syndrome, comprising diverse etiologies of kidney insults that result in high mortality and morbidity if not well managed. Although great efforts have been made to investigate underlying pathogenic mechanisms of AKI, there are limited therapeutic strategies available. Extracellular vesicles (EV) are membrane-bound vesicles secreted by various cell types, which can serve as cell-free therapy through transfer of bioactive molecules. In this review, we first overview the AKI syndrome and EV biology, with a particular focus on the technical aspects and therapeutic application of cell culture-derived EVs. Second, we illustrate how multi-omic approaches to EV miRNA, protein, and genomic cargo analysis can yield new insights into their mechanisms of action and address unresolved questions in the field. We then summarize major experimental evidence regarding the therapeutic potential of EVs in AKI, which we subdivide into stem cell and non-stem cell-derived EVs. Finally, we highlight the challenges and opportunities related to the clinical translation of animal studies into human patients.
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Affiliation(s)
- David J Lundy
- Graduate Institute of Biomedical Materials & Tissue Engineering, Taipei Medical University, Taipei 235603, Taiwan
- International PhD Program in Biomedical Engineering, Taipei Medical University, Taipei 235603, Taiwan
- Center for Cell Therapy, Taipei Medical University Hospital, Taipei 110301, Taiwan
| | - Barbara Szomolay
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Chia-Te Liao
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Research Center of Urology and Kidney, Taipei Medical University, Taipei 110, Taiwan
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10
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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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11
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Galichon P, Lannoy M, Li L, Serre J, Vandermeersch S, Legouis D, Valerius MT, Hadchouel J, Bonventre JV. Energy depletion by cell proliferation sensitizes the kidney epithelial cells to injury. Am J Physiol Renal Physiol 2024; 326:F326-F337. [PMID: 38205542 PMCID: PMC11207531 DOI: 10.1152/ajprenal.00023.2023] [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: 02/01/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 01/12/2024] Open
Abstract
Acute kidney injury activates both proliferative and antiproliferative pathways, the consequences of which are not fully elucidated. If an initial proliferation of the renal epithelium is necessary for the successful repair, the persistence of proliferation markers is associated with the occurrence of chronic kidney disease. We hypothesized that proliferation in stress conditions impacts cell viability and renal outcomes. We found that proliferation is associated with cell death after various stresses in kidney cells. In vitro, the ATP/ADP ratio oscillates reproducibly throughout the cell cycle, and cell proliferation is associated with a decreased intracellular ATP/ADP ratio. In vivo, transcriptomic data from transplanted kidneys revealed that proliferation was strongly associated with a decrease in the expression of the mitochondria-encoded genes of the oxidative phosphorylation pathway, but not of the nucleus-encoded ones. These observations suggest that mitochondrial function is a limiting factor for energy production in proliferative kidney cells after injury. The association of increased proliferation and decreased mitochondrial function was indeed associated with poor renal outcomes. In summary, proliferation is an energy-demanding process impairing the cellular ability to cope with an injury, highlighting proliferative repair and metabolic recovery as indispensable and interdependent features for successful kidney repair.NEW & NOTEWORTHY ATP depletion is a hallmark of acute kidney injury. Proliferation is instrumental to kidney repair. We show that ATP levels vary during the cell cycle and that proliferation sensitizes renal epithelial cells to superimposed injuries in vitro. More proliferation and less energy production by the mitochondria are associated with adverse outcomes in injured kidney allografts. This suggests that controlling the timing of kidney repair might be beneficial to mitigate the extent of acute kidney injury.
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Affiliation(s)
- Pierre Galichon
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
- Medical School, Sorbonne Université, Paris, France
| | - Morgane Lannoy
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Li Li
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Justine Serre
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Sophie Vandermeersch
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - David Legouis
- Laboratory of Nephrology, Division of Intensive Care, Department of Medicine and Cell Physiology, University Hospital of Geneva, Geneva, Switzerland
| | - M Todd Valerius
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Juliette Hadchouel
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
| | - Joseph V Bonventre
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
- Institut National de la Santé et de la Recherche Médicale (UMR_S1155), "Common and Rare and Kidney Diseases: From Molecular Events to Precision Medicine," Paris, France
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12
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Zhang H, Zheng C, Xu Y, Hu X. Comprehensive molecular and cellular characterization of endoplasmic reticulum stress-related key genes in renal ischemia/reperfusion injury. Front Immunol 2024; 15:1340997. [PMID: 38495888 PMCID: PMC10940334 DOI: 10.3389/fimmu.2024.1340997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Abstract
Background Renal ischemia-reperfusion injury (RIRI) is an inevitable complication in the process of kidney transplantation and lacks specific therapy. The study aims to determine the underlying mechanisms of RIRI to uncover a promising target for efficient renoprotection. Method Four bulk RNA-seq datasets including 495 renal samples of pre- and post-reperfusion were collected from the GEO database. The machine learning algorithms were utilized to ascertain pivotal endoplasmic reticulum stress genes. Then, we incorporated correlation analysis and determined the interaction pathways of these key genes. Considering the heterogeneous nature of bulk-RNA analysis, the single-cell RNA-seq analysis was performed to investigate the mechanisms of key genes at the single-cell level. Besides, 4-PBA was applied to inhibit endoplasmic reticulum stress and hence validate the pathological role of these key genes in RIRI. Finally, three clinical datasets with transcriptomic profiles were used to assess the prognostic role of these key genes in renal allograft outcomes after RIRI. Results In the bulk-RNA analysis, endoplasmic reticulum stress was identified as the top enriched pathway and three endoplasmic reticulum stress-related genes (PPP1R15A, JUN, and ATF3) were ranked as top performers in both LASSO and Boruta analyses. The three genes were found to significantly interact with kidney injury-related pathways, including apoptosis, inflammatory response, oxidative stress, and pyroptosis. For oxidative stress, these genes were more strongly related to oxidative markers compared with antioxidant markers. In single-cell transcriptome, the three genes were primarily upregulated in endothelium, distal convoluted tubule cells, and collecting duct principal cells among 12 cell types of renal tissues in RIRI. Furthermore, distal convoluted tubule cells and collecting duct principal cells exhibited pro-inflammatory status and the highest pyroptosis levels, suggesting their potential as main effectors of three key genes for mediating RIRI-associated injuries. Importantly, inhibition of these key genes using 4-phenyl butyric acid alleviated functional and histological damage in a mouse RIRI model. Finally, the three genes demonstrated highly prognostic value in predicting graft survival outcomes. Conclusion The study identified three key endoplasmic reticulum stress-related genes and demonstrated their prognostic value for graft survival, providing references for individualized clinical prevention and treatment of postoperative complications after renal transplantation.
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Affiliation(s)
- Hao Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Chaoyue Zheng
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Yue Xu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
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13
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Liu M, Chen J, Sun M, Zhang L, Yu Y, Mi W, Ma Y, Wang G. Protection of Ndrg2 deficiency on renal ischemia-reperfusion injury via activating PINK1/Parkin-mediated mitophagy. Chin Med J (Engl) 2024:00029330-990000000-00971. [PMID: 38407220 DOI: 10.1097/cm9.0000000000002957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Renal ischemia-reperfusion (R-I/R) injury is the most prevalent cause of acute kidney injury, with high mortality and poor prognosis. However, the underlying pathological mechanisms are not yet fully understood. Therefore, this study aimed to investigate the role of N-myc downstream-regulated gene 2 (Ndrg2) in R-I/R injury. METHODS We examined the expression of Ndrg2 in the kidney under normal physiological conditions and after R-I/R injury by immunofluorescence staining, real-time polymerase chain reaction, and western blotting. We then detected R-I/R injury in Ndrg2-deficient (Ndrg2-/-) mice and wild type (Ndrg2+/+) littermates in vivo, and detected oxygen and glucose deprivation and reperfusion injury (OGD-R) in HK-2 cells. We further conducted transcriptomic sequencing to investigate the role of Ndrg2 in R-I/R injury and detected levels of oxidative stress and mitochondrial damage by dihydroethidium staining, biochemical assays, and western blot. Finally, we measured the levels of mitophagy in Ndrg2+/+ and Ndrg2-/- mice after R-I/R injury or HK-2 cells in OGD-R injury. RESULTS We found that Ndrg2 was primarily expressed in renal proximal tubules and significantly decreased its expression 24 h after R-I/R injury. Ndrg2-/- mice exhibited significantly attenuated R-I/R injury compared to Ndrg2+/+ mice. Transcriptomics profiling showed that Ndrg2 deficiency induced perturbations of multiple signaling pathways, downregulated inflammatory responses and oxidative stress, and increased autophagy following R-I/R injury. Further studies revealed that Ndrg2 deficiency reduced oxidative stress and mitochondrial damage. Notably, Ndrg2 deficiency significantly activated phosphatase and tensin homologue on chromosome ten-induced putative kinase 1 (PINK1)/Parkin-mediated mitophagy. The downregulation of NDRG2 expression significantly increased cell viability after OGD-R injury, increased the expression of heme oxygenase-1, decreased the expression of nicotinamide adenine dinucleotide phosphate oxidase 4, and increased the expression of the PINK1/Parkin pathway. CONCLUSION Ndrg2 deficiency might become a therapy target for R-I/R injury by decreasing oxidative stress, maintaining mitochondrial homeostasis, and activating PINK1/Parkin-mediated mitophagy.
