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Brasileiro-Martins LM, Cavalcante SA, Nascimento TP, Silva-Neto AV, Mariano Santos MD, Camillo-Andrade AC, da Gama Fischer JDS, Ferreira CC, Oliveira LB, Sartim MA, Costa AG, Pucca MB, Wen FH, Moura-da-Silva AM, Sachett J, Carvalho PC, de Aquino PF, Monteiro WM. Urinary proteomics reveals biological processes related to acute kidney injury in Bothrops atrox envenomings. PLoS Negl Trop Dis 2024; 18:e0012072. [PMID: 38536893 PMCID: PMC11020875 DOI: 10.1371/journal.pntd.0012072] [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: 11/17/2023] [Revised: 04/16/2024] [Accepted: 03/14/2024] [Indexed: 04/18/2024] Open
Abstract
Acute kidney injury (AKI) is a critical systemic complication caused by Bothrops envenoming, a neglected health problem in the Brazilian Amazon. Understanding the underlying mechanisms leading to AKI is crucial for effectively mitigating the burden of this complication. This study aimed to characterize the urinary protein profile of Bothrops atrox snakebite victims who developed AKI. We analyzed three groups of samples collected on admission: healthy subjects (controls, n = 10), snakebite victims who developed AKI (AKI, n = 10), and those who did not evolve to AKI (No-AKI, n = 10). Using liquid-chromatography tandem mass spectrometry, we identified and quantified (label-free) 1190 proteins. A panel of 65 proteins was identified exclusively in the urine of snakebite victims, with 32 exclusives to the AKI condition. Proteins more abundant or exclusive in AKI's urine were associated with acute phase response, endopeptidase inhibition, complement cascade, and inflammation. Notable proteins include serotransferrin, SERPINA-1, alpha-1B-glycoprotein, and NHL repeat-containing protein 3. Furthermore, evaluating previously reported biomarkers candidates for AKI and renal injury, we found retinol-binding protein, beta-2-microglobulin, cystatin-C, and hepcidin to be significant in cases of AKI induced by Bothrops envenoming. This work sheds light on physiological disturbances caused by Bothrops envenoming, highlighting potential biological processes contributing to AKI. Such insights may aid in better understanding and managing this life-threatening complication.
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Affiliation(s)
- Lisele Maria Brasileiro-Martins
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
| | | | - Thaís Pinto Nascimento
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Leonidas and Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Brazil
| | - Alexandre Vilhena Silva-Neto
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
| | - Marlon Dias Mariano Santos
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | - Amanda C. Camillo-Andrade
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | | | | | | | - Marco Aurelio Sartim
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Department of Research, Nilton Lins University, Manaus, Brazil
| | - Allyson Guimarães Costa
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Nursing School, Amazonas Federal University, Manaus, Brazil
| | - Manuela B. Pucca
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Fan Hui Wen
- Immunopathology Laboratory, Butantan Institute, São Paulo, Brazil
| | | | - Jacqueline Sachett
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- Immunopathology Laboratory, Butantan Institute, São Paulo, Brazil
| | - Paulo Costa Carvalho
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | | | - Wuelton M. Monteiro
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
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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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Liu L, Liu H, Zhu K, Zhang L, Yin X, Han L, Wang M, Gao S, Xiao X, Yang J, Huang C, Huang Y. Proteome analysis reveals novel serum biomarkers for Henoch-Schönlein purpura in Chinese children. J Proteomics 2023; 276:104841. [PMID: 36796721 DOI: 10.1016/j.jprot.2023.104841] [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: 05/11/2022] [Revised: 12/30/2022] [Accepted: 01/29/2023] [Indexed: 02/16/2023]
Abstract
PURPOSE Henoch-Schönlein purpura (HSP) is diagnosed based on characteristic skin changes. This study aimed to identify the serum biomarkers of HSP in children. EXPERIMENTAL DESIGN We performed proteomic analysis of serum samples from 38 paired pre- and posttherapy HSP patients and 22 healthy controls using a combination of magnetic bead-based weak cation exchange and MALDI-TOF MS. ClinProTools was used to screen the differential peaks. Then, LC-ESI-MS/MS was performed to identify the proteins. ELISA was used to verify the expression of whole protein in the serum of 92 HSP patients, 14 peptic ulcer disease (PUD) patients and 38 healthy controls, which were prospectively collected. Finally, logistic regression analysis was performed to analyze the diagnostic value of the above predictors and existing clinical indicators. RESULTS Seven potential HSP serum biomarker peaks (m/z:1228.95, m/z:1781.22, m/z:1468.43, m/z:1619.53, m/z:1868.41, m/z:1694.05, m/z:1743.25) with higher expression in the pretherapy group and one peak (m/z:1947.41) with lower expression in the pretherapy group were all