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Pfister K, Young V, Frankel B, Silva Barbosa A, Burton J, Bons J, Zhang B, Chiba T, Uhlean R, Goetzman E, Schilling B, Sims-Lucas S. Succinylation of Park7 activates a protective metabolic response to acute kidney injury. Am J Physiol Renal Physiol 2024; 327:F128-F136. [PMID: 38695076 DOI: 10.1152/ajprenal.00062.2024] [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: 02/26/2024] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024] Open
Abstract
Acute kidney injury (AKI) is extremely prevalent among hospitalizations and presents a significant risk for the development of chronic kidney disease and increased mortality. Ischemia caused by shock, trauma, and transplant are common causes of AKI. To attenuate ischemic AKI therapeutically, we need a better understanding of the physiological and cellular mechanisms underlying damage. Instances of ischemia are most damaging in proximal tubule epithelial cells (PTECs) where hypoxic signaling cascades, and perhaps more rapidly, posttranslational modifications (PTMs), act in concert to change cellular metabolism. Here, we focus on the effects of the understudied PTM, lysine succinylation. We have previously shown a protective effect of protein hypersuccinylation on PTECs after depletion of the desuccinylase sirtuin5. General trends in the results suggested that hypersuccinylation led to upregulation of peroxisomal activity and was protective against kidney injury. Included in the list of changes was the Parkinson's-related deglycase Park7. There is little known about any links between peroxisome activity and Park7. In this study, we show in vitro and in vivo that Park7 has a crucial role in protection from AKI and upregulated peroxisome activity. These data in combination with published results of Park7's protective role in cardiovascular damage and chronic kidney disease lead us to hypothesize that succinylation of Park7 may ameliorate oxidative damage resulting from AKI and prevent disease progression. This novel mechanism provides a potential therapeutic mechanism that can be targeted.NEW & NOTEWORTHY Succinylation is an understudied posttranslational modification that has been shown to increase peroxisomal activity. Furthermore, increased peroxisomal activity has been shown to reduce oxidative stress and protect proximal tubules after acute kidney injury. Analysis of mass spectrometry succinylomic and proteomic data reveals a novel role for Parkinson's related Park7 in mediating Nrf2 antioxidant response after kidney injury. This novel protection pathway provides new insights for kidney injury prevention and development of novel therapeutics.
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Affiliation(s)
- Katherine Pfister
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Victoria Young
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Brendon Frankel
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Anne Silva Barbosa
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Jordan Burton
- Buck Institute for Research on Aging, Novato, California, United States
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California, United States
| | - Bob Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Takuto Chiba
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Rebecca Uhlean
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Eric Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States
| | - Sunder Sims-Lucas
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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Zhang R, Bons J, Rose JP, Schilling B, Verdin E. Protocol for mass spectrometric profiling of lysine malonylation by lysine acetyltransferase in CRISPRi K562 cell lines. STAR Protoc 2024; 5:103074. [PMID: 38771695 PMCID: PMC11135037 DOI: 10.1016/j.xpro.2024.103074] [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: 12/12/2023] [Revised: 03/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024] Open
Abstract
Lysine malonylation is a protein posttranslational modification. We present a protocol to generate stable gene-knockdown K562 cell lines through lentiviral infection of a CRISPR interference (CRISPRi) system followed by lysine malonylation measurement using mass spectrometry (MS). We detail guide RNA (gRNA) vector cloning, lentiviral infection, cell line purification, protein digestion, malonyl-lysine enrichment, desalting, and MS acquisition and analysis. For complete details on the use and execution of this protocol, please refer to Zhang et al.1 and Bons et al.2.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.
| | - Joanna Bons
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Jacob P Rose
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA.
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Silva Barbosa AC, Pfister KE, Chiba T, Bons J, Rose JP, Burton JB, King CD, O'Broin A, Young V, Zhang B, Sivakama B, Schmidt AV, Uhlean R, Oda A, Schilling B, Goetzman ES, Sims-Lucas S. Dicarboxylic Acid Dietary Supplementation Protects against AKI. J Am Soc Nephrol 2024; 35:135-148. [PMID: 38044490 PMCID: PMC10843194 DOI: 10.1681/asn.0000000000000266] [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: 03/17/2023] [Accepted: 10/20/2023] [Indexed: 12/05/2023] Open
Abstract
SIGNIFICANCE STATEMENT In this study, we demonstrate that a common, low-cost compound known as octanedioic acid (DC 8 ) can protect mice from kidney damage typically caused by ischemia-reperfusion injury or the chemotherapy drug cisplatin. This compound seems to enhance peroxisomal activity, which is responsible for breaking down fats, without adversely affecting mitochondrial function. DC 8 is not only affordable and easy to administer but also effective. These encouraging findings suggest that DC 8 could potentially be used to assist patients who are at risk of experiencing this type of kidney damage. BACKGROUND Proximal tubules are rich in peroxisomes, which are damaged during AKI. Previous studies demonstrated that increasing peroxisomal fatty acid oxidation (FAO) is renoprotective, but no therapy has emerged to leverage this mechanism. METHODS Mice were fed with either a control diet or a diet enriched with dicarboxylic acids, which are peroxisome-specific FAO substrates, then subjected to either ischemia-reperfusion injury-AKI or cisplatin-AKI models. Biochemical, histologic, genetic, and proteomic analyses were performed. RESULTS Both octanedioic acid (DC 8 ) and dodecanedioic acid (DC 12 ) prevented the rise of AKI markers in mice that were exposed to renal injury. Proteomics analysis demonstrated that DC 8 preserved the peroxisomal and mitochondrial proteomes while inducing extensive remodeling of the lysine succinylome. This latter finding indicates that DC 8 is chain shortened to the anaplerotic substrate succinate and that peroxisomal FAO was increased by DC 8 . CONCLUSIONS DC 8 supplementation protects kidney mitochondria and peroxisomes and increases peroxisomal FAO, thereby protecting against AKI.
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Affiliation(s)
- Anne C. Silva Barbosa
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Katherine E. Pfister
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Takuto Chiba
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Jacob P. Rose
- Buck Institute for Research on Aging, Novato, California
| | | | | | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, California
| | - Victoria Young
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bob Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bharathi Sivakama
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alexandra V. Schmidt
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rebecca Uhlean
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Akira Oda
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Eric S. Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sunder Sims-Lucas
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
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Salovska B, Liu Y. Post-translational modification and phenotype. Proteomics 2023; 23:e2200535. [PMID: 36799530 DOI: 10.1002/pmic.202200535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 02/18/2023]
Affiliation(s)
- Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, Connecticut, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
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