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Affiliation(s)
- Min Liu
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Jianwen Chen
- Department of Nephrology, The First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing 100853, China
| | - Miao Sun
- Department of Anesthesiology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, Liaoning 121000, China
| | - Lixia Zhang
- Department of Burn and Plastic Surgery, The Fourth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Yao Yu
- Department of Anesthesiology, Peking University Third Hospital, Beijing 100191, China
| | - Weidong Mi
- Department of Anesthesiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Yulong Ma
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Guyan Wang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
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14
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Aggarwal S, Wang Z, Fernandez Pacheco DR, Rinaldi A, Rajewski A, Callemeyn J, Van Loon E, Lamarthée B, Covarrubias AE, Hou J, Yamashita M, Akiyama H, Karumanchi SA, Svendsen CN, Noble PW, Jordan SC, Breunig J, Naesens M, Cippà PE, Kumar S. SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys. Science 2024; 383:eadd6371. [PMID: 38386758 PMCID: PMC11345873 DOI: 10.1126/science.add6371] [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: 06/24/2022] [Accepted: 01/11/2024] [Indexed: 02/24/2024]
Abstract
The steps governing healing with or without fibrosis within the same microenvironment are unclear. After acute kidney injury (AKI), injured proximal tubular epithelial cells activate SOX9 for self-restoration. Using a multimodal approach for a head-to-head comparison of injury-induced SOX9 lineages, we identified a dynamic SOX9 switch in repairing epithelia. Lineages that regenerated epithelia silenced SOX9 and healed without fibrosis (SOX9on-off). By contrast, lineages with unrestored apicobasal polarity maintained SOX9 activity in sustained efforts to regenerate, which were identified as a SOX9on-on Cadherin6pos cell state. These reprogrammed cells generated substantial single-cell WNT activity to provoke a fibroproliferative response in adjacent fibroblasts, driving AKI to chronic kidney disease. Transplanted human kidneys displayed similar SOX9/CDH6/WNT2B responses. Thus, we have uncovered a sensor of epithelial repair status, the activity of which determines regeneration with or without fibrosis.
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Affiliation(s)
- Shikhar Aggarwal
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhanxiang Wang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David Rincon Fernandez Pacheco
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anna Rinaldi
- Division of Nephrology, Ente Ospedaliero Cantonale, CH-6900 Lugano, Switzerland
| | - Alex Rajewski
- Applied Genomics, Computation, and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Baptiste Lamarthée
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Ambart Ester Covarrubias
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jean Hou
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michifumi Yamashita
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Haruhiko Akiyama
- Department of Orthopaedic Surgery, Gifu University Graduate School of Medicine, Gifu 500-8705, Japan
| | - S. Ananth Karumanchi
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N. Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W. Noble
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stanley C. Jordan
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Pietro E Cippà
- Division of Nephrology, Ente Ospedaliero Cantonale, CH-6900 Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Sanjeev Kumar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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15
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Mizuno H, Murakami N. Multi-omics Approach in Kidney Transplant: Lessons Learned from COVID-19 Pandemic. CURRENT TRANSPLANTATION REPORTS 2023; 10:173-187. [PMID: 38152593 PMCID: PMC10751044 DOI: 10.1007/s40472-023-00410-8] [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] [Accepted: 08/09/2023] [Indexed: 12/29/2023]
Abstract
Purpose of Review Multi-omics approach has advanced our knowledge on transplantation-associated clinical outcomes, such as acute rejection and infection, and emerging omics data are becoming available in kidney transplant and COVID-19. Herein, we discuss updated findings of multi-omics data on kidney transplant outcomes, as well as COVID-19 and kidney transplant. Recent Findings Transcriptomics, proteomics, and metabolomics revealed various inflammation pathways associated with kidney transplantation-related outcomes and COVID-19. Although multi-omics data on kidney transplant and COVID-19 is limited, activation of innate immune pathways and suppression of adaptive immune pathways were observed in the active phase of COVID-19 in kidney transplant recipients. Summary Multi-omics analysis has led us to a deeper exploration and a more comprehensive understanding of key biological pathways in complex clinical settings, such as kidney transplantation and COVID-19. Future multi-omics analysis leveraging multi-center biobank collaborative will further advance our knowledge on the precise immunological responses to allograft and emerging pathogens.
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Affiliation(s)
- Hiroki Mizuno
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
- Dvision of Nephrology and Rheumatology, Toranomon Hospital, Tokyo, Japan
| | - Naoka Murakami
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
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16
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Yang M, Lopez LN, Brewer M, Delgado R, Menshikh A, Clouthier K, Zhu Y, Vanichapol T, Yang H, Harris RC, Gewin L, Brooks CR, Davidson AJ, de Caestecker M. Inhibition of retinoic acid signaling in proximal tubular epithelial cells protects against acute kidney injury. JCI Insight 2023; 8:e173144. [PMID: 37698919 PMCID: PMC10619506 DOI: 10.1172/jci.insight.173144] [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: 06/15/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
Retinoic acid receptor (RAR) signaling is essential for mammalian kidney development but, in the adult kidney, is restricted to occasional collecting duct epithelial cells. We now show that there is widespread reactivation of RAR signaling in proximal tubular epithelial cells (PTECs) in human sepsis-associated acute kidney injury (AKI) and in mouse models of AKI. Genetic inhibition of RAR signaling in PTECs protected against experimental AKI but was unexpectedly associated with increased expression of the PTEC injury marker Kim1. However, the protective effects of inhibiting PTEC RAR signaling were associated with increased Kim1-dependent apoptotic cell clearance, or efferocytosis, and this was associated with dedifferentiation, proliferation, and metabolic reprogramming of PTECs. These data demonstrate the functional role that reactivation of RAR signaling plays in regulating PTEC differentiation and function in human and experimental AKI.
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Affiliation(s)
- Min Yang
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lauren N. Lopez
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Maya Brewer
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rachel Delgado
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anna Menshikh
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kelly Clouthier
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yuantee Zhu
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thitinee Vanichapol
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland, New Zealand
| | - Haichun Yang
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Raymond C. Harris
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Leslie Gewin
- Washington University in St. Louis School of Medicine and the St. Louis Veterans Affairs Hospital, St. Louis, Missouri, USA
| | - Craig R. Brooks
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alan J. Davidson
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland, New Zealand
| | - Mark de Caestecker
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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17
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Nørgård MØ, Svenningsen P. Acute Kidney Injury by Ischemia/Reperfusion and Extracellular Vesicles. Int J Mol Sci 2023; 24:15312. [PMID: 37894994 PMCID: PMC10607034 DOI: 10.3390/ijms242015312] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Acute kidney injury (AKI) is often caused by ischemia-reperfusion injury (IRI). IRI significantly affects kidney metabolism, which elicits pro-inflammatory responses and kidney injury. The ischemia/reperfusion of the kidney is associated with transient high mitochondrial-derived reactive oxygen species (ROS) production rates. Excessive mitochondrial-derived ROS damages cellular components and, together with other pathogenic mechanisms, elicits a range of acute injury mechanisms that impair kidney function. Mitochondrial-derived ROS production also stimulates epithelial cell secretion of extracellular vesicles (EVs) containing RNAs, lipids, and proteins, suggesting that EVs are involved in AKI pathogenesis. This literature review focuses on how EV secretion is stimulated during ischemia/reperfusion and how cell-specific EVs and their molecular cargo may modify the IRI process. Moreover, critical pitfalls in the analysis of kidney epithelial-derived EVs are described. In particular, we will focus on how the release of kidney epithelial EVs is affected during tissue analyses and how this may confound data on cell-to-cell signaling. By increasing awareness of methodological pitfalls in renal EV research, the risk of false negatives can be mitigated. This will improve future EV data interpretation regarding EVs contribution to AKI pathogenesis and their potential as biomarkers or treatments for AKI.
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Affiliation(s)
| | - Per Svenningsen
- Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark;
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18
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Li J, Han Z, Zhu Z, Wei L. LncRNA H19 aggravates primary graft dysfunction after lung transplantation via KLF5-mediated activation of CCL28. Am J Transplant 2023; 23:1536-1550. [PMID: 37394140 DOI: 10.1016/j.ajt.2023.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
The present study aims to elucidate the possible involvement of H19 in primary graft dysfunction (PGD) following lung transplantation (LT) and the underlying mechanism. The transcriptome data were obtained through high-throughput sequencing analysis, and the differential long noncoding RNAs and messenger RNAs were screened for coexpression analysis. The interaction among H19, KLF5 and CCL28 was analyzed. A hypoxia-induced human pulmonary microvascular endothelial cell injury model was established, in which H19 was knocked down to elucidate its effect on the lung function, inflammatory response, and cell apoptosis. An orthotopic left LT model was constructed for in vivo mechanistic validation. High-throughput transcriptome sequencing analysis revealed the involvement of the H19/KLF5/CCL28 signaling axis in PGD. Silencing of H19 reduced inflammatory response and thus improved PGD. CCL28 secreted by human pulmonary microvascular endothelial cells after LT recruited neutrophils and macrophages. Mechanistic investigations indicated that H19 augmented the expression of CCL28 by binding to the transcription factor KLF5. Abundant expression of CCL28 reversed the alleviating effect of H19 silencing on PGD. In conclusion, the results point out that H19 exerts a promoting effect on PGD through increasing KLF5 expression and the subsequent CCL28 expression. Our study provides a novel insight into the mechanism of action of H19.
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Affiliation(s)
- Jiwei Li
- Department of Thoracic Surgery, Zhengzhou Key Laboratory for Surgical Treatment for End-stage Lung Disease, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China.
| | - Zhijun Han
- Department of Thoracic Surgery, Zhengzhou Key Laboratory for Surgical Treatment for End-stage Lung Disease, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Zibo Zhu
- Department of Thoracic Surgery, Zhengzhou Key Laboratory for Surgical Treatment for End-stage Lung Disease, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Li Wei
- Department of Thoracic Surgery, Zhengzhou Key Laboratory for Surgical Treatment for End-stage Lung Disease, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
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19
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Sieckmann T, Schley G, Ögel N, Kelterborn S, Boivin FJ, Fähling M, Ashraf MI, Reichel M, Vigolo E, Hartner A, Lichtenberger FB, Breiderhoff T, Knauf F, Rosenberger C, Aigner F, Schmidt-Ott K, Scholz H, Kirschner KM. Strikingly conserved gene expression changes of polyamine regulating enzymes among various forms of acute and chronic kidney injury. Kidney Int 2023; 104:90-107. [PMID: 37121432 DOI: 10.1016/j.kint.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023]
Abstract
The polyamines spermidine and spermine and their common precursor molecule putrescine are involved in tissue injury and repair. Here, we test the hypothesis that impaired polyamine homeostasis contributes to various kidney pathologies in mice during experimental models of ischemia-reperfusion, transplantation, rhabdomyolysis, cyclosporine treatment, arterial hypertension, diabetes, unilateral ureteral obstruction, high oxalate feeding, and adenine-induced injuries. We found a remarkably similar pattern in most kidney pathologies with reduced expression of enzymes involved in polyamine synthesis together with increased expression of polyamine degrading enzymes. Transcript levels of amine oxidase copper-containing 1 (Aoc1), an enzyme which catalyzes the breakdown of putrescine, were barely detectable by in situ mRNA hybridization in healthy kidneys. Aoc1 was highly expressed upon various experimental kidney injuries resulting in a significant reduction of kidney putrescine content. Kidney levels of spermine were also significantly reduced, whereas spermidine was increased in response to ischemia-reperfusion injury. Increased Aoc1 expression in injured kidneys was mainly accounted for by an Aoc1 isoform that harbors 22 additional amino acids at its N-terminus and shows increased secretion. Mice with germline deletion of Aoc1 and injured kidneys showed no decrease of kidney putrescine content; although they displayed no overt phenotype, they had fewer tubular casts upon ischemia-reperfusion injury. Hyperosmotic stress stimulated AOC1 expression at the transcriptional and post-transcription levels in metanephric explants and kidney cell lines. AOC1 expression was also significantly enhanced after kidney transplantation in humans. These data demonstrate that the kidneys respond to various forms of injury with down-regulation of polyamine synthesis and activation of the polyamine breakdown pathway. Thus, an imbalance in kidney polyamines may contribute to various etiologies of kidney injury.