identified as peptide regions of albumin (ALB), complement C4-A precursor (C4A), tubulin beta chain (TUBB), isoform 1 of fibrinogen alpha chain (FGA), and ezrin (EZR). The expression of identified proteins was validated by ELISA. Multivariate logistic regression analysis showed that serum C4A EZR and ALB were independent risk factors for HSP, serum C4A and lgA were independent risk factors for HSPN, and serum D-dimer was an independent risk factor for abdominal HSP. CONCLUSIONS AND CLINICAL RELEVANCE These findings revealed the specific etiology of HSP from the perspective of serum proteomics. The identified proteins might serve as potential biomarkers for HSP and HSPN diagnoses. SIGNIFICANCE Henoch-Schönlein purpura (HSP) is the most common systemic vasculitis in children, and its diagnosis depends primarily on characteristic skin changes. Early diagnosis of non-rash patients is difficult, especially for abdominal and renal types (Henoch-Schönlein purpura nephritis, HSPN). HSPN has poor outcomes, is diagnosed based on urinary protein and/or haematuria, and cannot be detected early in HSP. Patients with an earlier diagnosis of HSPN appear to have better renal outcomes. Our plasma proteomic analysis of HSP in children revealed that HSP patients could be distinguished from healthy controls and peptic ulcer disease patients using complement C4-A precursor (C4A), ezrin, and albumin. C4A and IgA could distinguish HSPN from HSP in the early stages, and D-dimer was a sensitive index used to distinguish abdominal HSP; identifying these biomarkers could promote the early diagnosis of HSP, especially pediatric HSPN and abdominal HSP, thereby improving precision therapy.
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Affiliation(s)
- Li Liu
- Department of Pediatrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710061, PR China; Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China.
| | - Hailing Liu
- Department of Pediatrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710061, PR China; Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China
| | - Kaili Zhu
- Department of Pediatrics, Xi'an No 3 People's Hospital, Xi'an, Shaanxi Province 71006, PR China
| | - Lingyu Zhang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China
| | - Xiaomei Yin
- Department of Pediatrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710061, PR China
| | - Lin Han
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Miaomiao Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710061, PR China
| | - Shanfeng Gao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China
| | - Xuan Xiao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China
| | - Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Yanping Huang
- Department of Pediatrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710061, PR China.
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Venturini G, Alvim JM, Padilha K, Toepfer CN, Gorham JM, Wasson LK, Biagi D, Schenkman S, Carvalho VM, Salgueiro JS, Cardozo KHM, Krieger JE, Pereira AC, Seidman JG, Seidman CE. Cardiomyocyte infection by Trypanosoma cruzi promotes innate immune response and glycolysis activation. Front Cell Infect Microbiol 2023; 13:1098457. [PMID: 36814444 PMCID: PMC9940271 DOI: 10.3389/fcimb.2023.1098457] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Introduction Chagas cardiomyopathy, a disease caused by Trypanosoma cruzi (T. cruzi) infection, is a major contributor to heart failure in Latin America. There are significant gaps in our understanding of the mechanism for infection of human cardiomyocytes, the pathways activated during the acute phase of the disease, and the molecular changes that lead to the progression of cardiomyopathy. Methods To investigate the effects of T. cruzi on human cardiomyocytes during infection, we infected induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) with the parasite and analyzed cellular, molecular, and metabolic responses at 3 hours, 24 hours, and 48 hours post infection (hpi) using transcriptomics (RNAseq), proteomics (LC-MS), and metabolomics (GC-MS and Seahorse) analyses. Results Analyses of multiomic data revealed that cardiomyocyte infection caused a rapid increase in genes and proteins related to activation innate and adaptive immune systems and pathways, including alpha and gamma interferons, HIF-1α signaling, and glycolysis. These responses resemble prototypic responses observed in pathogen-activated immune cells. Infection also caused an activation of glycolysis that was dependent on HIF-1α signaling. Using gene editing and pharmacological inhibitors, we found that T. cruzi uptake was mediated in part by the glucose-facilitated transporter GLUT4 and that the attenuation of glycolysis, HIF-1α activation, or GLUT4 expression decreased T. cruzi infection. In contrast, pre-activation of pro-inflammatory immune responses with LPS resulted in increased infection rates. Conclusion These findings suggest that T. cruzi exploits a HIF-1α-dependent, cardiomyocyte-intrinsic stress-response activation of glycolysis to promote intracellular infection and replication. These chronic immuno-metabolic responses by cardiomyocytes promote dysfunction, cell death, and the emergence of cardiomyopathy.
