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Altman J, Bai S, Purohit S, White J, Steed D, Liu S, Hopkins D, She JX, Sharma A, Zhi W. A candidate panel of eight urinary proteins shows potential of early diagnosis and risk assessment for diabetic kidney disease in type 1 diabetes. J Proteomics 2024; 300:105167. [PMID: 38574989 DOI: 10.1016/j.jprot.2024.105167] [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: 11/17/2023] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Diabetic kidney disease (DKD) poses a significant health challenge for individuals with diabetes. At its initial stages, DKD often presents asymptomatically, and the standard for non-invasive diagnosis, the albumin-creatinine ratio (ACR), employs discrete categorizations (normal, microalbuminuria, macroalbuminuria) with limitations in sensitivity and specificity across diverse population cohorts. Single biomarker reliance further restricts the predictive value in clinical settings. Given the escalating prevalence of diabetes, our study uses proteomic technologies to identify novel urinary proteins as supplementary DKD biomarkers. A total of 158 T1D subjects provided urine samples, with 28 (15 DKD; 13 non-DKD) used in the discovery stage and 131 (45 DKD; 40 pDKD; 46 non-DKD) used in the confirmation. We identified eight proteins (A1BG, AMBP, AZGP1, BTD, RBP4, ORM2, GM2A, and PGCP), all of which demonstrated excellent area-under-the-curve (AUC) values (0.959 to 0.995) in distinguishing DKD from non-DKD. Furthermore, this multi-marker panel successfully segregated the most ambiguous group (microalbuminuria) into three distinct clusters, with 80% of subjects aligning either as DKD or non-DKD. The remaining 20% exhibited continued uncertainty. Overall, the use of these candidate urinary proteins allowed for the better classification of DKD and offered potential for significant improvements in the early identification of DKD in T1D populations.
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Affiliation(s)
- Jeremy Altman
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Sharad Purohit
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA; Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - John White
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - Dennis Steed
- Southeastern Endocrine and Diabetes, Atlanta, GA 30076, USA
| | - Su Liu
- Department of Endocrinology, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu Province
| | - Diane Hopkins
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA; Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - Jin-Xiong She
- Jinfiniti Precision Medicine, Augusta, GA 30901, USA.
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA; Department of Ophthalmology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
| | - Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA; Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
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2
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Hu X, Chen S, Ye S, Chen W, Zhou Y. New insights into the role of immunity and inflammation in diabetic kidney disease in the omics era. Front Immunol 2024; 15:1342837. [PMID: 38487541 PMCID: PMC10937589 DOI: 10.3389/fimmu.2024.1342837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Diabetic kidney disease (DKD) is becoming the leading cause of chronic kidney disease, especially in the industrialized world. Despite mounting evidence has demonstrated that immunity and inflammation are highly involved in the pathogenesis and progression of DKD, the underlying mechanisms remain incompletely understood. Substantial molecules, signaling pathways, and cell types participate in DKD inflammation, by integrating into a complex regulatory network. Most of the studies have focused on individual components, without presenting their importance in the global or system-based processes, which largely hinders clinical translation. Besides, conventional technologies failed to monitor the different behaviors of resident renal cells and immune cells, making it difficult to understand their contributions to inflammation in DKD. Recently, the advancement of omics technologies including genomics, epigenomics, transcriptomics, proteomics, and metabolomics has revolutionized biomedical research, which allows an unbiased global analysis of changes in DNA, RNA, proteins, and metabolites in disease settings, even at single-cell and spatial resolutions. They help us to identify critical regulators of inflammation processes and provide an overview of cell heterogeneity in DKD. This review aims to summarize the application of multiple omics in the field of DKD and emphasize the latest evidence on the interplay of inflammation and DKD revealed by these technologies, which will provide new insights into the role of inflammation in the pathogenesis of DKD and lead to the development of novel therapeutic approaches and diagnostic biomarkers.