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Affiliation(s)
- Tobias Sieckmann
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gunnar Schley
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Neslihan Ögel
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Simon Kelterborn
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix J Boivin
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michael Fähling
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Muhammad I Ashraf
- Department of Surgery, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Reichel
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Emilia Vigolo
- Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Andrea Hartner
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander University Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Falk-Bach Lichtenberger
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tilman Breiderhoff
- Department of Pediatrics, Division of Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christian Rosenberger
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Felix Aigner
- Department of Surgery, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Department of Surgery, St. John of God Hospital Graz, Graz, Austria
| | - Kai Schmidt-Ott
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Molecular and Translational Kidney Research, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Holger Scholz
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Karin M Kirschner
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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20
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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: 134] [Impact Index Per Article: 134.0] [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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21
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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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22
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Yang M, Lopez LN, Brewer M, Delgado R, Menshikh A, Clouthier K, Zhu Y, Vanichapol T, Yang H, Harris R, Gewin L, Brooks C, Davidson A, de Caestecker MP. Inhibition of Retinoic Acid Signaling in Proximal Tubular Epithelial cells Protects against Acute Kidney Injury by Enhancing Kim-1-dependent Efferocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545113. [PMID: 37398101 PMCID: PMC10312711 DOI: 10.1101/2023.06.15.545113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Retinoic acid receptor (RAR) signaling is essential for mammalian kidney development, but in the adult kidney is restricted to occasional collecting duct epithelial cells. We now show there is widespread reactivation of RAR signaling in proximal tubular epithelial cells (PTECs) in human sepsis-associated acute kidney injury (AKI), and in mouse models of AKI. Genetic inhibition of RAR signaling in PTECs protects against experimental AKI but is associated with increased expression of the PTEC injury marker, Kim-1. However, Kim-1 is also expressed by de-differentiated, proliferating PTECs, and protects against injury by increasing apoptotic cell clearance, or efferocytosis. We show that the protective effect of inhibiting PTEC RAR signaling is mediated by increased Kim-1 dependent efferocytosis, and that this is associated with de-differentiation, proliferation, and metabolic reprogramming of PTECs. These data demonstrate a novel functional role that reactivation of RAR signaling plays in regulating PTEC differentiation and function in human and experimental AKI. Graphical abstract
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23
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Bi Q, Wu JY, Qiu XM, Li YQ, Yan YY, Sun ZJ, Wang W. Identification of potential necroinflammation-associated necroptosis-related biomarkers for delayed graft function and renal allograft failure: a machine learning-based exploration in the framework of predictive, preventive, and personalized medicine. EPMA J 2023; 14:307-328. [PMID: 37275548 PMCID: PMC10141843 DOI: 10.1007/s13167-023-00320-w] [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: 01/06/2023] [Accepted: 04/07/2023] [Indexed: 06/07/2023]
Abstract
Delayed graft function (DGF) is one of the key post-operative challenges for a subset of kidney transplantation (KTx) patients. Graft survival is significantly lower in recipients who have experienced DGF than in those who have not. Assessing the risk of chronic graft injury, predicting graft rejection, providing personalized treatment, and improving graft survival are major strategies for predictive, preventive, and personalized medicine (PPPM/3PM) to promote the development of transplant medicine. However, since PPPM aims to accurately identify disease by integrating multiple omics, current methods to predict DGF and graft survival can still be improved. Renal ischemia/reperfusion injury (IRI) is a pathological process experienced by all KTx recipients that can result in varying occurrences of DGF, chronic rejection, and allograft failure depending on its severity. During this process, a necroinflammation-mediated necroptosis-dependent secondary wave of cell death significantly contributes to post-IRI tubular cell loss. In this article, we obtained the expression matrices and corresponding clinical data from the GEO database. Subsequently, nine differentially expressed necroinflammation-associated necroptosis-related genes (NiNRGs) were identified by correlation and differential expression analysis. The subtyping of post-KTx IRI samples relied on consensus clustering; the grouping of prognostic risks and the construction of predictive models for DGF (the area under the receiver operating characteristic curve (AUC) of the internal validation set and the external validation set were 0.730 and 0.773, respectively) and expected graft survival after a biopsy (the internal validation set's 1-year AUC: 0.770; 2-year AUC: 0.702; and 3-year AUC: 0.735) were based on the least absolute shrinkage and selection operator regression algorithms. The results of the immune infiltration analysis showed a higher infiltration abundance of myeloid immune cells, especially neutrophils, macrophages, and dendritic cells, in the cluster A subtype and prognostic high-risk groups. Therefore, in the framework of PPPM, this work provides a comprehensive exploration of the early expression landscape, related pathways, immune features, and prognostic impact of NiNRGs in post-KTx patients and assesses their capabilities as.predictors of post-KTx DGF and graft loss,targets of the vicious loop between regulated tubular cell necrosis and necroinflammation for targeted secondary and tertiary prevention, andreferences for personalized immunotherapy. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-023-00320-w.
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Affiliation(s)
- Qing Bi
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Ji-Yue Wu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Xue-Meng Qiu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
- Third Clinical Medical College, Capital Medical University, Beijing, China
| | - Yu-Qing Li
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Yu-Yao Yan
- Department of Anesthesiology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Ze-Jia Sun
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Wei Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
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24
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Gerhardt LM, Koppitch K, van Gestel J, Guo J, Cho S, Wu H, Kirita Y, Humphreys BD, McMahon AP. Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury. J Am Soc Nephrol 2023; 34:554-571. [PMID: 36735940 PMCID: PMC10103206 DOI: 10.1681/asn.0000000000000057] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/17/2022] [Indexed: 01/22/2023] Open
Abstract
SIGNIFICANCE STATEMENT Understanding the mechanisms underlying adaptive and maladaptive renal repair after AKI and their long-term consequences is critical to kidney health. The authors used lineage tracing of cycling cells and single-nucleus multiomics (profiling transcriptome and chromatin accessibility) after AKI. They demonstrated that AKI triggers a cell-cycle response in most epithelial and nonepithelial kidney cell types. They also showed that maladaptive proinflammatory proximal tubule cells (PTCs) persist until 6 months post-AKI, although they decreased in abundance over time, in part, through cell death. Single-nucleus multiomics of lineage-traced cells revealed regulatory features of adaptive and maladaptive repair. These included activation of cell state-specific transcription factors and cis-regulatory elements, and effects in PTCs even after adaptive repair, weeks after the injury event. BACKGROUND AKI triggers a proliferative response as part of an intrinsic cellular repair program, which can lead to adaptive renal repair, restoring kidney structure and function, or maladaptive repair with the persistence of injured proximal tubule cells (PTCs) and an altered kidney structure. However, the cellular and molecular understanding of these repair programs is limited. METHODS To examine chromatin and transcriptional responses in the same cell upon ischemia-reperfusion injury (IRI), we combined genetic fate mapping of cycling ( Ki67+ ) cells labeled early after IRI with single-nucleus multiomics-profiling transcriptome and chromatin accessibility in the same nucleus-and generated a dataset of 83,315 nuclei. RESULTS AKI triggered a broad cell cycle response preceded by cell type-specific and global transcriptional changes in the nephron, the collecting and vascular systems, and stromal and immune cell types. We observed a heterogeneous population of maladaptive PTCs throughout proximal tubule segments 6 months post-AKI, with a marked loss of maladaptive cells from 4 weeks to 6 months. Gene expression and chromatin accessibility profiling in the same nuclei highlighted differences between adaptive and maladaptive PTCs in the activity of cis-regulatory elements and transcription factors, accompanied by corresponding changes in target gene expression. Adaptive repair was associated with reduced expression of genes encoding transmembrane transport proteins essential to kidney function. CONCLUSIONS Analysis of genome organization and gene activity with single-cell resolution using lineage tracing and single-nucleus multiomics offers new insight into the regulation of renal injury repair. Weeks to months after mild-to-moderate IRI, maladaptive PTCs persist with an aberrant epigenetic landscape, and PTCs exhibit an altered transcriptional profile even following adaptive repair.