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Affiliation(s)
- Gabriela Venturini
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Juliana M. Alvim
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Kallyandra Padilha
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Christopher N. Toepfer
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | | | - Sergio Schenkman
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, São Paulo, Brazil
| | | | | | | | - Jose E. Krieger
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States,Howard Hughes Medical Institute, Chevy Chase, MD, United States,*Correspondence: Christine E. Seidman,
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Wei L, Han Y, Tu C. Molecular Pathways of Diabetic Kidney Disease Inferred from Proteomics. Diabetes Metab Syndr Obes 2023; 16:117-128. [PMID: 36760602 PMCID: PMC9842482 DOI: 10.2147/dmso.s392888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023] Open
Abstract
Diabetic kidney disease (DKD) affects an estimated 20-40% of type 2 diabetes patients and is among the most prevalent microvascular complications in this patient population, contributing to high morbidity and mortality rates. Currently, changes in albuminuria status are thought to be a primary indicator of the onset or progression of DKD, yet progressive nephropathy and renal impairment can occur in certain diabetic individuals who exhibit normal urinary albumin levels, emphasizing the lack of sensitivity and specificity associated with the use of albuminuria as a biomarker for detecting diabetic kidney disease and predicting DKD risk. According to the study, a non-invasive method for early detection or prediction of DKD may involve combining proteomic analytical techniques such second generation sequencing, mass spectrometry, two-dimensional gel electrophoresis, and other advanced system biology algorithms. Another category of proteins of relevance may now be provided by renal tissue biomarkers. The establishment of reliable proteomic biomarkers of DKD represents a novel approach to improving the diagnosis, prognostic evaluation, and treatment of affected patients. In the present review, a series of protein biomarkers that have been characterized to date are discussed, offering a theoretical foundation for future efforts to aid patients suffering from this debilitating microvascular complication.
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Affiliation(s)
- Lan Wei
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Chao Tu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
- Correspondence: Chao Tu, Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, 213000, People’s Republic of China, Email
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Tang X, Zheng W, Hu J, Deng H, Tang L, Zou Z, Liu Y, Qin H, Ye Y, Chen H. Proteomics-based analysis of potential therapeutic targets in patients with peritoneal dialysis-associated peritonitis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140796. [PMID: 35661691 DOI: 10.1016/j.bbapap.2022.140796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Peritoneal dialysis-associated peritonitis (PDAP) is the most common complication in peritoneal dialysis patients. We propose screening for characteristic expressed proteins in the dialysate of PDAP patients to provide clues for the diagnosis of PDAP and its therapeutic targets. METHODS Dialysate samples were collected from patients with a first diagnosis of PDAP (n = 15) and from patients who had not experienced peritonitis (Control, n = 15). Data-independent acquisition (DIA) proteomic analysis was used to screen for differentially expressed proteins (DEPs). Co-expression networks were constructed via weighted gene co-expression network analysis (WGCNA) for detection of gene modules. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used for functional annotation of DEPs and gene modules. Hub proteins were validated using the parallel reaction monitoring (PRM) method. RESULTS A total of 142 DEPs in the dialysate of PDAP patients were identified. 70 proteins were upregulated and 72 proteins were downregulated. GO and KEGG analysis showed that DEPs were mainly enriched in cell metabolism, glycolysis/glycogenesis and hypoxia-inducible factor-1 signaling pathway. Subsequently, a co-expression network was constructed and four gene modules were detected. Myeloperoxidase (MPO) and myeloperoxidase (HP) were the key proteins of the blue and turquoise modules, respectively. Additionally, PRM analysis showed that the expression of MPO and HP was significantly upregulated in the PDAP group compared to the non-peritonitis group, which was consistent with our proteomics data. CONCLUSION MPO and HP were differentially expressed in the dialysate of PDAP patients and may be potential diagnostic and therapeutic targets for PDAP.
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Affiliation(s)
- Xingming Tang
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China.