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Affiliation(s)
- Xinrong Hu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Sixiu Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Siyang Ye
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Yi Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
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3
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Zhuang X, Sun Z, Du H, Zhou T, Zou J, Fu W. Metformin inhibits high glucose-induced apoptosis of renal podocyte through regulating miR-34a/SIRT1 axis. Immun Inflamm Dis 2024; 12:e1053. [PMID: 38270305 PMCID: PMC10797654 DOI: 10.1002/iid3.1053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/21/2023] [Accepted: 10/09/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Previous studies have reported SIRT1 was inversely modulated by miR-34a, However, mechanism of metformin (MFN)'s renal podocyte protection under high glucose (HG) conditions and the connection between miR-34a and SIRT1 expression in diabetic nephropathy (DN) remain unclear. METHOD We aimed to further elucidate the role of miR-34a in HG-treated podocytes in DN. A conditionally immortalized human podocyte cell line was cultivated in d-glucose (30 mM). RESULTS Microarray and RT-qPCR revealed that miR-34a was downregulated in HG-treated podocytes. Additionally, miR-34a levels increased in MFN-treated HG-induced podocytes. CCK-8 assay, colony formation assay, flow cytometry, and Western blot detection showed that HG treatment reduced cell viability and promoted via HG treatment, and MFN treatment reversed this phenotypic change. MiR-34a upregulation caused restored cell viability and suppressed cell apoptosis in HG-treated podocytes, and miR-34a downregulation led to damaged cell survival and induced apoptosis in MFN-administered and HG-treated podocytes. The dual luciferase reporter assay showed that SIRT1 3'-UTR was a direct miR-34a target. Further studies demonstrated an elevation in SIRT1 levels in HG-exposed podocytes, whereas MFN treatment decreased SIRT1 levels. In addition, miR-34a upregulation led to reduced SIRT1 expression, whereas miR-34a inhibition increased SIRT1 levels in cells. MFN-induced miR-34a suppresses podocyte apoptosis under HG conditions by acting on SIRT1. CONCLUSION This study proposes a promising approach to interpret the mechanisms of action of the MFN-miR-34a axis involved in DN.
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Affiliation(s)
- Xudong Zhuang
- Department of DialysisLinyi Traditional Chinese Medicine HospitalLinyiShandongChina
| | - Zhuye Sun
- Department of PharmacyRizhao Hospital of Traditional Chinese MedicineRizhaoShandongChina
| | - Huasheng Du
- Department of NephrologyQingdao Municipal HospitalQingdaoShandongChina
| | - Tianhui Zhou
- Beijing University of Chinese MedicineBeijingChina
| | - Jing Zou
- Department of DialysisLinyi Traditional Chinese Medicine HospitalLinyiShandongChina
| | - Wei Fu
- Department of Drug DispensingZibo Central HospitalZiboShandongChina
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4
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Kononikhin AS, Brzhozovskiy AG, Bugrova AE, Chebotareva NV, Zakharova NV, Semenov S, Vinogradov A, Indeykina MI, Moiseev S, Larina IM, Nikolaev EN. Targeted MRM Quantification of Urinary Proteins in Chronic Kidney Disease Caused by Glomerulopathies. Molecules 2023; 28:molecules28083323. [PMID: 37110557 PMCID: PMC10142111 DOI: 10.3390/molecules28083323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Glomerulopathies with nephrotic syndrome that are resistant to therapy often progress to end-stage chronic kidney disease (CKD) and require timely and accurate diagnosis. Targeted quantitative urine proteome analysis by mass spectrometry (MS) with multiple-reaction monitoring (MRM) is a promising tool for early CKD diagnostics that could replace the invasive biopsy procedure. However, there are few studies regarding the development of highly multiplexed MRM assays for urine proteome analysis, and the two MRM assays for urine proteomics described so far demonstrate very low consistency. Thus, the further development of targeted urine proteome assays for CKD is actual task. Herein, a BAK270 MRM assay previously validated for blood plasma protein analysis was adapted for urine-targeted proteomics. Because proteinuria associated with renal impairment is usually associated with an increased diversity of plasma proteins being present in urine, the use of this panel was appropriate. Another advantage of the BAK270 MRM assay is that it includes 35 potential CKD markers described previously. Targeted LC-MRM MS analysis was performed for 69 urine samples from 46 CKD patients and 23 healthy controls, revealing 138 proteins that were found in ≥2/3 of the samples from at least one of the groups. The results obtained confirm 31 previously proposed CKD markers. Combination of MRM analysis with machine learning for data processing was performed. As a result, a highly accurate classifier was developed (AUC = 0.99) that enables distinguishing between mild and severe glomerulopathies based on the assessment of only three urine proteins (GPX3, PLMN, and A1AT or SHBG).