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Affiliation(s)
- Louisa M.S. Gerhardt
- 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, California
| | - 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, California
| | - Jordi van Gestel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jinjin 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, California
| | - Sam Cho
- 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, California
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri
| | - 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, California
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25
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Chen RY, Li DW, Xie H, Liu XW, Zhuang SY, Wu HY, Wu JJ, Sun N, Qu JW, Miao JY, Zhong C, Huang YH, Yuan XD, Zhang M, Zhang WJ, Hou JQ. Gene signature and prediction model of the mitophagy-associated immune microenvironment in renal ischemia-reperfusion injury. Front Immunol 2023; 14:1117297. [PMID: 37056767 PMCID: PMC10086170 DOI: 10.3389/fimmu.2023.1117297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
BackgroundRenal ischemia-reperfusion injury (IRI) is an inevitable occurrence during kidney transplantation. Mitophagy, ferroptosis, and the associated immune microenvironment (IME) have been shown to play important roles in renal IRI. However, the role of mitophagy-associated IME genes in IRI remains unclear. In this study, we aimed to construct a prediction model of IRI prognosis based on mitophagy-associated IME genes.MethodThe specific biological characteristics of the mitophagy-associated IME gene signature were comprehensively analyzed using public databases such as GEO, Pathway Unification, and FerrDb. Correlations between the expression of prognostic genes and immune-related genes and IRI prognosis were determined by Cox regression, LASSO analysis, and Pearson’s correlation. Molecular validation was performed using human kidney 2 (HK2) cells and culture supernatant as well as the serum and kidney tissues of mice after renal IRI. Gene expression was measured by PCR, and inflammatory cell infiltration was examined by ELISA and mass cytometry. Renal tissue damage was characterized using renal tissue homogenate and tissue sections.ResultsThe expression of the mitophagy-associated IME gene signature was significantly correlated with IRI prognosis. Excessive mitophagy and extensive immune infiltration were the primary factors affecting IRI. In particular, FUNDC1, SQSTM1, UBB, UBC, KLF2, CDKN1A, and GDF15 were the key influencing factors. In addition, B cells, neutrophils, T cells, and M1 macrophages were the key immune cells present in the IME after IRI. A prediction model for IRI prognosis was constructed based on the key factors associated with the mitophagy IME. Validation experiments in cells and mice indicated that the prediction model was reliable and applicable.ConclusionWe clarified the relationship between the mitophagy-related IME and IRI. The IRI prognostic prediction model based on the mitophagy-associated IME gene signature provides novel insights on the prognosis and treatment of renal IRI.
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Affiliation(s)
- Ruo-Yang Chen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Da-Wei Li
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Hui Xie
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Xiao-Wen Liu
- Department of Institute of Molecular Medicine, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Shao-Yong Zhuang
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Hao-Yu Wu
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Jia-Jin Wu
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Nan Sun
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Jun-Wen Qu
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Jia-Yi Miao
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Chen Zhong
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Yu-Hua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiao-Dong Yuan
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
- *Correspondence: Xiao-Dong Yuan, ; Ming Zhang, ; Wei-Jie Zhang, ; Jian-Quan Hou,
| | - Ming Zhang
- Department of Urology, Renji Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
- *Correspondence: Xiao-Dong Yuan, ; Ming Zhang, ; Wei-Jie Zhang, ; Jian-Quan Hou,
| | - Wei-Jie Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Xiao-Dong Yuan, ; Ming Zhang, ; Wei-Jie Zhang, ; Jian-Quan Hou,
| | - Jian-Quan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Urology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
- *Correspondence: Xiao-Dong Yuan, ; Ming Zhang, ; Wei-Jie Zhang, ; Jian-Quan Hou,
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26
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Chromatin accessibility dynamics dictate renal tubular epithelial cell response to injury. Nat Commun 2022; 13:7322. [PMID: 36443310 PMCID: PMC9705299 DOI: 10.1038/s41467-022-34854-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Renal tubular epithelial cells (TECs) can initiate an adaptive response to completely recover from mild acute kidney injury (AKI), whereas severe injury often leads to persistence of maladaptive repair and progression to kidney fibrosis. Through profiling of active DNA regulatory elements by ATAC-seq, we reveal widespread, dynamic changes in the chromatin accessibility of TECs after ischemia-reperfusion injury. We show that injury-specific domains of regulatory chromatin become accessible prior to gene activation, creating poised chromatin states to activate the consequent gene expression program and injury response. We further identify RXRα as a key transcription factor in promoting adaptive repair. Activation of RXRα by bexarotene, an FDA-approved RXRα agonist, restores the chromatin state and gene expression program to protect TECs against severe kidney injury. Together, our findings elucidate a chromatin-mediated mechanism underlying differential responses of TECs to varying injuries and identify RXRα as a therapeutic target of acute kidney injury.
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27
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Van den Eynde J, Jacquemyn X, Cloet N, Noé D, Gillijns H, Lox M, Gsell W, Himmelreich U, Luttun A, McCutcheon K, Janssens S, Oosterlinck W. Arteriovenous Fistulae in Chronic Kidney Disease and the Heart: Physiological, Histological, and Transcriptomic Characterization of a Novel Rat Model. J Am Heart Assoc 2022; 11:e027593. [PMID: 36205249 DOI: 10.1161/jaha.122.027593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Arteriovenous fistulae (AVFs) are the gold standard for vascular access in those requiring hemodialysis but may put an extra hemodynamic stress on the cardiovascular system. The complex interactions between the heart, kidney, and AVFs remain incompletely understood. Methods and Results We characterized a novel rat model of five-sixths partial nephrectomy (NX) and AVFs. NX induced increases in urea, creatinine, and hippuric acid. The addition of an AVF (AVF+NX) further increased urea and a number of uremic toxins such as trimethylamine N-oxide and led to increases in cardiac index, left and right ventricular volumes, and right ventricular mass. Plasma levels of uremic toxins correlated well with ventricular morphology and function. Heart transcriptomes identified altered expression of 8 genes following NX and 894 genes following AVF+NX, whereas 290 and 1431 genes were altered in the kidney transcriptomes, respectively. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed gene expression changes related to cell division and immune activation in both organs, suppression of ribosomes and transcriptional activity in the heart, and altered renin-angiotensin signaling as well as chronodisruption in the kidney. All except the latter were worsened in AVF+NX compared with NX. Conclusions Inflammation and organ dysfunction in chronic kidney disease are exacerbated following AVF creation. Furthermore, our study provides important information for the discovery of novel biomarkers and therapeutic targets in the management of cardiorenal syndrome.
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Affiliation(s)
| | | | - Nicolas Cloet
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Dries Noé
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Hilde Gillijns
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Marleen Lox
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Willy Gsell
- MoSAIC, Biomedical MRI, Department of Imaging and Pathology KU Leuven Leuven Belgium
| | - Uwe Himmelreich
- MoSAIC, Biomedical MRI, Department of Imaging and Pathology KU Leuven Leuven Belgium
| | - Aernout Luttun
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium.,Endothelial Cell Biology Unit, Center for Molecular and Vascular Biology KU Leuven Leuven Belgium
| | - Keir McCutcheon
- Department of Cardiology Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle University Newcastle United Kingdom
| | - Stefan Janssens
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium.,Department of Cardiovascular Diseases University Hospitals Leuven Leuven Belgium
| | - Wouter Oosterlinck
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium.,Department of Cardiovascular Diseases University Hospitals Leuven Leuven Belgium
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28
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He S, He L, Yan F, Li J, Liao X, Ling M, Jing R, Pan L. Identification of hub genes associated with acute kidney injury induced by renal ischemia-reperfusion injury in mice. Front Physiol 2022; 13:951855. [PMID: 36246123 PMCID: PMC9557154 DOI: 10.3389/fphys.2022.951855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Acute kidney injury (AKI) is a severe clinical syndrome, and ischemia-reperfusion injury is an important cause of acute kidney injury. The aim of the present study was to investigate the related genes and pathways in the mouse model of acute kidney injury induced by ischemia-reperfusion injury (IRI-AKI). Method: Two public datasets (GSE39548 and GSE131288) originating from the NCBI Gene Expression Omnibus (GEO) database were analyzed using the R software limma package, and differentially expressed genes (DEGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genomes (KEGG) and gene set enrichment analysis (GSEA) were performed using the differentially expressed genes. Furthermore, a protein-protein interaction (PPI) network was constructed to investigate hub genes, and transcription factor (TF)-hub gene and miRNA-hub gene networks were constructed. Drugs and molecular compounds that could interact with hub genes were predicted using the DGIdb. Result: A total of 323 common differentially expressed genes were identified in the renal ischemia-reperfusion injury group compared with the control group. Among these, 260 differentially expressed genes were upregulated and 66 differentially expressed genes were downregulated. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis results showed that these common differentially expressed genes were enriched in positive regulation of cytokine production, muscle tissue development, and other biological processes, indicating that they were involved in mitogen-activated protein kinase (MAPK), PI3K-Akt, TNF, apoptosis, and Epstein-Barr virus infection signaling pathways. Protein-protein interaction analysis showed 10 hub genes, namely, Jun, Stat3, MYC, Cdkn1a, Hif1a, FOS, Atf3, Mdm2, Egr1, and Ddit3. Using the STRUST database, starBase database, and DGIdb database, it was predicted that 34 transcription factors, 161 mi-RNAs, and 299 drugs or molecular compounds might interact with hub genes. Conclusion: Our findings may provide novel potential biomarkers and insights into the pathogenesis of ischemia-reperfusion injury-acute kidney injury through a comprehensive analysis of Gene Expression Omnibus data, which may provide a reliable basis for early diagnosis and treatment of ischemia-reperfusion injury-acute kidney injury.
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Affiliation(s)
- Sheng He
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
- Guangxi Engineering Research Center for Tissue and Organ Injury and Repair Medicine, Nanning, China
- Guangxi Key Laboratory for Basic Science and Prevention of Perioperative Organ Disfunction, Nanning, China
- Guangxi Clinical Research Center for Anesthesiology, Nanning, China
- Department of Anesthesiology, The First Affiliated Hospital of Southern China University, Hengyang, China
| | - Lili He
- Department of Anesthesiology, The Second Affiliated Hospital of Southern China University, Hengyang, China
| | - Fangran Yan
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Junda Li
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xiaoting Liao
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Maoyao Ling
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Ren Jing
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Linghui Pan
- Department of Anesthesiology, Guangxi Medical University Cancer Hospital, Nanning, China
- Guangxi Engineering Research Center for Tissue and Organ Injury and Repair Medicine, Nanning, China
- Guangxi Key Laboratory for Basic Science and Prevention of Perioperative Organ Disfunction, Nanning, China
- Guangxi Clinical Research Center for Anesthesiology, Nanning, China
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29
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Zhao JL, Qiao XH, Mao JH, Liu F, Fu HD. The interaction between cellular senescence and chronic kidney disease as a therapeutic opportunity. Front Pharmacol 2022; 13:974361. [PMID: 36091755 PMCID: PMC9459105 DOI: 10.3389/fphar.2022.974361] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/03/2022] [Indexed: 01/10/2023] Open
Abstract
Chronic kidney disease (CKD) is an increasingly serious public health problem in the world, but the effective therapeutic approach is quite limited at present. Cellular senescence is characterized by the irreversible cell cycle arrest, senescence-associated secretory phenotype (SASP) and senescent cell anti-apoptotic pathways (SCAPs). Renal senescence shares many similarities with CKD, including etiology, mechanism, pathological change, phenotype and outcome, however, it is difficult to judge whether renal senescence is a trigger or a consequence of CKD, since there is a complex correlation between them. A variety of cellular signaling mechanisms are involved in their interactive association, which provides new potential targets for the intervention of CKD, and then extends the researches on senotherapy. Our review summarizes the common features of renal senescence and CKD, the interaction between them, the strategies of senotherapy, and the open questions for future research.