| | - Wei Zheng
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Jieping Hu
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Huizhao Deng
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Liwen Tang
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Ziliang Zou
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Yinglin Liu
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Hui Qin
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Yuqiu Ye
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
| | - Huimin Chen
- Department of Nephropathy and Rheumatism, Dongguan Tungwah Hospital, Dongguan, China
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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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Urinary proteomics investigations into contrast-induced acute kidney injury. PLoS One 2021; 16:e0258736. [PMID: 34669736 PMCID: PMC8528309 DOI: 10.1371/journal.pone.0258736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022] Open
Abstract
Some patients have a decline in renal function after contrast medium injection, and this phenomenon is called contrast-induced acute kidney injury (CI-AKI); a small number of people even suffer severe renal failure. To date, the mechanism of CI-AKI remains unclear. We aimed to identify novel potential biomarkers in the urine of patients with CI-AKI through LC-MS/MS and bioinformatics analysis. We enrolled patients who underwent coronary angiography (contrast agent: iohexol). The CI-AKI group included 4 cases, and the non-CI-AKI group included 20 cases. We mixed the 4 CI-AKI samples and 20 non-CI-AKI samples. Then, a 0.6 ml urine sample was used for proteome analysis with LC-MS/MS approach. Metascape, ExPASy, and the Human Protein Atlas were utilized for bioinformatics analysis. We obtained 724 and 830 urine proteins from the CI-AKI and non-CI-AKI groups, respectively. The distribution of the pI values and molecular weights (MWs) of postoperative urine proteins showed no significant difference between the CI-AKI group and the non-CI-AKI group. A total of 99differentially expressed proteins (DEPs) were detected, among which 18 proteins were detected only in tubule cells, and 19 proteins were detected in both tubule cells and glomeruli. With GO analysis, the GEPs were mainly associated with immune response and inflammation. Although biomarkers cannot be asserted from this single pilot study, our results may help advance the understanding of the mechanisms of CI-AKI and identify potential novel biomarkers for further investigation.
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9
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Saito R, Hirayama A, Akiba A, Kamei Y, Kato Y, Ikeda S, Kwan B, Pu M, Natarajan L, Shinjo H, Akiyama S, Tomita M, Soga T, Maruyama S. Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry. Metabolites 2021; 11:671. [PMID: 34677386 PMCID: PMC8540909 DOI: 10.3390/metabo11100671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/29/2022] Open
Abstract
Acute kidney injury (AKI) is defined as a rapid decline in kidney function. The associated syndromes may lead to increased morbidity and mortality, but its early detection remains difficult. Using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS), we analyzed the urinary metabolomic profile of patients admitted to the intensive care unit (ICU) after invasive surgery. Urine samples were collected at six time points: before surgery, at ICU admission and 6, 12, 24 and 48 h after. First, urine samples from 61 initial patients (non-AKI: 23, mild AKI: 24, severe AKI: 14) were measured, followed by the measurement of urine samples from 60 additional patients (non-AKI: 40, mild AKI: 20). Glycine and ethanolamine were decreased in patients with AKI compared with non-AKI patients at 6-24 h in the two groups. The linear statistical model constructed at each time point by machine learning achieved the best performance at 24 h (median AUC, area under the curve: 89%, cross-validated) for the 1st group. When cross-validated between the two groups, the AUC showed the best value of 70% at 12 h. These results identified metabolites and time points that show patterns specific to subjects who develop AKI, paving the way for the development of better biomarkers.
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Affiliation(s)
- Rintaro Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Arisa Akiba
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Yushi Kamei
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Yuyu Kato
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Brian Kwan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA; (B.K.); (M.P.); (L.N.)
| | - Minya Pu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA; (B.K.); (M.P.); (L.N.)
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA; (B.K.); (M.P.); (L.N.)
| | - Hibiki Shinjo
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (H.S.); (S.A.); (S.M.)
| | - Shin’ichi Akiyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (H.S.); (S.A.); (S.M.)
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (H.S.); (S.A.); (S.M.)
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10
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Abstract
Pigs represent a potentially attractive model for medical research. Similar body size and physiological patterns of kidney injury that more closely mimic those described in humans make larger animals attractive for experimentation. Using larger animals, including pigs, to investigate the pathogenesis of acute kidney injury (AKI) also serves as an experimental bridge, narrowing the gap between clinical disease and preclinical discoveries. This article compares the advantages and disadvantages of large versus small AKI animal models and provides a comprehensive overview of the development and application of porcine models of AKI induced by clinically relevant insults, including ischemia-reperfusion, sepsis, and nephrotoxin exposure. The primary focus of this review is to evaluate the use of pigs for AKI studies by current investigators, including areas where more information is needed.
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Affiliation(s)
- Jianni Huang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - George Bayliss
- Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, Rhode Island
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11
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Rymut HE, Rund LA, Bolt CR, Villamil MB, Bender DE, Southey BR, Johnson RW, Rodriguez-Zas SL. Biochemistry and Immune Biomarkers Indicate Interacting Effects of Pre- and Postnatal Stressors in Pigs across Sexes. Animals (Basel) 2021; 11:987. [PMID: 33915976 PMCID: PMC8067328 DOI: 10.3390/ani11040987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
The effects of maternal immune activation (MIA) elicited by a prenatal stressor and postnatal metabolic or immune stressors on chemical and inflammatory biomarkers were studied in male and female pigs. Pigs exposed to MIA elicited by porcine reproductive and respiratory syndrome virus and matching controls were assigned at two months of age to fasting stress, immune stress, or a saline group. The serum levels of over 30 chemistry and immune analytes were studied. Significantly low levels of blood urea nitrogen were detected in females exposed to MIA, while the highest creatinine levels were identified in fasting females exposed to MIA. The levels of interferon gamma and interleukin 8 were highest in pigs exposed to postnatal immune challenge. The profiles suggest that MIA may sensitize pigs to postnatal stressors for some indicators while making them more tolerant of other stressors. Effectiveness of practices to ameliorate the impact of postnatal stressors on the physiology of the pig could be enhanced by considering the prenatal stress circumstances.
