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Shi Q, Xiao Z, Cai W, Chen Y, Liang H, Ye Z, Li Z, Liang X. Quantitative proteomics analysis reveals the protective role of S14G-humanin in septic acute kidney injury using 4D-label-free and PRM Approaches. Biochem Biophys Res Commun 2024; 733:150630. [PMID: 39332154 DOI: 10.1016/j.bbrc.2024.150630] [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: 06/12/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/29/2024]
Abstract
Mitochondrial dysfunction contributes to septic acute kidney injury (S-AKI), making mitochondrial protection a potential therapeutic strategy. This study investigates the effects of S14G-humanin (HNG) in S-AKI, utilizing 4D-label-free and parallel reaction monitoring (PRM) techniques for proteomic analysis. An S-AKI model was created in male C57BL/6 mice using lipopolysaccharide (LPS) injection, followed by HNG administration. After 24 h, kidney tissues were analyzed for histology, biochemistry, mitochondrial function, and proteomics. HNG treatment improved renal function, reduced tubular injury, and decreased pro-inflammatory cytokines and oxidative stress markers. Proteomic analysis identified 5900 proteins, with 5111 quantifiable. HNG altered the expression of 132 proteins, with 18 selected for PRM validation. Ten of these proteins were linked to key pathways, including fatty acid degradation and PPAR signaling. This study is the first to show HNG's protective effects in S-AKI, providing insights into its mechanisms through advanced proteomic techniques.
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Affiliation(s)
- Qingying Shi
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China
| | - Zhenmeng Xiao
- Blood Purification Center, the People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, 450003, China
| | - Wenjing Cai
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China
| | - Yuanhan Chen
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, 106th, Zhongshan Road II, Guangzhou, 510080, China
| | - Huaban Liang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, 106th, Zhongshan Road II, Guangzhou, 510080, China
| | - Zhiming Ye
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, 106th, Zhongshan Road II, Guangzhou, 510080, China
| | - Zhilian Li
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, 106th, Zhongshan Road II, Guangzhou, 510080, China.
| | - Xinling Liang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106th, Zhongshan Road II, Guangzhou, 510080, China; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, 106th, Zhongshan Road II, Guangzhou, 510080, China.
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2
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Luo X, Dai W, Lin T, Li L, Zhang Y. Role of Deoxyribonucleic Acid Origami for Alleviating Kidney and Liver Injury in Diabetic Sepsis. J Proteome Res 2024; 23:4626-4636. [PMID: 39264033 DOI: 10.1021/acs.jproteome.4c00543] [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] [Indexed: 09/13/2024]
Abstract
Treating diabetic sepsis (DS) can be challenging because of the persistent infection of multiple organs. To address this complicated pathological condition, it is necessary to develop advanced materials and gain a better understanding of their roles. In this study, we developed a two-dimensional planar material with a rectangular deoxyribonucleic acid origami nanostructure (termed Rec-DON). Rec-DON was used to improve liver and renal function in DS mice, as it preferentially accumulates in these organs, and has superior anti-inflammatory activity and the ability to scavenge reactive oxygen species. The role of Rec-DON in the treatment of DS mice was investigated via quantitative proteomics. This study revealed that Rec-DON can regulate key proteins located primarily in the cytoplasm and mitochondrion, involved in protein transport, antigen processing and presentation, and steroid metabolic process, and can also bind to various proteins to restore liver and renal function in DS mice. This study presented Rec-DON as a liver and kidney targeting material and revealed its role in alleviating multiorgan injury in DS.