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Affiliation(s)
- Jing-Li Zhao
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiao-Hui Qiao
- Department of Pediatric Internal Medicine, Ningbo Women and Children’s Hospital, Ningbo, China
| | - Jian-Hua Mao
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- *Correspondence: Jian-Hua Mao,
| | - Fei Liu
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Hai-Dong Fu
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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30
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Rinaldi A, Lazareth H, Poindessous V, Nemazanyy I, Sampaio JL, Malpetti D, Bignon Y, Naesens M, Rabant M, Anglicheau D, Cippà PE, Pallet N. Impaired fatty acid metabolism perpetuates lipotoxicity along the transition to chronic kidney injury. JCI Insight 2022; 7:161783. [PMID: 35998043 DOI: 10.1172/jci.insight.161783] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Energy metabolism failure in proximal tubule cells (PTC) is a hallmark of chronic kidney injury. We combined transcriptomic, metabolomic and lipidomic approaches in experimental models and patient cohorts to investigate the molecular bases of the progression to chronic kidney allograft injury initiated by ischemia-reperfusion injury (IRI). The urinary metabolome of kidney transplant recipients with chronic allograft injury and who experienced severe IRI was significantly enriched with long chain fatty acids (FA). We identified a renal FA-related gene signature with low levels of Cpt2 and Acsm5 and high levels of Acsl4 and Acsm5 associated with IRI, transition to chronic injury, and established CKD in mouse models and kidney transplant recipients. The findings were consistent with the presence of Cpt2-, Acsl4+, Acsl5+, Acsm5- PTC failing to recover from IRI as identified by snRNAseq. In vitro experiments indicated that endoplasmic reticulum (ER) stress contributes to CPT2 repression, which, in turn, promotes lipids accumulation, drives profibrogenic epithelial phenotypic changes, and activates the unfolded protein response. ER stress through CPT2 inhibition and lipid accumulation, engages an auto-amplification loop leading to lipotoxicity and self-sustained cellular stress. Thus, IRI imprints a persistent FA metabolism disturbance in the proximal tubule sustaining the progression to chronic kidney allograft injury.
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Affiliation(s)
- Anna Rinaldi
- Department of Medicine, Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Hélène Lazareth
- Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
| | | | - Ivan Nemazanyy
- PMM: The Metabolism-Metabolome Platform, Necker Federative Research Structu, INSERM US24/CNRS, UMS3633, Paris, France
| | - Julio L Sampaio
- CurieCoreTech Metabolomics and Lipidomics Technology Platform, Paris, France
| | - Daniele Malpetti
- Instituto Dalle Molle di Studi sull'Intelligenza Artificiale, Lugano, Switzerland
| | - Yohan Bignon
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marion Rabant
- Department of Pathology, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Dany Anglicheau
- Department of Kidney Transplantation, Necker Hospital, Paris, France
| | - Pietro E Cippà
- Department of Medicine, Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Nicolas Pallet
- Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
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31
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Imenez Silva PH, Mohebbi N. Kidney metabolism and acid-base control: back to the basics. Pflugers Arch 2022; 474:919-934. [PMID: 35513635 PMCID: PMC9338915 DOI: 10.1007/s00424-022-02696-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 01/18/2023]
Abstract
Kidneys are central in the regulation of multiple physiological functions, such as removal of metabolic wastes and toxins, maintenance of electrolyte and fluid balance, and control of pH homeostasis. In addition, kidneys participate in systemic gluconeogenesis and in the production or activation of hormones. Acid-base conditions influence all these functions concomitantly. Healthy kidneys properly coordinate a series of physiological responses in the face of acute and chronic acid-base disorders. However, injured kidneys have a reduced capacity to adapt to such challenges. Chronic kidney disease patients are an example of individuals typically exposed to chronic and progressive metabolic acidosis. Their organisms undergo a series of alterations that brake large detrimental changes in the homeostasis of several parameters, but these alterations may also operate as further drivers of kidney damage. Acid-base disorders lead not only to changes in mechanisms involved in acid-base balance maintenance, but they also affect multiple other mechanisms tightly wired to it. In this review article, we explore the basic renal activities involved in the maintenance of acid-base balance and show how they are interconnected to cell energy metabolism and other important intracellular activities. These intertwined relationships have been investigated for more than a century, but a modern conceptual organization of these events is lacking. We propose that pH homeostasis indissociably interacts with central pathways that drive progression of chronic kidney disease, such as inflammation and metabolism, independent of etiology.
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Affiliation(s)
- Pedro Henrique Imenez Silva
- Institute of Physiology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- National Center of Competence in Research NCCR Kidney.CH, Zurich, Switzerland.
| | - Nilufar Mohebbi
- National Center of Competence in Research NCCR Kidney.CH, Zurich, Switzerland
- Praxis Und Dialysezentrum Zurich, Zurich, Switzerland
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32
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Lai D, Wang L, Li JR, Chen C, Zhao WL, Yuan Q, Ma X, Zhang X. Transcriptional progressive patterns from mild to severe renal ischemia/reperfusion-induced kidney injury in mice. Front Genet 2022; 13:874189. [PMID: 35938014 PMCID: PMC9355309 DOI: 10.3389/fgene.2022.874189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/01/2022] [Indexed: 12/02/2022] Open
Abstract
The renal ischemia/reperfusion (I/R)-induced acute kidney injury incidence after nephron-sparing surgery for localized renal tumors is 20%, but the biological determinant process of postoperative acute kidney injury remains unclear. Using Gene Expression Omnibus database (GSE192883) and several bioinformatics analyses (discrete time points analysis, gene set enrichment analysis, dynamic network biomarker analysis, etc), combined with the establishment of the I/R model for verification, we identified three progressive patterns involving five core pathways confirmed using gene set enrichment analysis and six key genes (S100a10, Pcna, Abat, Kmo, Acadm, and Adhfe1) verified using quantitative polymerase chain reaction The dynamic network biomarker (DNB) subnetwork composite index value is the highest in the 22-min ischemia group, suggesting the transcriptome expression level fluctuated sharply in this group, which means 22-min ischemia is an critical warning point. This study illustrates the core molecular progressive patterns from mild to severe I/R kidney injury, laying the foundation for precautionary biomarkers and molecular intervention targets for exploration. In addition, the safe renal artery blocking time of nephron-sparing surgery that we currently accept may not be safe anymore.
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Affiliation(s)
- Dong Lai
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Lei Wang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jia-Rui Li
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Wen-Lei Zhao
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qing Yuan
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xin Ma
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xu Zhang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, China
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33
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Owen A, Patel JM, Parekh D, Bangash MN. Mechanisms of Post-critical Illness Cardiovascular Disease. Front Cardiovasc Med 2022; 9:854421. [PMID: 35911546 PMCID: PMC9334745 DOI: 10.3389/fcvm.2022.854421] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Prolonged critical care stays commonly follow trauma, severe burn injury, sepsis, ARDS, and complications of major surgery. Although patients leave critical care following homeostatic recovery, significant additional diseases affect these patients during and beyond the convalescent phase. New cardiovascular and renal disease is commonly seen and roughly one third of all deaths in the year following discharge from critical care may come from this cluster of diseases. During prolonged critical care stays, the immunometabolic, inflammatory and neurohumoral response to severe illness in conjunction with resuscitative treatments primes the immune system and parenchymal tissues to develop a long-lived pro-inflammatory and immunosenescent state. This state is perpetuated by persistent Toll-like receptor signaling, free radical mediated isolevuglandin protein adduct formation and presentation by antigen presenting cells, abnormal circulating HDL and LDL isoforms, redox and metabolite mediated epigenetic reprogramming of the innate immune arm (trained immunity), and the development of immunosenescence through T-cell exhaustion/anergy through epigenetic modification of the T-cell genome. Under this state, tissue remodeling in the vascular, cardiac, and renal parenchymal beds occurs through the activation of pro-fibrotic cellular signaling pathways, causing vascular dysfunction and atherosclerosis, adverse cardiac remodeling and dysfunction, and proteinuria and accelerated chronic kidney disease.
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Affiliation(s)
- Andrew Owen
- Department of Critical Care, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, United Kingdom
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Jaimin M. Patel
- Department of Critical Care, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, United Kingdom
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Dhruv Parekh
- Department of Critical Care, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, United Kingdom
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Mansoor N. Bangash
- Department of Critical Care, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, United Kingdom
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- *Correspondence: Mansoor N. Bangash
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34
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Caloric restriction reduces the pro-inflammatory eicosanoid 20- hydroxyeicosatetraenoic acid to protect from acute kidney injury. Kidney Int 2022; 102:560-576. [PMID: 35654224 DOI: 10.1016/j.kint.2022.04.033] [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: 04/13/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022]
Abstract
Acute kidney injury is a frequent complication in the clinical setting and associated with significant morbidity and mortality. Preconditioning with short-term caloric restriction is highly protective against kidney injury in rodent ischemia reperfusion injury models. However, the underlying mechanisms are unknown hampering clinical translation. Here, we examined the molecular basis of caloric restriction-mediated protection to elucidate the principles of kidney stress resistance. Analysis of an RNAseq dataset after caloric restriction identified Cyp4a12a, a cytochrome exclusively expressed in male mice, to be strongly downregulated after caloric restriction. Kidney ischemia reperfusion injury robustly induced acute kidney injury in male mice and this damage could be markedly attenuated by pretreatment with caloric restriction. In females, damage was significantly less pronounced and preconditioning with caloric restriction had only little effect. Tissue concentrations of the metabolic product of Cyp4a12a, 20-hydroxyeicosatetraenoic acid (20-HETE), were found to be significantly reduced by caloric restriction. Conversely, intraperitoneal supplementation of 20-HETE in preconditioned males partly abrogated the protective potential of caloric restriction. Interestingly, this effect was accompanied by a partial reversal of caloric restriction-induced changes in protein but not RNA expression pointing towards inflammation, endoplasmic reticulum stress and lipid metabolism. Thus, our findings provide an insight into the mechanisms underlying kidney protection by caloric restriction. Hence, understanding the mediators of preconditioning is an important pre-requisite for moving towards translation to the clinical setting.