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Affiliation(s)
- Haley E. Rymut
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.E.R.); (L.A.R.); (C.R.B.); (B.R.S.); (R.W.J.)
| | - Laurie A. Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.E.R.); (L.A.R.); (C.R.B.); (B.R.S.); (R.W.J.)
| | - Courtni R. Bolt
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.E.R.); (L.A.R.); (C.R.B.); (B.R.S.); (R.W.J.)
| | - María B. Villamil
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Diane E. Bender
- Bursky Center for Human Immunology & Immunotherapy, Washington University, St. Louis, MO 63110, USA;
| | - Bruce R. Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.E.R.); (L.A.R.); (C.R.B.); (B.R.S.); (R.W.J.)
| | - Rodney W. Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.E.R.); (L.A.R.); (C.R.B.); (B.R.S.); (R.W.J.)
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.E.R.); (L.A.R.); (C.R.B.); (B.R.S.); (R.W.J.)
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 618012, USA
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12
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Fang X, Lu M, Xia Z, Gao C, Cao Y, Wang R, Wang M, Wu H. Use of liquid chromatography-tandem mass spectrometry to perform urinary proteomic analysis of children with IgA nephropathy and Henoch-Schönlein purpura nephritis. J Proteomics 2020; 230:103979. [PMID: 32932007 DOI: 10.1016/j.jprot.2020.103979] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 08/27/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022]
Abstract
The emerging technology of urinary proteomics has become an efficient biological approach for identifying biomarkers and characterizing pathogenesis in renal involvement. In this study, we attempted to elucidate the relationship between IgAN and HSPN in children, employing LC-MS/MS to perform urinary proteomic analyses using the DIA method. Early-morning spot urine was collected from patients with biopsy-proven IgAN (n = 19) and HSPN (n = 19) prior to treatment and renal biopsy in the Department of Pediatrics, Jinling Hospital, Nanjing, China, and did healthy volunteers (n = 14), from June 2018 to December 2019. Two hundred seventy-six urinary proteins and 125 urinary proteins were determined to be differentially expressed in children with IgAN (n = 4) and HSPN (n = 4), respectively, compared to the urinary proteins of healthy children (n = 4) (p < 0.05). GO analysis demonstrated that the differentially expressed proteins of the two groups, which were located in the extracellular matrix and cell membrane, were primarily involved in biological processes, including metabolic processes, immune system processes, cellular adhesion, cell proliferation, signaling, and biological regulation. KEGG analysis revealed that the differentially expressed proteins of the two groups were associated with cell adhesion molecules, ECM-receptor interactions, the PI3K-Akt signaling pathway, the complement and coagulation cascades, regulation of actin cytoskeleton, cholesterol metabolism, and platelet activation. The target proteins (alpha-1B-glycoprotein (A1BG) and afamin (AFM)), which participated in the complement and coagulation cascades and the regulation of complement activation, were further investigated in the independent validation cohort by ELISA. These proteins were significantly increased in children with IgAN (n = 15) and HSPN (n = 15) compared with the proteins observed in healthy controls (n = 10, P < 0.05). The validated results were consistent with the mass spectrometry results. SIGNIFICANCE: IgAN and HSPN both result from the glomerular deposition of abnormally glycosylated IgA1 with mesangial proliferative changes, and both diseases are common glomerulopathies in the pediatric population that are believed to be correlated. Interestingly, our data, by combining urinary proteomic analyses, showed that several uniform enrichment pathways played an important role in the progression of IgAN and HSPN, suggesting that we might reduce the renal involvement of the two diseases in children through these pathways. The same urinary proteins along these pathways were observed to be differentially expressed in children with IgAN and HSPN, implying that these proteins may be potential biomarkers to identify the two diseases. Future studies examining larger cohorts are warranted to confirm the validity of our findings.