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Affiliation(s)
- Xinmei Luo
- Health Management Center, General Practice Medical Center and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenshu Dai
- Health Management Center, General Practice Medical Center and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Li
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yong Zhang
- Health Management Center, General Practice Medical Center and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
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3
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Shaheed SU, McGivern H, Oliveira M, Snashall C, Sutton CW, Tam KH, Knight S, Abbas SH, Kers J, Cross S, Ploeg R, Hunter J. Research biopsies in kidney transplantation: an evaluation of surgical techniques and optimal tissue mass allowing molecular and histological analyses. Clin Proteomics 2024; 21:55. [PMID: 39271970 PMCID: PMC11401365 DOI: 10.1186/s12014-024-09508-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Research biopsies have great potential to advance scientific knowledge by helping to establish predictors of favourable or unfavourable outcomes in kidney transplantation. We evaluated punch and core biopsies of different sizes to determine the optimal size for clinical use. METHODS A total of 54 punch biopsies and 18 core needle biopsies were retrieved by three transplant surgeons. Each surgeon obtained three separate 2 mm, 3 mm and 4 mm punch biopsy samples and three 23 mm (length) core needle biopsies from two pig kidneys. RESULTS 4 mm punch biopsies yielded the greatest amount of protein (2.11 ± 0.41 mg) with good reproducibility between surgeons and biopsy types (Coefficient of Variation ∼ 22.13%). All surgeons found 2 mm biopsies technically challenging to obtain and sample processing was difficult due to the sample size. Shotgun proteomics identified 3853 gene products with no significant difference in the quantitative proteome of 2 mm and 3 mm punch biopsies. However, the expression of 158 Kidney enriched genes, was higher in bigger and deeper 4 mm punch and core needle biopsies compared to 2 mm biopsy. Only 80% of 2 mm biopsies demonstrated the presence of glomeruli, whereas glomeruli were present in 100% of all other biopsy sizes. CONCLUSIONS The 2 mm punch biopsy has been shown to be challenging to use and frequently provides inadequate tissue for histology and proteomics while 3 mm research biopsies were the smallest size that were technically obtainable with adequate tissue for molecular studies.
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Affiliation(s)
- Sadr Ul Shaheed
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Hannah McGivern
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Bodleian Health Care Libraries, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - Marta Oliveira
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - Corinna Snashall
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
| | - Chris W Sutton
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Ka Ho Tam
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Simon Knight
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Syed Hussain Abbas
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Jesper Kers
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Pathology, Leiden Transplant Center, Leiden University Medical Center, Leiden, Netherlands
| | - Sarah Cross
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - Rutger Ploeg
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - James Hunter
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
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4
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Martin KR, Le HT, Abdelgawad A, Yang C, Lu G, Keffer JL, Zhang X, Zhuang Z, Asare-Okai PN, Chan CS, Batish M, Yu Y. Development of an efficient, effective, and economical technology for proteome analysis. CELL REPORTS METHODS 2024; 4:100796. [PMID: 38866007 PMCID: PMC11228373 DOI: 10.1016/j.crmeth.2024.100796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome.
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Affiliation(s)
- Katherine R Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Canyuan Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Guotao Lu
- CDS Analytical, LLC, Oxford, PA 19363, USA
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA
| | | | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Papa Nii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA; School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA.
| | - Yanbao Yu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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5
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Gui Y, Yu Y, Wang W, Wang Y, Lu H, Mozdzierz S, Eskander K, Lin YH, Li H, Tian XJ, Liu S, Zhou D. Proteome characterization of liver-kidney comorbidity after microbial sepsis. FASEB J 2024; 38:e23597. [PMID: 38581235 DOI: 10.1096/fj.202302520r] [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: 12/06/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
Sepsis is a life-threatening condition that occurs when the body responds to an infection but subsequently triggers widespread inflammation and impaired blood flow. These pathologic responses can rapidly cause multiple organ dysfunction or failure either one by one or simultaneously. The fundamental common mechanisms involved in sepsis-induced multiple organ dysfunction remain unclear. Here, employing quantitative global and phosphoproteomics, we examine the liver's temporal proteome and phosphoproteome changes after moderate sepsis induced by cecum ligation and puncture. In total, 4593 global proteins and 1186 phosphoproteins according to 3275 phosphosites were identified. To characterize the liver-kidney comorbidity after sepsis, we developed a mathematical model and performed cross-analyses of liver and kidney proteome data obtained from the same set of mice. Beyond immune response, we showed the commonly disturbed pathways and key regulators of the liver-kidney comorbidity are linked to energy metabolism and consumption. Our data provide open resources to understand the communication between the liver and kidney as they work to fight infection and maintain homeostasis.