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35
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Gerhardt LMS, McMahon AP. Identifying Common Molecular Mechanisms in Experimental and Human Acute Kidney Injury. Semin Nephrol 2022; 42:151286. [PMID: 36402654 PMCID: PMC11017289 DOI: 10.1016/j.semnephrol.2022.10.012] [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: 11/19/2022]
Abstract
Acute kidney injury (AKI) is a highly prevalent, heterogeneous syndrome, associated with increased short- and long-term mortality. A multitude of different factors cause AKI including ischemia, sepsis, nephrotoxic drugs, and urinary tract obstruction. Upon injury, the kidney initiates an intrinsic repair program that can result in adaptive repair with regeneration of damaged nephrons and functional recovery of epithelial activity, or maladaptive repair and persistence of damaged epithelial cells with a characteristic proinflammatory, profibrotic molecular signature. Maladaptive repair is linked to disease progression from AKI to chronic kidney disease. Despite extensive efforts, no therapeutic strategies provide consistent benefit to AKI patients. Since kidney biopsies are rarely performed in the acute injury phase in humans, most of our understanding of AKI pathophysiology is derived from preclinical AKI models. This raises the question of how well experimental models of AKI reflect the molecular and cellular mechanisms underlying human AKI? Here, we provide a brief overview of available AKI models, discuss their strengths and limitations, and consider important aspects of the AKI response in mice and humans, with a particular focus on the role of proximal tubule cells in adaptive and maladaptive repair.
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Affiliation(s)
- Louisa M S Gerhardt
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA.
| | - 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, University of Southern California, Los Angeles, CA
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36
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Verissimo T, Faivre A, Rinaldi A, Lindenmeyer M, Delitsikou V, Veyrat-Durebex C, Heckenmeyer C, Fernandez M, Berchtold L, Dalga D, Cohen C, Naesens M, Ricksten SE, Martin PY, Pugin J, Merlier F, Haupt K, Rutkowski JM, Moll S, Cippà PE, Legouis D, de Seigneux S. Decreased Renal Gluconeogenesis Is a Hallmark of Chronic Kidney Disease. J Am Soc Nephrol 2022; 33:810-827. [PMID: 35273087 PMCID: PMC8970457 DOI: 10.1681/asn.2021050680] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION CKD is associated with alterations of tubular function. Renal gluconeogenesis is responsible for 40% of systemic gluconeogenesis during fasting, but how and why CKD affects this process and the repercussions of such regulation are unknown. METHODS We used data on the renal gluconeogenic pathway from more than 200 renal biopsies performed on CKD patients and from 43 kidney allograft patients, and studied three mouse models, of proteinuric CKD (POD-ATTAC), of ischemic CKD, and of unilateral urinary tract obstruction. We analyzed a cohort of patients who benefitted from renal catheterization and a retrospective cohort of patients hospitalized in the intensive care unit. RESULTS Renal biopsies of CKD and kidney allograft patients revealed a stage-dependent decrease in the renal gluconeogenic pathway. Two animal models of CKD and one model of kidney fibrosis confirm gluconeogenic downregulation in injured proximal tubule cells. This shift resulted in an alteration of renal glucose production and lactate clearance during an exogenous lactate load. The isolated perfused kidney technique in animal models and renal venous catheterization in CKD patients confirmed decreased renal glucose production and lactate clearance. In CKD patients hospitalized in the intensive care unit, systemic alterations of glucose and lactate levels were more prevalent and associated with increased mortality and a worse renal prognosis at follow-up. Decreased expression of the gluconeogenesis pathway and its regulators predicted faster histologic progression of kidney disease in kidney allograft biopsies. CONCLUSION Renal gluconeogenic function is impaired in CKD. Altered renal gluconeogenesis leads to systemic metabolic changes with a decrease in glucose and increase in lactate level, and is associated with a worse renal prognosis.
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Affiliation(s)
- Thomas Verissimo
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Anna Faivre
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Anna Rinaldi
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Maja Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vasiliki Delitsikou
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Christelle Veyrat-Durebex
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carolyn Heckenmeyer
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Marylise Fernandez
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Lena Berchtold
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Delal Dalga
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Clemens Cohen
- Nephrological Center, Medical Clinic and Polyclinic IV, University of Munich, Munich, Germany
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Sven-Erik Ricksten
- Department of Anesthesiology and Intensive Care, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre-Yves Martin
- Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jérôme Pugin
- Division of Intensive Care, Department of Acute Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Franck Merlier
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Compiègne, France
| | - Karsten Haupt
- Université de Technologie de Compiègne, CNRS Laboratory for Enzyme and Cell Engineering, Compiègne, France
| | - Joseph M Rutkowski
- Department of Medical Physiology, Texas A&M University Health Science Center, Bryan, Texas
| | - Solange Moll
- Service of Clinical Pathology, Department of Pathology and Immunology, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Pietro E Cippà
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - David Legouis
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.,Division of Intensive Care, Department of Acute Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Sophie de Seigneux
- Department of Medicine and Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland .,Service of Nephrology, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
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37
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Experimental models of acute kidney injury for translational research. Nat Rev Nephrol 2022; 18:277-293. [PMID: 35173348 DOI: 10.1038/s41581-022-00539-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/20/2022]
Abstract
Preclinical models of human disease provide powerful tools for therapeutic discovery but have limitations. This problem is especially apparent in the field of acute kidney injury (AKI), in which clinical trial failures have been attributed to inaccurate modelling performed largely in rodents. Multidisciplinary efforts such as the Kidney Precision Medicine Project are now starting to identify molecular subtypes of human AKI. In addition, over the past decade, there have been developments in human pluripotent stem cell-derived kidney organoids as well as zebrafish, rodent and large animal models of AKI. These organoid and AKI models are being deployed at different stages of preclinical therapeutic development. However, the traditionally siloed, preclinical investigator-driven approaches that have been used to evaluate AKI therapeutics to date rarely account for the limitations of the model systems used and have given rise to false expectations of clinical efficacy in patients with different AKI pathophysiologies. To address this problem, there is a need to develop more flexible and integrated approaches, involving teams of investigators with expertise in a range of different model systems, working closely with clinical investigators, to develop robust preclinical evidence to support more focused interventions in patients with AKI.
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38
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Tanemoto F, Mimura I. Therapies Targeting Epigenetic Alterations in Acute Kidney Injury-to-Chronic Kidney Disease Transition. Pharmaceuticals (Basel) 2022; 15:ph15020123. [PMID: 35215236 PMCID: PMC8877070 DOI: 10.3390/ph15020123] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Acute kidney injury (AKI) was previously thought to be a merely transient event; however, recent epidemiological evidence supports the existence of a causal relationship between AKI episodes and subsequent progression to chronic kidney disease (CKD). Although the pathophysiology of this AKI-to-CKD transition is not fully understood, it is mediated by the interplay among multiple components of the kidney including tubular epithelial cells, endothelial cells, pericytes, inflammatory cells, and myofibroblasts. Epigenetic alterations including histone modification, DNA methylation, non-coding RNAs, and chromatin conformational changes, are also expected to be largely involved in the pathophysiology as a “memory” of the initial injury that can persist and predispose to chronic progression of fibrosis. Each epigenetic modification has a great potential as a therapeutic target of AKI-to-CKD transition; timely and target-specific epigenetic interventions to the various temporal stages of AKI-to-CKD transition will be the key to future therapeutic applications in clinical practice. This review elaborates on the latest knowledge of each mechanism and the currently available therapeutic agents that target epigenetic modification in the context of AKI-to-CKD transition. Further studies will elucidate more detailed mechanisms and novel therapeutic targets of AKI-to-CKD transition.
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A Review of Current and Emerging Trends in Donor Graft-Quality Assessment Techniques. J Clin Med 2022; 11:jcm11030487. [PMID: 35159939 PMCID: PMC8836899 DOI: 10.3390/jcm11030487] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
The number of patients placed on kidney transplant waiting lists is rapidly increasing, resulting in a growing gap between organ demand and the availability of kidneys for transplantation. This organ shortage has forced medical professionals to utilize marginal kidneys from expanded criteria donors (ECD) to broaden the donor pool and shorten wait times for patients with end-stage renal disease. However, recipients of ECD kidney grafts tend to have worse outcomes compared to those receiving organs from standard criteria donors (SCD), specifically increased risks of delayed graft function (DGF) and primary nonfunction incidence. Thus, representative methods for graft-quality assessment are strongly needed, especially for ECDs. Currently, graft-quality evaluation is limited to interpreting the donor’s recent laboratory tests, clinical risk scores, the visual evaluation of the organ, and, in some cases, a biopsy and perfusion parameters. The last few years have seen the emergence of many new technologies designed to examine organ function, including new imaging techniques, transcriptomics, genomics, proteomics, metabolomics, lipidomics, and new solutions in organ perfusion, which has enabled a deeper understanding of the complex mechanisms associated with ischemia-reperfusion injury (IRI), inflammatory process, and graft rejection. This review summarizes and assesses the strengths and weaknesses of current conventional diagnostic methods and a wide range of new potential strategies (from the last five years) with respect to donor graft-quality assessment, the identification of IRI, perfusion control, and the prediction of DGF.