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Affiliation(s)
- Xiang Fang
- Department of Pediatrics, Jinling Hospital, Nanjing 210002, Jiangsu, China
| | - Mei Lu
- Department of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Zhengkun Xia
- Department of Pediatrics, Jinling Hospital, Nanjing 210002, Jiangsu, China.
| | - Chunlin Gao
- Department of Pediatrics, Jinling Hospital, Nanjing 210002, Jiangsu, China.
| | - Yan Cao
- Nanjing Maternal and Child Health Institute, the Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 210004, Jiangsu, China
| | - Ren Wang
- Department of Pediatrics, Jinling Hospital, Nanjing 210002, Jiangsu, China
| | - Meiqiu Wang
- Department of Pediatrics, Jinling Hospital, Nanjing 210002, Jiangsu, China
| | - Heyan Wu
- Department of Pediatrics, Jinling Hospital, Nanjing 210002, Jiangsu, China
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13
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Fang X, Wu H, Lu M, Cao Y, Wang R, Wang M, Gao C, Xia Z. Urinary proteomics of Henoch-Schönlein purpura nephritis in children using liquid chromatography-tandem mass spectrometry. Clin Proteomics 2020; 17:10. [PMID: 32190014 PMCID: PMC7066733 DOI: 10.1186/s12014-020-09274-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Henoch-Schönlein purpura nephritis (HSPN) is the principal cause of morbidity and mortality in children with Henoch-Schönlein purpura (HSP). However, the criteria for risk assessment currently used is not satisfactory. The urine proteome may provide important clues to indicate the development of HSPN. METHODS Here, we detected and compared the urine proteome of patients with HSPN and healthy controls by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the data-independent acquisition (DIA) mode. The differentially expressed proteins were analysed by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. For validation, enzyme-linked immunosorbent assay (ELISA) was used to analyse the selected proteins. RESULTS A total of 125 proteins (29 upregulated and 96 downregulated) were found to be differentially expressed in children with HSPN compared with the controls. Forty-one proteins were predicted to have direct interactions. The enriched pathways mainly included focal adhesion, cell adhesion molecules, the PI3K-Akt signalling pathway, ECM-receptor interactions and so on. Cell adhesion related to the pathogenesis of HSPN was the main biological process identified in this study. The decrease in two proteins (integrin beta-1 and tenascin) was validated by ELISA. CONCLUSIONS Our study provides new insights into the assessment of HSPN progression in children, as well as new potential biomarkers. The data confirm the value of the urinary proteome in capturing the emergence of HSPN.
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Affiliation(s)
- Xiang Fang
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
- Department of Clinical Medicine, Anqing Medical College, Anqing, 246052 Anhui China
| | - Heyan Wu
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
| | - Mei Lu
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
| | - Yan Cao
- Nanjing Maternity and Child Health Care Institute, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004 Jiangsu China
| | - Ren Wang
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
| | - Meiqiu Wang
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
| | - Chunlin Gao
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
| | - Zhengkun Xia
- Department of Pediatrics, Jinling Hospital, the First School of Clinical Medicine, Southern Medical University, No. 305 Zhongshan East Road, Nanjing, 210002 Jiangsu China
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14
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Tajima S, Yamamoto N, Masuda S. Clinical prospects of biomarkers for the early detection and/or prediction of organ injury associated with pharmacotherapy. Biochem Pharmacol 2019; 170:113664. [PMID: 31606409 DOI: 10.1016/j.bcp.2019.113664] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/08/2019] [Indexed: 12/31/2022]
Abstract
Several biomarkers are used to monitor organ damage caused by drug toxicity. Traditional markers of kidney function, such as serum creatinine and blood urea nitrogen are commonly used to estimate glomerular filtration rate. However, these markers have several limitations including poor specificity and sensitivity. A number of serum and urine biomarkers have recently been described to detect kidney damage caused by drugs such as cisplatin, gentamicin, vancomycin, and tacrolimus. Neutrophil gelatinase-associated lipocalin (NGAL), liver-type fatty acid-binding protein (L-FABP), kidney injury molecule-1 (KIM-1), monocyte chemotactic protein-1 (MCP-1), and cystatin C have been identified as biomarkers for early kidney damage. Hy's Law is widely used as to predict a high risk of severe drug-induced liver injury caused by drugs such as acetaminophen. Recent reports have indicated that glutamate dehydrogenase (GLDH), high-mobility group box 1 (HMGB-1), Keratin-18 (k18), MicroRNA-122 and ornithine carbamoyltransferase (OCT) are more sensitive markers of hepatotoxicity compared to the traditional markers including the blood levels of amiotransferases and total bilirubin. Additionally, the rapid development of proteomic technologies in biofluids and tissue provides a new multi-marker panel, leading to the discovery of more sensitive biomarkers. In this review, an update topics of biomarkers for the detection of kidney or liver injury associated with pharmacotherapy.