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Affiliation(s)
- Yuan Gui
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Yanbao Yu
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Wenjia Wang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuanyuan Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Hanyue Lu
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Sarah Mozdzierz
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Kirollos Eskander
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Yi-Han Lin
- National Center for Advancing Translational Sciences, Bethesda, Maryland, USA
| | - Hanwen Li
- Department of Statistics, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dong Zhou
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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Xiong J, Zhao J. Pyroptosis: The Determinator of Cell Death and Fate in Acute Kidney Injury. KIDNEY DISEASES (BASEL, SWITZERLAND) 2024; 10:118-131. [PMID: 38751798 PMCID: PMC11095617 DOI: 10.1159/000535894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/15/2023] [Indexed: 05/18/2024]
Abstract
Background Acute kidney injury (AKI) is kidney damage that leads to a rapid decline in function. AKI primarily occurs when the tubular epithelium is damaged, causing swelling, loss of brush margin, and eventual apoptosis. Research has shown that tubular epithelial cell damage in AKI is linked to cell cycle arrest, autophagy, and regulation of cell death. Summary Pyroptosis, a type of programmed cell death triggered by inflammation, is believed to play a role in the pathophysiology of AKI. Cumulative evidence has shown that pyroptosis is the main cause of tubular cell death in AKI. Thus, targeted intervention of pyroptosis may be a promising therapeutic approach for AKI. This review delves deep into the cutting-edge research surrounding pyroptosis in the context of AKI, shedding light on its intricate mechanisms and potential implications for clinical practice. Additionally, we explore the exciting realm of potential preclinical treatment options for AKI, aiming to pave the way for future therapeutic advancements. Key Messages Pyroptosis, a highly regulated form of cell death, plays a crucial role in determining the fate of cells during the development of AKI. This intricate process involves the activation of inflammasomes, which are multi-protein complexes that initiate pyroptotic cell death. By understanding the mechanisms underlying pyroptosis, researchers aim to gain insights into the pathogenesis of AKI and potentially identify new therapeutic targets for this condition.
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Affiliation(s)
- Jiachuan Xiong
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, PR China
| | - Jinghong Zhao
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, PR China
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7
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Xu J, Li J, Li Y, Shi X, Zhu H, Chen L. Multidimensional Landscape of SA-AKI Revealed by Integrated Proteomics and Metabolomics Analysis. Biomolecules 2023; 13:1329. [PMID: 37759729 PMCID: PMC10526551 DOI: 10.3390/biom13091329] [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: 04/29/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Sepsis-associated acute kidney injury (SA-AKI) is a severe and life-threatening condition with high morbidity and mortality among emergency patients, and it poses a significant risk of chronic renal failure. Clinical treatments for SA-AKI remain reactive and non-specific, lacking effective diagnostic biomarkers or treatment targets. In this study, we established an SA-AKI mouse model using lipopolysaccharide (LPS) and performed proteomics and metabolomics analyses. A variety of bioinformatic analyses, including gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), protein and protein interactions (PPI), and MetaboAnalyst analysis, were conducted to investigate the key molecules of SA-AKI. Integrated proteomics and metabolomics analysis revealed that sepsis led to impaired renal mitochondrial function and metabolic disorders. Immune-related pathways were found to be activated in kidneys upon septic infection. The catabolic products of polyamines accumulated in septic kidneys. Overall, our integrated analysis provides a multidimensional understanding of SA-AKI and identifies potential pathways for this condition.
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Affiliation(s)
- Jiatong Xu
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (J.X.); (Y.L.)
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Jiaying Li
- Department of Nephrology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (J.L.); (X.S.)
| | - Yan Li
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (J.X.); (Y.L.)
| | - Xiaoxiao Shi
- Department of Nephrology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (J.L.); (X.S.)
| | - Huadong Zhu
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (J.X.); (Y.L.)
| | - Limeng Chen
- Department of Nephrology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (J.L.); (X.S.)
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8
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Molinari MDC, Fuganti-Pagliarini R, Yu Y, Florentino LH, Mertz-Henning LM, Lima RN, Bittencourt DMDC, Freire MO, Rech E. Exploring the Proteomic Profile of Soybean Bran: Unlocking the Potential for Improving Protein Quality and Quantity. PLANTS (BASEL, SWITZERLAND) 2023; 12:2704. [PMID: 37514318 PMCID: PMC10383420 DOI: 10.3390/plants12142704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Soybean is a rich source of vegetal protein for both animal and human consumption. Despite the high levels of protein in soybean seeds, industrial processing to obtain soybean bran significantly decreases the final protein content of the byproducts. To overcome this problem, cultivars with higher protein contents must be developed. However, selecting the target proteins is difficult because of the lack of information on the proteome profile of soybean bran. Therefore, this study obtained the comparative proteomic profiles of both natural coatless seeds and defatted bran from an elite tropical-soybean cultivar. Thus, their extracts were characterized using LC-MS/MS and a total of 550 proteins were identified. Among these, 526 proteins were detected in coatless seeds and 319 proteins in defatted bran. Moreover, a total of 139 proteins were identified as presenting different levels of content in coatless seeds and defatted bran. Among them, only 46 were retained after the seed processing. These proteins were clustered in several important metabolic pathways, such as amino-acid biosynthesis, sugar biosynthesis, and antioxidant activity, meaning that they could act as targets for bioactive products or genome editing to improve protein quality and quantity in soybean grains. These findings can enhance our understanding regarding protein robustness for both soybean crops and the commercial bran improvement because target proteins must remain intact after processing and must be bioactive when overexpressed. Overall, the soybean bran proteomic profile was explored for the first time, providing a valuable catalogue of target proteins that can tolerate the industrial process.