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Affiliation(s)
- Alexey S Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Alexander G Brzhozovskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of the Ministry of Health, 117997 Moscow, Russia
| | - Anna E Bugrova
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of the Ministry of Health, 117997 Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Kosygina Str. 4, 119334 Moscow, Russia
| | - Natalia V Chebotareva
- Nephrology Department, Sechenov First Moscow State Medical University, Trubezkaya 8, 119048 Moscow, Russia
- Department of Internal Medicine, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Natalia V Zakharova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Kosygina Str. 4, 119334 Moscow, Russia
| | - Savva Semenov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anatoliy Vinogradov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Internal Medicine, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Maria I Indeykina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Kosygina Str. 4, 119334 Moscow, Russia
| | - Sergey Moiseev
- Nephrology Department, Sechenov First Moscow State Medical University, Trubezkaya 8, 119048 Moscow, Russia
| | - Irina M Larina
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, Khoroshevskoe Shosse 76A, 123007 Moscow, Russia
| | - Evgeny N Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
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Urinary microRNA in Diabetic Kidney Disease: A Literature Review. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59020354. [PMID: 36837555 PMCID: PMC9962090 DOI: 10.3390/medicina59020354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023]
Abstract
Diabetic kidney disease is the most common primary disease of end-stage kidney disease globally; however, a sensitive and accurate biomarker to predict this disease remains awaited. microRNAs are endogenous single-stranded noncoding RNAs that have intervened in different post-transcriptional regulations of various cellular biological functions. Previous literatures have reported its potential role in the pathophysiology of diabetic kidney disease, including regulation of Transforming Growth Factor-β1-mediated fibrosis, extracellular matrix and cell adhesion proteins, cellular hypertrophy, growth factor, cytokine production, and redox system activation. Urinary microRNAs have emerged as a novel, non-invasive liquid biopsy for disease diagnosis. In this review, we describe the available experimental and clinical evidence of urinary microRNA in the context of diabetic kidney disease and discuss the future application of microRNA in routine practice.
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Liu H, Feng J, Tang L. Early renal structural changes and potential biomarkers in diabetic nephropathy. Front Physiol 2022; 13:1020443. [PMID: 36425298 PMCID: PMC9679365 DOI: 10.3389/fphys.2022.1020443] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/26/2022] [Indexed: 08/10/2023] Open
Abstract
Diabetic nephropathy is one of the most serious microvascular complications of diabetes mellitus, with increasing prevalence and mortality. Currently, renal function is assessed clinically using albumin excretion rate and glomerular filtration rate. But before the appearance of micro-albumin, the glomerular structure has been severely damaged. Glomerular filtration rate based on serum creatinine is a certain underestimate of renal status. Early diagnosis of diabetic nephropathy has an important role in improving kidney function and delaying disease progression with drugs. There is an urgent need for biomarkers that can characterize the structural changes associated with the kidney. In this review, we focus on the early glomerular and tubular structural alterations, with a detailed description of the glomerular injury markers SMAD1 and Podocalyxin, and the tubular injury markers NGAL, Netrin-1, and L-FABP in the context of diabetic nephropathy. We have summarized the currently studied protein markers and performed bioprocess analysis. Also, a brief review of proteomic and scRNA-seq method in the search of diabetic nephropathy.
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Affiliation(s)
- Hao Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University; Laboratory of Anesthesiology, Southwest Medical University, Luzhou, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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7
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Maghbooli Z, Ebrahimi Meimand S, Malek Hosseini AA, Shirvani A. Alterations in circulating levels of vitamin D binding protein, total and bioavailability of vitamin D in diabetic retinopathy patients. BMC Endocr Disord 2022; 22:169. [PMID: 35778716 PMCID: PMC9250226 DOI: 10.1186/s12902-022-01084-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/22/2022] [Indexed: 12/04/2022] Open
Abstract
AIMS This study aimed to investigate the association between circulating levels of vitamin D binding protein (VDBP) and its genotypes and diabetic retinopathy risk. METHODS This case-control study recruited 154 patients with type 2 diabetes mellitus; 62 with diabetic retinopathy (DR) and 92 without DR and diabetic nephropathy (DN). Circulating levels of 25-hydroxyvitamin D3 and VDBP levels were measured in the patients. The genotype and phenotype of VDBP were evaluated based on two common VDBP variations; rs7041 and rs4588. RESULTS Serum levels of VDBP were significantly lower in patients with DR than in patients without DR and/or DN (Ln-VDBP (μg/ml): 6.14 ± 0.92 vs. 6.73 ± 1.45, p = 0.001) even after adjustment for age, sex, body mass index, disease duration, estimated glomerular filtration rate (eGFR), HbA1C, insulin therapy profile, and serum levels of 25(OH)D. The distribution of VDBP phenotypes and genotypes in the two studied groups were nearly the same, and the distribution was similar to that of the general population. CONCLUSIONS In this study, we found the association between lower circulating levels of VDBP and risk of DR. However, the precise mechanism linking these two remains unknown. Further and more in-depth research is needed to find out the underlying causes of the relationship.