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Affiliation(s)
- Soichiro Tajima
- Department of Pharmacy, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Nanae Yamamoto
- Department of Pharmacy, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Satohiro Masuda
- Department of Pharmacy, Kyushu University Hospital, Fukuoka 812-8582, Japan; Department of Clinical Pharmacology and Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Department of Pharmacy, International University of Health and Welfare Narita Hospital, Japan; Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, International University of Health and Welfare Narita Hospital, Japan.
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15
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Abstract
Acute kidney injury (AKI) is a severe and frequent condition in hospitalized patients. Currently, no efficient therapy of AKI is available. Therefore, efforts focus on early prevention and potentially early initiation of renal replacement therapy to improve the outcome in AKI. The detection of AKI in hospitalized patients implies the need for early, accurate, robust, and easily accessible biomarkers of AKI evolution and outcome prediction because only a narrow window exists to implement the earlier-described measures. Even more challenging is the multifactorial origin of AKI and the fact that the changes of molecular expression induced by AKI are difficult to distinguish from those of the diseases associated or causing AKI as shock or sepsis. During the past decade, a considerable number of protein biomarkers for AKI have been described and we expect from recent advances in the field of omics technologies that this number will increase further in the future and be extended to other sorts of biomolecules, such as RNAs, lipids, and metabolites. However, most of these biomarkers are poorly defined by their AKI-associated molecular context. In this review, we describe the state-of-the-art tissue and biofluid proteomic and metabolomic technologies and new bioinformatics approaches for proteomic and metabolomic pathway and molecular interaction analysis. In the second part of the review, we focus on AKI-associated proteomic and metabolomic biomarkers and briefly outline their pathophysiological context in AKI.
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16
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Navarrete M, Ho J, Dwivedi RC, Choi N, Ezzati P, Spicer V, Arora RC, Rigatto C, Wilkins JA. Activity-Based Protein Profiling of Intraoperative Serine Hydrolase Activities during Cardiac Surgery. J Proteome Res 2018; 17:3547-3556. [PMID: 30192561 DOI: 10.1021/acs.jproteome.8b00500] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The processes involved in the initiation of acute kidney injury (AKI) following cardiopulmonary bypass (CPB) are thought to occur during the intraoperative period. Such a rapid development might indicate that some of the inductive events are not dependent on de novo protein synthesis, raising the possibility that changes in activities of pre-existing enzymes could contribute to the development of AKI. Activity-based protein profiling (ABPP) was used to compare the serine hydrolase enzyme activities present in the urines of CPB patients who subsequently developed AKI versus those who did not (non-AKI) during the intra- and immediate postoperative periods. Sequential urines collected from a nested case-control cohort of AKI and non-AKI patients were reacted with a serine hydrolase activity probe, fluorophosphonate-TAMRA, and separated by SDS-PAGE. The patterns and levels of probe-labeled proteins in the two groups were initially comparable. However, within 1 h of CPB there were significant pattern changes in the AKI group. Affinity purification and mass spectrometry-based analysis of probe-labeled enzymes in AKI urines at 1 h CPB and arrival to the intensive care unit (ICU) identified 28 enzymes. Quantitative analysis of the activity of one of the identified enzymes, kallikrein-1, revealed some trends suggesting differences in the levels and temporal patterns of enzyme activity between a subset of patients who developed AKI and those who did not. A comparative analysis of affinity-purified probe reacted urinary proteins from these patient groups during the intraoperative period suggested the presence of both shared and unique enzyme patterns. These results indicate that there are intraoperative changes in the levels and types of serine hydrolase activities in patients who subsequently develop AKI. However, the role of these activity differences in the development of AKI remains to be determined.