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Affiliation(s)
| | | | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Lilian Hasegawa Florentino
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Distrito Federal 70770-917, Brazil
| | | | - Rayane Nunes Lima
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Distrito Federal 70770-917, Brazil
| | | | | | - Elibio Rech
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Distrito Federal 70770-917, Brazil
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Yu Y, Martin K, Le H, Yang C, Lu G, Zhang X, Grimes C, Zhuang Z, Asare-Okai PN. Development of an Efficient, Effective, and Economical Technology for Proteome Analysis. RESEARCH SQUARE 2023:rs.3.rs-3165690. [PMID: 37502920 PMCID: PMC10371162 DOI: 10.21203/rs.3.rs-3165690/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Proteomics experiments have typically high economic and technical barriers to broad biomedical scientists, which not only result in costly supplies and accessories for sample preparation but also the reluctance to adapt new techniques. In the present study, we present an effective and efficient, yet economical technology, which we call E3technology, for proteomics sample preparation. By immobilizing silica microparticles into a polytetrafluoroethylene (PTFE) matrix, we developed a novel medium, which could be used as a robust and reliable proteomics platform to generate LCMS-friendly samples in a rapid and low-cost fashion. Using different formats of E3technology, including E3tip, E3filter, E3cartridge, and E3plate, we explored a variety of sample types in varied complexity, quantity, volume, and size, including bacterial, fungi, mammalian cells, mouse tissue, and human body fluids. We benchmark their performance against several established approaches. Our data suggest that E3technology outperforms many of the currently available techniques in terms of proteome identification and quantitation. It is widely applicable, highly reproducible, readily scalable and automatable, and is user-friendly and stress-free to non-expert proteomics laboratories. It does not require specialized expertise and equipment, and significantly lowers the technical and economical barrier to proteomics experiments. An enhanced version, E4technology, also opens new avenues to sample preparation for low input and/or low-cell proteomics analysis. The presented technologies by our study represent a breakthrough innovation in biomedical science, and we anticipate widespread adoption by the proteomics community.
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Chen J, Zheng QY, Wang LM, Luo J, Chen KH, He YN. Proteomics reveals defective peroxisomal fatty acid oxidation during the progression of acute kidney injury and repair. Heliyon 2023; 9:e18134. [PMID: 37539197 PMCID: PMC10395357 DOI: 10.1016/j.heliyon.2023.e18134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023] Open
Abstract
Acute kidney injury (AKI) is characterized by a rapid decrease in renal function with high mortality and risk of progression to chronic kidney disease (CKD). Ischemia and reperfusion injury (IRI) is one of the major causes of AKI. However, the cellular and molecular responses of the kidney to IRI are complex and not fully understood. Herein, we conducted unbiased proteomics and bioinformatics analyses in an IRI mouse model on days 3, 7, and 21, and validated the results using IRI, unilateral ureteral obstruction (UUO), and biopsies from patients with AKI or CKD. The results indicated an obvious temporal expression profile of differentially expressed proteins and highlighted impaired lipid metabolism during the progression of AKI to CKD. Acyl-coenzyme A oxidase 1 (Acox1), the first rate-limiting enzyme of peroxisomal fatty acid beta-oxidation, was then selected, and its disturbed expression in the two murine models validated the proteomic findings. Accordingly, Acox1 expression was significantly downregulated in renal biopsies from patients with AKI or CKD, and its expression was negatively correlated with kidney injury score. Furthermore, in contrast to the decreased Acox1 expression, lipid droplet accumulation was remarkably increased in these renal tissues, suggesting dysregulation of fatty acid oxidation. In conclusion, our results suggest that defective peroxisomal fatty acid oxidation might be a common pathological feature in the transition from AKI to CKD, and that Acox1 is a promising intervention target for kidney injury and repair.