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Affiliation(s)
- Zhila Maghbooli
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | | | - Ali-Asghar Malek Hosseini
- Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Prediction of Type 2 Diabetes at Pre-diabetes Stage by Mass Spectrometry: A Preliminary Study. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10419-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Urinary Protein and Peptide Markers in Chronic Kidney Disease. Int J Mol Sci 2021; 22:ijms222212123. [PMID: 34830001 PMCID: PMC8625140 DOI: 10.3390/ijms222212123] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic kidney disease (CKD) is a non-specific type of kidney disease that causes a gradual decline in kidney function (from months to years). CKD is a significant risk factor for death, cardiovascular disease, and end-stage renal disease. CKDs of different origins may have the same clinical and laboratory manifestations but different progression rates, which requires early diagnosis to determine. This review focuses on protein/peptide biomarkers of the leading causes of CKD: diabetic nephropathy, IgA nephropathy, lupus nephritis, focal segmental glomerulosclerosis, and membranous nephropathy. Mass spectrometry (MS) approaches provided the most information about urinary peptide and protein contents in different nephropathies. New analytical approaches allow urinary proteomic-peptide profiles to be used as early non-invasive diagnostic tools for specific morphological forms of kidney disease and may become a safe alternative to renal biopsy. MS studies of the key pathogenetic mechanisms of renal disease progression may also contribute to developing new approaches for targeted therapy.
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10
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Diabetic nephropathy: A twisted thread to unravel. Life Sci 2021; 278:119635. [PMID: 34015285 DOI: 10.1016/j.lfs.2021.119635] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022]
Abstract
Diabetic nephropathy (DN), a persistent microvascular problem of diabetes mellitus is described as an elevated level of albumin excretion in urine and impaired renal activity. The morbidity and mortality of type-1 diabetics and type-2 diabetics due to end stage renal disease is also a result of the increased prevalence of DN. DN typically occurs as a consequence of an association among metabolic and hemodynamic variables, activating specific pathways leading to renal injury. According to current interventions, intensive glucose regulation decreases the threat of DN incidence and growth, and also suppressing the renin-angiotensin system (RAS) is a significant goal for hemodynamic and metabolism-related deformities in DN. However, the pathogenesis of DN is multifactorial so novel approaches other than glucose and blood pressure control are required for treatment. This review briefly summarizes the reported pathogenesis of DN, current interventions for its treatment, and possible novel interventions to unweave the thread of DN.
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11
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Masood A, Benabdelkamel H, Jammah AA, Ekhzaimy AA, Alfadda AA. Identification of Protein Changes in the Urine of Hypothyroid Patients Treated with Thyroxine Using Proteomics Approach. ACS OMEGA 2021; 6:2367-2378. [PMID: 33521475 PMCID: PMC7841925 DOI: 10.1021/acsomega.0c05686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
The thyroid gland and thyroid hormones control a multitude of homeostatic functions including maintenance of fluid and electrolyte balance and normal functioning of the kidneys. Thyroid dysfunction alters the sytemic hemodynamic and metabolic balance, thereby affecting the kidney. In this study, we aimed to identify and characterize the urinary proteome of the patients with hypothyroidism. An untargeted proteomic approach with network analysis was used to identify changes in total urinary proteome in patients with newly diagnosed overt hypothyroidism. Urine samples were collected from nine age-matched patients' before and after l-thyroxine treatment. Differences in the abundance of urinary proteins between hypothyroid and euthyroid states were determined using a two-dimensional difference in gel electrophoresis (2D-DIGE) coupled to matrix-assisted laser desorption and ionization time-of-flight (MALDI TOF) mass spectrometry. Alterations in the abundance of urinary proteins, analyzed by Progenesis software, revealed statistically significant differential abundance in a total of 49 spots corresponding to 42 proteins, 28 up and 14 down (≥1.5-fold change, analysis of variance (ANOVA), p ≤ 0.05). The proteins identified in the study are known to regulate processes related to transport, acute phase response, oxidative stress, generation of reactive oxygen species, cellular proliferation, and endocytosis. Bioinformatic analysis using Ingenuity Pathway Analysis (IPA) identified dysregulation of pathways related to amino acid metabolism, molecular transport, and small-molecule biochemistry and involved the MAPK kinase, vascular endothelial growth factor (VEGF), PI3 kinase/Akt, protein kinase C (PKC), signaling pathways. The identified proteins were involved in the regulation of thyroglobulin (Tg) and thyrotropin (TSH) metabolism. Alterations in their levels indicate the presence of a compensatory mechanism aimed at increasing the regulation of Tg in the hypothyroid state.