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Verissimo T, Faivre A, Sgardello S, Naesens M, de Seigneux S, Criton G, Legouis D. Estimated Renal Metabolomics at Reperfusion Predicts One-Year Kidney Graft Function. Metabolites 2022; 12:57. [PMID: 35050179 PMCID: PMC8778290 DOI: 10.3390/metabo12010057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/26/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Renal transplantation is the gold-standard procedure for end-stage renal disease patients, improving quality of life and life expectancy. Despite continuous advancement in the management of post-transplant complications, progress is still needed to increase the graft lifespan. Early identification of patients at risk of rapid graft failure is critical to optimize their management and slow the progression of the disease. In 42 kidney grafts undergoing protocol biopsies at reperfusion, we estimated the renal metabolome from RNAseq data. The estimated metabolites' abundance was further used to predict the renal function within the first year of transplantation through a random forest machine learning algorithm. Using repeated K-fold cross-validation we first built and then tuned our model on a training dataset. The optimal model accurately predicted the one-year eGFR, with an out-of-bag root mean square root error (RMSE) that was 11.8 ± 7.2 mL/min/1.73 m2. The performance was similar in the test dataset, with a RMSE of 12.2 ± 3.2 mL/min/1.73 m2. This model outperformed classic statistical models. Reperfusion renal metabolome may be used to predict renal function one year after allograft kidney recipients.
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Affiliation(s)
- Thomas Verissimo
- Laboratory of Nephrology, Department of Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; (T.V.); (A.F.); (S.d.S.)
| | - Anna Faivre
- Laboratory of Nephrology, Department of Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; (T.V.); (A.F.); (S.d.S.)
| | - Sebastian Sgardello
- Department of Surgery, University Hospital of Geneva, 1205 Geneva, Switzerland;
| | - Maarten Naesens
- Service of Nephrology, University Hospitals of Leuven, 3000 Leuven, Belgium;
| | - Sophie de Seigneux
- Laboratory of Nephrology, Department of Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; (T.V.); (A.F.); (S.d.S.)
- Service of Nephrology, Department of Internal Medicine Specialties, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Gilles Criton
- Geneva School of Economics and Management, University of Geneva, 1205 Geneva, Switzerland;
| | - David Legouis
- Laboratory of Nephrology, Department of Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; (T.V.); (A.F.); (S.d.S.)
- Division of Intensive Care, Department of Acute Medicine, University hospital of Geneva, 1205 Geneva, Switzerland
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41
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Little MH, Humphreys BD. Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney. J Am Soc Nephrol 2022; 33:15-32. [PMID: 34789545 PMCID: PMC8763179 DOI: 10.1681/asn.2021081073] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
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Affiliation(s)
- Melissa H. Little
- Murdoch Children’s Research Institute, Parkville, Melbourne, Victoria, Australia,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Melbourne, Victoria, Australia,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, Missouri
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42
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Kakade VR, Weiss M, Cantley LG. Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues. Front Physiol 2021; 12:817181. [PMID: 35002783 PMCID: PMC8727440 DOI: 10.3389/fphys.2021.817181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/25/2021] [Indexed: 12/30/2022] Open
Abstract
In the evolving landscape of highly multiplexed imaging techniques that can be applied to study complex cellular microenvironments, this review characterizes the use of imaging mass cytometry (IMC) to study the human kidney. We provide technical details for antibody validation, cell segmentation, and data analysis specifically tailored to human kidney samples, and elaborate on phenotyping of kidney cell types and novel insights that IMC can provide regarding pathophysiological processes in the injured or diseased kidney. This review will provide the reader with the necessary background to understand both the power and the limitations of IMC and thus support better perception of how IMC analysis can improve our understanding of human disease pathogenesis and can be integrated with other technologies such as single cell sequencing and proteomics to provide spatial context to cellular data.
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Affiliation(s)
| | | | - Lloyd G. Cantley
- Section of Nephrology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
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CCN2 Aggravates the Immediate Oxidative Stress-DNA Damage Response following Renal Ischemia-Reperfusion Injury. Antioxidants (Basel) 2021; 10:antiox10122020. [PMID: 34943123 PMCID: PMC8698829 DOI: 10.3390/antiox10122020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 01/10/2023] Open
Abstract
AKI, due to the fact of altered oxygen supply after kidney transplantation, is characterized by renal ischemia–reperfusion injury (IRI). Recent data suggest that AKI to CKD progression may be driven by cellular senescence evolving from prolonged DNA damage response (DDR) following oxidative stress. Cellular communication factor 2 (CCN2, formerly called CTGF) is a major contributor to CKD development and was found to aggravate DNA damage and the subsequent DDR–cellular senescence–fibrosis sequence following renal IRI. We therefore investigated the impact of CCN2 inhibition on oxidative stress and DDR in vivo and in vitro. Four hours after reperfusion, full transcriptome RNA sequencing of mouse IRI kidneys revealed CCN2-dependent enrichment of several signaling pathways, reflecting a different immediate stress response to IRI. Furthermore, decreased staining for γH2AX and p-p53 indicated reduced DNA damage and DDR in tubular epithelial cells of CCN2 knockout (KO) mice. Three days after IRI, DNA damage and DDR were still reduced in CCN2 KO, and this was associated with reduced oxidative stress, marked by lower lipid peroxidation, protein nitrosylation, and kidney expression levels of Nrf2 target genes (i.e., HMOX1 and NQO1). Finally, silencing of CCN2 alleviated DDR and lipid peroxidation induced by anoxia-reoxygenation injury in cultured PTECs. Together, our observations suggest that CCN2 inhibition might mitigate AKI by reducing oxidative stress-induced DNA damage and the subsequent DDR. Thus, targeting CCN2 might help to limit post-IRI AKI.
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44
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Gerhardt LMS, McMahon AP. Multi-omic approaches to acute kidney injury and repair. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100344. [PMID: 35005326 PMCID: PMC8740908 DOI: 10.1016/j.cobme.2021.100344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The kidney has a remarkable regenerative capacity. In response to ischemic or toxic injury, proximal tubule cells can proliferate to rebuild damaged tubules and restore kidney function. However, severe acute kidney injury (AKI) or recurrent AKI events can lead to maladaptive repair and disease progression from AKI to chronic kidney disease (CKD). The application of single cell technologies has identified injured proximal tubule cell states weeks after AKI, distinguished by a pro-inflammatory senescent molecular signature. Epigenetic studies highlighted dynamic changes in the chromatin landscape of the kidney following AKI and described key transcription factors linked to the AKI response. The integration of multi-omic technologies opens new possibilities to improve our understanding of AKI and the driving forces behind the AKI-to-CKD transition, with the ultimate goal of designing tailored diagnostic and therapeutic strategies to improve AKI outcomes and prevent kidney disease progression.
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Affiliation(s)
- Louisa M. S. Gerhardt
- 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 90033, 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 90033, USA
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Bignon Y, Rinaldi A, Nadour Z, Poindessous V, Nemazanyy I, Lenoir O, Fohlen B, Weill-Raynal P, Hertig A, Karras A, Galichon P, Naesens M, Anglicheau D, Cippà PE, Pallet N. Cell stress response impairs de novo NAD+ biosynthesis in the kidney. JCI Insight 2021; 7:153019. [PMID: 34793337 PMCID: PMC8765040 DOI: 10.1172/jci.insight.153019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
The biosynthetic routes leading to de novo nicotinamide adenine dinucleotide (NAD+) production are involved in acute kidney injury (AKI), with a critical role for quinolinate phosphoribosyl transferase (QPRT), a bottleneck enzyme of de novo NAD+ biosynthesis. The molecular mechanisms determining reduced QPRT in AKI, and the role of impaired NAD+ biosynthesis in the progression to chronic kidney disease (CKD), are unknown. We demonstrate that a high urinary quinolinate-to-tryptophan ratio, an indirect indicator of impaired QPRT activity and reduced de novo NAD+ biosynthesis in the kidney, is a clinically applicable early marker of AKI after cardiac surgery and is predictive of progression to CKD in kidney transplant recipients. We also provide evidence that the endoplasmic reticulum (ER) stress response may impair de novo NAD+ biosynthesis by repressing QPRT transcription. In conclusion, NAD+ biosynthesis impairment is an early event in AKI embedded with the ER stress response, and persistent reduction of QPRT expression is associated with AKI to CKD progression. This finding may lead to identification of noninvasive metabolic biomarkers of kidney injury with prognostic and therapeutic implications.
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Affiliation(s)
- Yohan Bignon
- Centre de Recherche des Cordeliers, Université de Paris, INSERM UMRS1138, Paris, France
| | - Anna Rinaldi
- Department of Medicine, Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Zahia Nadour
- Service de Biochimie, AP-HP Hôpital Européen Georges Pompidou, Paris, France
| | | | - Ivan Nemazanyy
- Plateforme d'analyses du métabolisme, INSERM US24/CNRS UMS3633, Paris, France
| | - Olivia Lenoir
- Department of Renal, Paris Cardiovascular Research Centre, Inserm UMRS970, Paris, France
| | - Baptiste Fohlen
- Service d'Anesthésie Réanimation Chrirugicale, AP-HP Hôpital Européen Georges Pompidou, Paris, France
| | - Pierre Weill-Raynal
- Service d'Anesthésie Réanimation Chrirugicale, AP-HP Hôpital Européen Georges Pompidou, Paris, France
| | | | - Alexandre Karras
- Service de Néphrologie, AP-HP Hôpital Européen Georges Pompidou, Paris, France
| | - Pierre Galichon
- Maladies Rénales Fréquentes et Rares, Sorbonne Universités, INSERM UMRS1155, Paris, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Dany Anglicheau
- Service de Néphrologie et Transplantation, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Pietro E Cippà
- Department of Medicine, Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Nicolas Pallet
- Centre de Recherche des Cordeliers, Université de Paris, INSERM UMRS1138, Paris, France
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Li X, Zhang Y, Dong X, Zhou G, Sang Y, Gao L, Zhou X, Sun Z. DNA methylation changes induced by BDE-209 are related to DNA damage response and germ cell development in GC-2spd. J Environ Sci (China) 2021; 109:161-170. [PMID: 34607665 DOI: 10.1016/j.jes.2021.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 06/13/2023]
Abstract
Decabrominated diphenyl ether (BDE-209) is generally utilized in multiple polymer materials as common brominated flame retardant. BDE-209 has been listed as persistent organic pollutants (POPs), which was considered to be reproductive toxin in the environment. But it still remains unclear about the effects of BDE-209 on DNA methylation and the induced-male reproductive toxicity. Due to the extensive epigenetic regulation in germ line development, we hypothesize that BDE-209 exposure impacts the statue of DNA methylation in spermatocytes in vitro. Therefore, the mouse GC-2spd (GC-2) cells were used for the genome wide DNA methylation analysis after treated with 32 μg/mL BDE-209 for 24 hr. The results showed that BDE-209 caused genomic methylation changes with 32,083 differentially methylated CpGs in GC-2 cells, including 16,164 (50.38%) hypermethylated and 15,919 (49.62%) hypomethylated sites. With integrated analysis of DNA methylation data and functional enrichment, we found that BDE-209 might affect the functional transcription in cell growth and sperm development by differential gene methylation. qRT-PCR validation demonstrated the involvement of p53-dependent DNA damage response in the GC-2 cells after BDE-209 exposure. In general, our findings indicated that BDE-209-induced genome wide methylation changes could be interrelated with reproductive dysfunction. This study might provide new insights into the mechanisms of male reproductive toxicity under the environmental exposure to BDE-209.