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Affiliation(s)
- Jia Chen
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Quan-you Zheng
- Department of Nephrology and Urology, The 958th Hospital, The First Affiliated Hospital, Army Medical University, Chongqing, 400020, China
| | - Li-ming Wang
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jia Luo
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ke-hong Chen
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ya-ni He
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, 400042, China
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Heininen J, Erbacher C, Kotiaho T, Kostiainen R, Teppo J. Enzymatic Phosphorylation of Oxidized Tyrosine Residues. J Proteome Res 2023. [PMID: 37146082 DOI: 10.1021/acs.jproteome.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Post-translational modifications (PTMs) alter the function and fate of proteins and cells in almost every conceivable way. Protein modifications can occur as a result of specific regulating actions of enzymes, such as tyrosine kinases phosphorylating tyrosine residues or by nonenzymatic reactions, such as oxidation related to oxidative stress and diseases. While many studies have addressed the multisite, dynamic, and network-like properties of PTMs, only little is known of the interplay of the same site modifications. In this work, we studied the enzymatic phosphorylation of oxidized tyrosine (l-DOPA) residues using synthetic insulin receptor peptides, in which tyrosine residues were replaced with l-DOPA. The phosphorylated peptides were identified by liquid chromatography-high-resolution mass spectrometry and the site of phosphorylation by tandem mass spectrometry. The results clearly show that the oxidized tyrosine residues are phosphorylated, displaying a specific immonium ion peak in the MS2 spectra. Furthermore, we detected this modification in our reanalysis (MassIVE ID: MSV000090106) of published bottom-up phosphoproteomics data. The modification, where both oxidation and phosphorylation take place at the same amino acid, has not yet been published in PTM databases. Our data indicate that there can be multiple PTMs that do not exclude each other at the same modification site.
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Affiliation(s)
- Juho Heininen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Catharina Erbacher
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Tapio Kotiaho
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Risto Kostiainen
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Jaakko Teppo
- Drug Research Program and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
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12
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Gui Y, Wang Y, Palanza Z, Wang JL, Gupta P, Tao J, Qiao Y, Hargis G, Kreutzer DL, Bastacky SI, Yu Y, Wang Y, Liu S, Fu H, Zhou D. Calponin 2 harnesses metabolic reprogramming to determine kidney fibrosis. Mol Metab 2023; 71:101712. [PMID: 36963615 PMCID: PMC10090436 DOI: 10.1016/j.molmet.2023.101712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023] Open
Abstract
OBJECTIVE In the fibrotic kidneys, the extent of a formed deleterious microenvironment is determined by cellular mechanical forces. This process requires metabolism for energy. However, how cellular mechanics and metabolism are connected remains unclear. METHODS A multi-disciplinary approach was employed: the fibrotic kidney disease models were induced by renal ischemia-reperfusion injury and unilateral ureteral obstruction in Calponin 2 (CNN2) knockdown mice. Proteomics, bioinformatics, and in vivo and in vitro molecular experimental pathology studies were performed. RESULT Our proteomics revealed that actin filament binding and cell metabolism are the two most dysregulated events in the fibrotic kidneys. As a prominent actin stabilizer, CNN2 was predominantly expressed in fibroblasts and pericytes. In CKD patients, CNN2 levels was markedly induced in blood. In mice, CNN2 knockdown preserves kidney function and alleviates fibrosis. Global proteomics profiled that CNN2 knockdown enhanced the activities of the key rate-limiting enzymes and regulators of fatty acid oxidation (FAO) in the diseased kidneys. Inhibiting carnitine palmitoyltransferase 1α in the FAO pathway resulted in lipid accumulation and extracellular matrix deposition in the fibrotic kidneys, which were restored after CNN2 knockdown. Bioinformatics and chromatin immunoprecipitation showed that CNN2 interactor, estrogen receptor 2 (ESR2), binds peroxisome proliferator-activated receptor-α (PPARα) to transcriptionally regulate FAO downstream target genes expression amid kidney fibrosis. In vitro, ESR2 knockdown repressed the mRNA levels of PPARα and the key genes in the FAO pathway. Conversely, activation of PPARα reduced CNN2-induced matrix inductions. CONCLUSIONS Our results suggest that balancing cell mechanics and metabolism is crucial to develop therapeutic strategies to halt kidney fibrosis.