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Affiliation(s)
- Mario Navarrete
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada
| | - Julie Ho
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada.,Department of Internal Medicine, Section of Nephrology , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada.,Department of Internal Medicine, Section of Biomedical Proteomics , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada.,Department of Immunology , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - Ravi C Dwivedi
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada
| | - Nora Choi
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada.,Department of Immunology , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - Peyman Ezzati
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada
| | - Rakesh C Arora
- Department of Surgery , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada.,Cardiac Sciences Program , St Boniface Hospital , Winnipeg , Manitoba R2H 2A6 , Canada
| | - Claudio Rigatto
- Department of Internal Medicine, Section of Nephrology , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - John A Wilkins
- Manitoba Centre for Proteomics & Systems Biology , University of Manitoba & Health Sciences Centre , Winnipeg , Manitoba R3E 3P4 , Canada.,Department of Internal Medicine, Section of Biomedical Proteomics , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
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17
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Reperfusion Activates AP-1 and Heat Shock Response in Donor Kidney Parenchyma after Warm Ischemia. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5717913. [PMID: 30186861 PMCID: PMC6116402 DOI: 10.1155/2018/5717913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/28/2018] [Accepted: 07/16/2018] [Indexed: 01/19/2023]
Abstract
Utilization of kidneys from extended criteria donors leads to an increase in average warm ischemia time (WIT), which is associated with larger degrees of ischemia-reperfusion injury (IRI). Kidney resuscitation by extracorporeal perfusion in situ allows up to 60 minutes of asystole after the circulatory death. Molecular studies of kidney grafts from human donors with critically expanded WIT are warranted. Transcriptomes of two human kidneys from two different donors were profiled after 35-45 minutes of WIT and after 120 minutes of normothermic perfusion and compared. Baseline gene expression patterns in ischemic grafts display substantial intrinsic differences. IRI does not lead to substantial change in overall transcription landscape but activates a highly connected protein network with hubs centered on Jun/Fos/ATF transcription factors and HSP1A/HSPA5 heat shock proteins. This response is regulated by positive feedback. IRI networks are enriched in soluble proteins and biofluids assayable substances, thus, indicating feasibility of the longitudinal, minimally invasive assessment in vivo. Mapping of IRI related molecules in ischemic and reperfused kidneys provides a rationale for possible organ conditioning during machine assisted ex vivo normothermic perfusion. A study of natural diversity of the transcriptional landscapes in presumably normal, transplantation-suitable human organs is warranted.
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18
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Proteo-metabolomics reveals compensation between ischemic and non-injured contralateral kidneys after reperfusion. Sci Rep 2018; 8:8539. [PMID: 29867102 PMCID: PMC5986744 DOI: 10.1038/s41598-018-26804-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/18/2018] [Indexed: 12/18/2022] Open
Abstract
Ischaemia and reperfusion injury (IRI) is the leading cause of acute kidney injury (AKI), which contributes to high morbidity and mortality rates in a wide range of injuries as well as the development of chronic kidney disease. The cellular and molecular responses of the kidney to IRI are complex and not fully understood. Here, we used an integrated proteomic and metabolomic approach to investigate the effects of IRI on protein abundance and metabolite levels. Rat kidneys were subjected to 45 min of warm ischaemia followed by 4 h and 24 h reperfusion, with contralateral and separate healthy kidneys serving as controls. Kidney tissue proteomics after IRI revealed elevated proteins belonging to the acute phase response, coagulation and complement pathways, and fatty acid (FA) signalling. Metabolic changes were already evident after 4 h reperfusion and showed increased level of glycolysis, lipids and FAs, whilst mitochondrial function and ATP production was impaired after 24 h. This deficit was partially compensated for by the contralateral kidney. Such a metabolic balance counteracts for the developing energy deficit due to reduced mitochondrial function in the injured kidney.
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19
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Pang L, Li Q, Li Y, Liu Y, Duan N, Li H. Urine proteomics of primary membranous nephropathy using nanoscale liquid chromatography tandem mass spectrometry analysis. Clin Proteomics 2018; 15:5. [PMID: 29445323 PMCID: PMC5801694 DOI: 10.1186/s12014-018-9183-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
Background Primary membranous nephropathy (PMN) is an important cause of nephrotic syndrome in adults. Urine proteome may provide important clues of pathophysiological mechanisms in PMN. In the current study, we analyzed and compared the proteome of urine from patients with PMN and normal controls. Methods We performed two technical replicates (TMT1 and TMT2) to analyze and compare the urine proteome from patients with PMN and normal controls by tandem mass tag (TMT) technology coupled with nanoscale liquid chromatography tandem mass spectrometry analysis (LC–MS/MS). Gene ontology (GO) enrichment analysis was performed to analyse general characterization of the proteins. The proteins were also matched against the database of Kyoto Encyclopedia of Genes and Genomes (KEGG). For validation, Western blot was used to analyze the selected proteins. Results A total of 509 proteins and 411 proteins were identified in TMT1 and TMT2, respectively. 249 proteins were both identified in two technical replicates. GO analysis and KEGG analysis revealed immunization and coagulation were predominantly involved. Among the differential protein, the overexcretion of alpha-1-antitrypsin (A1AT) and afamin (AFM) were validated by Western blot analysis. Conclusions Our data showed the important role of immunologic mechanism in the development of PMN, and the value of urinary A1AT and AFM in biomarker discovery of patients with PMN. The discovery of the overexcretion of A1AT and AFM in the urine can help to further elucidate pathogenetic mechanisms involved in PMN. Electronic supplementary material The online version of this article (10.1186/s12014-018-9183-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lu Pang
- 1Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Qianqian Li
- 2Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- 2Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yi Liu
- 1Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Nan Duan
- 1Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Haixia Li
- 1Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
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