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Affiliation(s)
- Xiangyang Li
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yue Zhang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Xiaomin Dong
- Experimental Center for basic medical teaching, Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Guiqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Yujian Sang
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Leqiang Gao
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Xianqing Zhou
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
| | - Zhiwei Sun
- Department of Toxicology and Hygienic Chemistry, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
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Zhang D, Wang Y, Zeng S, Zhang M, Zhang X, Wang Y, Zhang Z, Wang X, Hu X. Integrated Analysis of Prognostic Genes Associated With Ischemia-Reperfusion Injury in Renal Transplantation. Front Immunol 2021; 12:747020. [PMID: 34557203 PMCID: PMC8452995 DOI: 10.3389/fimmu.2021.747020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Background Ischemia–reperfusion injury (IRI) remains an inevitable and major challenge in renal transplantation. The current study aims to obtain deep insights into underlying mechanisms and seek prognostic genes as potential therapeutic targets for renal IRI (RIRI). Methods After systematically screening the Gene Expression Omnibus (GEO) database, we collected gene expression profiles of over 1,000 specimens from 11 independent cohorts. Differentially expressed genes (DEGs) were identified by comparing allograft kidney biopsies taken before and after reperfusion in the discovery cohort and further validated in another two independent transplant cohorts. Then, graft survival analysis and immune cell analysis of DEGs were performed in another independent renal transplant cohort with long-term follow-ups to further screen out prognostic genes. Cell type and time course analyses were performed for investigating the expression pattern of prognostic genes in more dimensions utilizing a mouse RIRI model. Finally, two novel genes firstly identified in RIRI were verified in the mouse model and comprehensively analyzed to investigate potential mechanisms. Results Twenty DEGs upregulated in the process of RIRI throughout different donor types (living donors, cardiac and brain death donors) were successfully identified and validated. Among them, upregulation of 10 genes was associated with poor long-term allograft outcomes and exhibited strong correlations with prognostic immune cells, like macrophages. Furthermore, certain genes were found to be only differentially expressed in specific cell types and remained with high expression levels even months after RIRI in the mouse model, which processed the potential to serve as therapeutic targets. Importantly, two newly identified genes in RIRI, Btg2 and Rhob, were successfully confirmed in the mouse model and found to have strong connections with NF-κB signaling. Conclusions We successfully identified and validated 10 IRI-associated prognostic genes in renal transplantation across different donor types, and two novel genes with crucial roles in RIRI were recognized for the first time. Our findings offered promising potential therapeutic targets for RIRI in renal transplantation.
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Affiliation(s)
- Di Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Yicun Wang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Song Zeng
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Min Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Xin Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Yuxuan Wang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Zijian Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
| | - Xi Wang
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Beijing Key Laboratory for Cancer Invasion and Metastasis, Capital Medical University, Beijing, China.,Department of Oncology, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China.,Institute of Urology, Capital Medical University, Beijing, China
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Tubular Cell Dropout in Preimplantation Deceased Donor Biopsies as a Predictor of Delayed Graft Function. Transplant Direct 2021; 7:e716. [PMID: 34476295 PMCID: PMC8384397 DOI: 10.1097/txd.0000000000001168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/16/2021] [Accepted: 04/01/2021] [Indexed: 12/17/2022] Open
Abstract
Supplemental Digital Content is available in the text. Background. Delayed graft function (DGF) affects over 25% of deceased donor kidney transplants (DDKTs) and is associated with increased cost, worsened graft outcomes, and mortality. While approaches to preventing DGF have focused on minimizing cold ischemia, donor factors such as acute tubular injury can influence risk. There are currently no pharmacologic therapies to modify DGF risk or promote repair, in part due to our incomplete understanding of the biology of preimplantation tubular injury. Methods. We collected intraoperative, preimplantation kidney biopsies from 11 high-risk deceased donors and 10 living donors and followed transplant recipients for graft function. We performed quantitative high-dimensional histopathologic analysis using imaging mass cytometry to determine the cellular signatures that distinguished deceased and living donor biopsies as well as deceased donor biopsies which either did or did not progress to DGF. Results. We noted decreased tubular cells (P < 0.0001) and increased macrophage infiltration (P = 0.0037) in high-risk DDKT compared with living donor biopsies. For those high-risk DDKTs that developed postimplant DGF (n = 6), quantitative imaging mass cytometry analysis showed a trend toward reduced tubular cells (P = 0.02) and increased stromal cells (P = 0.04) versus those that did not (n = 5). Notably, these differences were not identified by conventional histopathologic evaluation. Conclusions. The current study identifies donor tubular cell loss as a precursor of DGF pathogenesis and highlights an area for further investigation and potential therapeutic intervention.
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Ide S, Kobayashi Y, Ide K, Strausser SA, Abe K, Herbek S, O'Brien LL, Crowley SD, Barisoni L, Tata A, Tata PR, Souma T. Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair. eLife 2021; 10:68603. [PMID: 34279220 PMCID: PMC8318592 DOI: 10.7554/elife.68603] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/17/2021] [Indexed: 12/14/2022] Open
Abstract
Overwhelming lipid peroxidation induces ferroptotic stress and ferroptosis, a non-apoptotic form of regulated cell death that has been implicated in maladaptive renal repair in mice and humans. Using single-cell transcriptomic and mouse genetic approaches, we show that proximal tubular (PT) cells develop a molecularly distinct, pro-inflammatory state following injury. While these inflammatory PT cells transiently appear after mild injury and return to their original state without inducing fibrosis, after severe injury they accumulate and contribute to persistent inflammation. This transient inflammatory PT state significantly downregulates glutathione metabolism genes, making the cells vulnerable to ferroptotic stress. Genetic induction of high ferroptotic stress in these cells after mild injury leads to the accumulation of the inflammatory PT cells, enhancing inflammation and fibrosis. Our study broadens the roles of ferroptotic stress from being a trigger of regulated cell death to include the promotion and accumulation of proinflammatory cells that underlie maladaptive repair.
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Affiliation(s)
- Shintaro Ide
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University School of Medicine, Durham, United States
| | - Kana Ide
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Sarah A Strausser
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Koki Abe
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Savannah Herbek
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Lori L O'Brien
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Steven D Crowley
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States
| | - Laura Barisoni
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States.,Department of Pathology, Duke University School of Medicine, Durham, United States
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, United States
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, United States.,Regeneration Next, Duke University, Durham, United States.,Duke Cancer Institute, Duke University School of Medicine, Durham, United States
| | - Tomokazu Souma
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, United States.,Regeneration Next, Duke University, Durham, United States
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Single-nuclear transcriptomics reveals diversity of proximal tubule cell states in a dynamic response to acute kidney injury. Proc Natl Acad Sci U S A 2021; 118:2026684118. [PMID: 34183416 PMCID: PMC8271768 DOI: 10.1073/pnas.2026684118] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A single acute kidney injury event increases the risk of progression to chronic kidney disease (CKD). Combining single-nucleus RNA sequencing with genetic tracing of injured proximal tubule cells identified a spatially dynamic, evolving injury response following ischemia–reperfusion injury. Failed proximal tubule repair leads to the persistence of a profibrotic, proinflammatory Vcam1+/Ccl2+ cell type exhibiting a senescence-associated secretory phenotype and a marked transcriptional activation of NF-κB and AP-1 pathway signatures, but no signs of G2/M cell cycle arrest. Insights from this study can inform strategies to improve renal repair and prevent CKD progression. Acute kidney injury (AKI), commonly caused by ischemia, sepsis, or nephrotoxic insult, is associated with increased mortality and a heightened risk of chronic kidney disease (CKD). AKI results in the dysfunction or death of proximal tubule cells (PTCs), triggering a poorly understood autologous cellular repair program. Defective repair associates with a long-term transition to CKD. We performed a mild-to-moderate ischemia–reperfusion injury (IRI) to model injury responses reflective of kidney injury in a variety of clinical settings, including kidney transplant surgery. Single-nucleus RNA sequencing of genetically labeled injured PTCs at 7-d (“early”) and 28-d (“late”) time points post-IRI identified specific gene and pathway activity in the injury–repair transition. In particular, we identified Vcam1+/Ccl2+ PTCs at a late injury stage distinguished by marked activation of NF-κB–, TNF-, and AP-1–signaling pathways. This population of PTCs showed features of a senescence-associated secretory phenotype but did not exhibit G2/M cell cycle arrest, distinct from other reports of maladaptive PTCs following kidney injury. Fate-mapping experiments identified spatially and temporally distinct origins for these cells. At the cortico-medullary boundary (CMB), where injury initiates, the majority of Vcam1+/Ccl2+ PTCs arose from early replicating PTCs. In contrast, in cortical regions, only a subset of Vcam1+/Ccl2+ PTCs could be traced to early repairing cells, suggesting late-arising sites of secondary PTC injury. Together, these data indicate even moderate IRI is associated with a lasting injury, which spreads from the CMB to cortical regions. Remaining failed-repair PTCs are likely triggers for chronic disease progression.
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