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Affiliation(s)
- Yuan Gui
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Yuanyuan Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Zachary Palanza
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Jack L Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Priya Gupta
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Jianling Tao
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yi Qiao
- Department of Surgery, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Geneva Hargis
- University of Connecticut, School of Medicine, Farmington, CT, 06030, USA
| | - Donald L Kreutzer
- Department of Surgery, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Sheldon I Bastacky
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Yanbao Yu
- Department of Chemistry & Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Yanlin Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Haiyan Fu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Dong Zhou
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
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13
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Gui Y, Tao J, Wang Y, Palanza Z, Qiao Y, Hargis G, Kreutzer DL, Liu S, Bastacky SI, Wang Y, Yu Y, Fu H, Zhou D. Calponin 2 harnesses metabolic reprogramming to determine kidney fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522608. [PMID: 36711748 PMCID: PMC9881848 DOI: 10.1101/2023.01.03.522608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the fibrotic kidneys, the extent of a formed deleterious microenvironment is determined by cellular mechanical forces. This process requires metabolism for energy; however, how cellular mechanics and metabolism are connected remains unclear. Our proteomics revealed that actin filament binding and cell metabolism are the two most dysregulated events in the fibrotic kidneys. As a prominent actin stabilizer, Calponin 2 (CNN2) is predominantly expressed in fibroblasts and pericytes. CNN2 knockdown preserves kidney function and alleviates fibrosis. Global proteomics profiled that CNN2 knockdown enhanced the activities of the key rate-limiting enzymes and regulators of fatty acid oxidation (FAO) in diseased kidneys. Inhibiting carnitine palmitoyltransferase 1α in the FAO pathway results in lipid accumulation and extracellular matrix deposition in the fibrotic kidneys, which were restored after CNN2 knockdown. In patients, increased serum CNN2 levels are correlated with lipid content. Bioinformatics and chromatin immunoprecipitation showed that CNN2 interactor, estrogen receptor 2 (ESR2) binds peroxisome proliferator-activated receptor-α (PPARα) to transcriptionally regulate FAO downstream target genes expression amid kidney fibrosis. In vitro , ESR2 knockdown repressed the mRNA levels of PPARα and the key genes in the FAO pathway. Conversely, activation of PPARα reduced CNN2-induced matrix inductions. Our results suggest that balancing cell mechanics and metabolism is crucial to develop therapeutic strategies to halt kidney fibrosis.
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14
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Bai Y, Li Y, Tang Z, Hu L, Jiang X, Chen J, Huang S, Wu K, Xu W, Chen C. Urinary proteome analysis of acute kidney injury in post-cardiac surgery patients using enrichment materials with high-resolution mass spectrometry. Front Bioeng Biotechnol 2022; 10:1002853. [PMID: 36177176 PMCID: PMC9513377 DOI: 10.3389/fbioe.2022.1002853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Cardiac surgery-associated acute kidney injury (CSA-AKI) may increase the mortality and incidence rates of chronic kidney disease in critically ill patients. This study aimed to investigate the underlying correlations between urinary proteomic changes and CSA-AKI. Methods: Nontargeted proteomics was performed using nano liquid chromatography coupled with Orbitrap Exploris mass spectrometry (MS) on urinary samples preoperatively and postoperatively collected from patients with CSA-AKI. Gemini C18 silica microspheres were used to separate and enrich trypsin-hydrolysed peptides under basic mobile phase conditions. Differential analysis was conducted to screen out urinary differential expressed proteins (DEPs) among patients with CSA-AKI for bioinformatics. Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis was adopted to identify the altered signal pathways associated with CSA-AKI. Results: Approximately 2000 urinary proteins were identified and quantified through data-independent acquisition MS, and 324 DEPs associated with AKI were screened by univariate statistics. According to KEGG enrichment analysis, the signal pathway of protein processing in the endoplasmic reticulum was enriched as the most up-regulated DEPs, and cell adhesion molecules were enriched as the most down-regulated DEPs. In protein–protein interaction analysis, the three hub targets in the up-regulated DEPs were α-1-antitrypsin, β-2-microglobulin and angiotensinogen, and the three key down-regulated DEPs were growth arrest-specific protein 6, matrix metalloproteinase-9 and urokinase-type plasminogen activator. Conclusion: Urinary protein disorder was observed in CSA-AKI due to ischaemia and reperfusion. The application of Gemini C18 silica microspheres can improve the protein identification rate to obtain highly valuable resources for the urinary DEPs of AKI. This work provides valuable knowledge about urinary proteome biomarkers and essential resources for further research on AKI.
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Affiliation(s)
- Yunpeng Bai
- Center of Scientific Research, Maoming People’s Hospital, Maoming, China
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming, China
| | - Ying Li
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhizhong Tang
- Department of Urology, Maoming People’s Hospital, Maoming, China
| | - Linhui Hu
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming, China
| | - Xinyi Jiang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Jingchun Chen
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Sumei Huang
- Center of Scientific Research, Maoming People’s Hospital, Maoming, China
- Department of Emergency, Maoming People’s Hospital, Maoming, China
- Biological Resource Center of Maoming People’s Hospital, Maoming, China
| | - Kunyong Wu
- Center of Scientific Research, Maoming People’s Hospital, Maoming, China
- Biological Resource Center of Maoming People’s Hospital, Maoming, China
| | - Wang Xu
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Critical Care Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chunbo Chen
- Department of Emergency, Maoming People’s Hospital, Maoming, China
- Department of Critical Care Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou, China
- *Correspondence: Chunbo Chen, , orcid.org/0000-0001-5662-497X
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15
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Qiao J, Cui L. Multi-Omics Techniques Make it Possible to Analyze Sepsis-Associated Acute Kidney Injury Comprehensively. Front Immunol 2022; 13:905601. [PMID: 35874763 PMCID: PMC9300837 DOI: 10.3389/fimmu.2022.905601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/10/2022] [Indexed: 12/29/2022] Open
Abstract
Sepsis-associated acute kidney injury (SA-AKI) is a common complication in critically ill patients with high morbidity and mortality. SA-AKI varies considerably in disease presentation, progression, and response to treatment, highlighting the heterogeneity of the underlying biological mechanisms. In this review, we briefly describe the pathophysiology of SA-AKI, biomarkers, reference databases, and available omics techniques. Advances in omics technology allow for comprehensive analysis of SA-AKI, and the integration of multiple omics provides an opportunity to understand the information flow behind the disease. These approaches will drive a shift in current paradigms for the prevention, diagnosis, and staging and provide the renal community with significant advances in precision medicine in SA-AKI analysis.
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Affiliation(s)
- Jiao Qiao
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
- *Correspondence: Liyan Cui,
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16
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Several Alkaloids in Chinese Herbal Medicine Exert Protection in Acute Kidney Injury: Focus on Mechanism and Target Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2427802. [PMID: 35602100 PMCID: PMC9122709 DOI: 10.1155/2022/2427802] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/03/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
Abstract
Objectives Acute kidney injury (AKI) is a loose set of kidney diseases accompanied by a variety of syndromes, which is a serious threat to human life and health. Some alkaloids are derived from various Chinese herbs have been widely concerned in the improvement of AKI. This review provides the research progress of alkaloids in AKI experimental models and discusses the related molecular mechanisms. Key Findings. Alkaloids can protect AKI through various mechanisms including antioxidant stress, improvement of mitochondrial damage, reduction of cell death, induction of autophagy, and inhibition of inflammation. These mechanisms are mainly related to the activation of Nrf2/HO-1 signaling pathway, inhibition of ferroptosis and apoptosis, regulation of PINK1/Parkin pathway, inhibition of TLR4/NF-κB pathway and NLRP3 inflammatory bodies, upregulation of Klotho protein level and so on. In addition, there are a few alkaloids that have certain toxicity on the kidney. Conclusion Alkaloids have been shown to significantly improve AKI, but only in pharmacological studies. This paper summarizes the main experimental models currently used in AKI research and describes some representative alkaloids based on recent research. Their potential roles in the prevention and treatment of AKI through different mechanisms are highlighted.
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17
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A New Role of Acute Phase Proteins: Local Production Is an Ancient, General Stress-Response System of Mammalian Cells. Int J Mol Sci 2022; 23:ijms23062972. [PMID: 35328392 PMCID: PMC8954921 DOI: 10.3390/ijms23062972] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/20/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
The prevailing general view of acute-phase proteins (APPs) is that they are produced by the liver in response to the stress of the body as part of a systemic acute-phase response. We demonstrated a coordinated, local production of these proteins upon cell stress by the stressed cells. The local, stress-induced APP production has been demonstrated in different tissues (kidney, breast cancer) and with different stressors (hypoxia, fibrosis and electromagnetic heat). Thus, this local acute-phase response (APR) seems to be a universal mechanism. APP production is an ancient defense mechanism observed in nematodes and fruit flies as well. Local APP production at the tissue level is also supported by sporadic literature data for single proteins; however, the complex, coordinated, local appearance of this stress response has been first demonstrated only recently. Although a number of literature data are available for the local production of single acute-phase proteins, their interpretation as a local, coordinated stress response is new. A better understanding of the role of APPs in cellular stress response may also be of diagnostic/prognostic and therapeutic significance.
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18
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Lohia S, Vlahou A, Zoidakis J. Microbiome in Chronic Kidney Disease (CKD): An Omics Perspective. Toxins (Basel) 2022; 14:toxins14030176. [PMID: 35324673 PMCID: PMC8951538 DOI: 10.3390/toxins14030176] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/14/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022] Open
Abstract
Chronic kidney disease (CKD) is predominant in 10% of the world’s adult population, and is increasingly considered a silent epidemic. Gut microbiota plays an essential role in maintaining host energy homeostasis and gut epithelial integrity. Alterations in gut microbiota composition, functions and, specifically, production of metabolites causing uremic toxicity are often associated with CKD onset and progression. Here, we present the latest omics (transcriptomics, proteomics and metabolomics) studies that explore the connection between CKD and gut microbiome. A review of the available literature using PubMed was performed using the keywords “microb*”, “kidney”, “proteom”, “metabolom” and “transcript” for the last 10 years, yielding a total of 155 publications. Following selection of the relevant studies (focusing on microbiome in CKD), a predominance of metabolomics (n = 12) over transcriptomics (n = 1) and proteomics (n = 6) analyses was observed. A consensus arises supporting the idea that the uremic toxins produced in the gut cause oxidative stress, inflammation and fibrosis in the kidney leading to CKD. Collectively, findings include an observed enrichment of Eggerthella lenta, Enterobacteriaceae and Clostridium spp., and a depletion in Bacteroides eggerthii, Roseburia faecis and Prevotella spp. occurring in CKD models. Bacterial species involved in butyrate production, indole synthesis and mucin degradation were also related to CKD. Consequently, strong links between CKD and gut microbial dysbiosis suggest potential therapeutic strategies to prevent CKD progression and portray the gut as a promising therapeutic target.
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Affiliation(s)
- Sonnal Lohia
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (S.L.); (A.V.)
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Antonia Vlahou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (S.L.); (A.V.)
| | - Jerome Zoidakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; (S.L.); (A.V.)
- Correspondence:
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Tracz J, Luczak M. Applying Proteomics and Integrative "Omics" Strategies to Decipher the Chronic Kidney Disease-Related Atherosclerosis. Int J Mol Sci 2021; 22:7492. [PMID: 34299112 PMCID: PMC8305100 DOI: 10.3390/ijms22147492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Patients with chronic kidney disease (CKD) are at increased risk of atherosclerosis and premature mortality, mainly due to cardiovascular events. However, well-known risk factors, which promote "classical" atherosclerosis are alone insufficient to explain the high prevalence of atherosclerosis-related to CKD (CKD-A). The complexity of the molecular mechanisms underlying the acceleration of CKD-A is still to be defied. To obtain a holistic picture of these changes, comprehensive proteomic approaches have been developed including global protein profiling followed by functional bioinformatics analyses of dysregulated pathways. Furthermore, proteomics surveys in combination with other "omics" techniques, i.e., transcriptomics and metabolomics as well as physiological assays provide a solid ground for interpretation of observed phenomena in the context of disease pathology. This review discusses the comprehensive application of various "omics" approaches, with emphasis on proteomics, to tackle the molecular mechanisms underlying CKD-A progression. We summarize here the recent findings derived from global proteomic approaches and underline the potential of utilizing integrative systems biology, to gain a deeper insight into the pathogenesis of CKD-A and other disorders.
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Affiliation(s)
| | - Magdalena Luczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
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20
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Gunne S, Heinicke U, Parnham MJ, Laux V, Zacharowski K, von Knethen A. Nrf2-A Molecular Target for Sepsis Patients in Critical Care. Biomolecules 2020; 10:biom10121688. [PMID: 33348637 PMCID: PMC7766194 DOI: 10.3390/biom10121688] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
The transcription factor NF-E2 p45-related factor 2 (Nrf2) is an established master regulator of the anti-oxidative and detoxifying cellular response. Thus, a role in inflammatory diseases associated with the generation of large amounts of reactive oxygen species (ROS) seems obvious. In line with this, data obtained in cell culture experiments and preclinical settings have shown that Nrf2 is important in regulating target genes that are necessary to ensure cellular redox balance. Additionally, Nrf2 is involved in the induction of phase II drug metabolizing enzymes, which are important both in degrading and converting drugs into active forms, and into putative carcinogens. Therefore, Nrf2 has also been implicated in tumorigenesis. This must be kept in mind when new therapy approaches are planned for the treatment of sepsis. Therefore, this review highlights the function of Nrf2 in sepsis with a special focus on the translation of rodent-based results into sepsis patients in the intensive care unit (ICU).
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Affiliation(s)
- Sandra Gunne
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany; (S.G.); (M.J.P.); (V.L.)
| | - Ulrike Heinicke
- Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; (U.H.); (K.Z.)
| | - Michael J. Parnham
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany; (S.G.); (M.J.P.); (V.L.)
| | - Volker Laux
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany; (S.G.); (M.J.P.); (V.L.)
| | - Kai Zacharowski
- Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; (U.H.); (K.Z.)
| | - Andreas von Knethen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany; (S.G.); (M.J.P.); (V.L.)
- Department of Anaesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; (U.H.); (K.Z.)
- Correspondence: ; Tel.: +49-69-6301-87824
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