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Affiliation(s)
- Afshan Masood
- Proteomics
Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Hicham Benabdelkamel
- Proteomics
Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Anwar A. Jammah
- Department
of Medicine, College of Medicine and King Saud Medical City, King Saud University, Riyadh 12372, Saudi Arabia
| | - Aishah A. Ekhzaimy
- Department
of Medicine, College of Medicine and King Saud Medical City, King Saud University, Riyadh 12372, Saudi Arabia
| | - Assim A. Alfadda
- Proteomics
Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
- Department
of Medicine, College of Medicine and King Saud Medical City, King Saud University, Riyadh 12372, Saudi Arabia
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12
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Wang L, Liu K, Li S, Tang H. A Fast and Memory-Efficient Spectral Library Search Algorithm Using Locality-Sensitive Hashing. Proteomics 2020; 20:e2000002. [PMID: 32415809 PMCID: PMC7669687 DOI: 10.1002/pmic.202000002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/17/2020] [Indexed: 01/07/2023]
Abstract
With the accumulation of MS/MS spectra collected in spectral libraries, the spectral library searching approach emerges as an important approach for peptide identification in proteomics, complementary to the commonly used protein database searching approach, in particular for the proteomic analyses of well-studied model organisms, such as human. Existing spectral library searching algorithms compare a query MS/MS spectrum with each spectrum in the library with matched precursor mass and charge state, which may become computationally intensive with the rapidly growing library size. Here, the software msSLASH, which implements a fast spectral library searching algorithm based on the Locality-Sensitive Hashing (LSH) technique, is presented. The algorithm first converts the library and query spectra into bit-strings using LSH functions, and then computes the similarity between the spectra with highly similar bit-string. Using the spectral library searching of large real-world MS/MS spectra datasets, it is demonstrated that the algorithm significantly reduced the number of spectral comparisons, and as a result, achieved 2-9X speedup in comparison with existing spectral library searching algorithm SpectraST. The spectral searching algorithm is implemented in C/C++, and is ready to be used in proteomic data analyses.
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Affiliation(s)
- Lei Wang
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - Kaiyuan Liu
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - Sujun Li
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
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13
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Beige J, Drube J, von der Leyen H, Pape L, Rupprecht H. Früherkennung mittels Urinproteomanalyse. Internist (Berl) 2020; 61:1094-1105. [DOI: 10.1007/s00108-020-00863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Reckoning the Dearth of Bioinformatics in the Arena of Diabetic Nephropathy (DN)—Need to Improvise. Processes (Basel) 2020. [DOI: 10.3390/pr8070808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Diabetic nephropathy (DN) is a recent rising concern amongst diabetics and diabetologist. Characterized by abnormal renal function and ending in total loss of kidney function, this is becoming a lurking danger for the ever increasing population of diabetics. This review touches upon the intensity of this complication and briefly reviews the role of bioinformatics in the area of diabetes. The advances made in the area of DN using proteomic approaches are presented. Compared to the enumerable inputs observed through the use of bioinformatics resources in the area of proteomics and even diabetes, the existing scenario of skeletal application of bioinformatics advances to DN is highlighted and the reasons behind this discussed. As this review highlights, almost none of the well-established tools that have brought breakthroughs in proteomic research have been applied into DN. Laborious, voluminous, cost expensive and time-consuming methodologies and advances in diagnostics and biomarker discovery promised through beckoning bioinformatics mechanistic approaches to improvise DN research and achieve breakthroughs. This review is expected to sensitize the researchers to fill in this gap, exploiting the available inputs from bioinformatics resources.
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Urinary peptidomics and bioinformatics for the detection of diabetic kidney disease. Sci Rep 2020; 10:1242. [PMID: 31988353 PMCID: PMC6985249 DOI: 10.1038/s41598-020-58067-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/07/2020] [Indexed: 01/15/2023] Open
Abstract
The aim of this study was to establish a peptidomic profile based on LC-MS/MS and random forest (RF) algorithm to distinguish the urinary peptidomic scenario of type 2 diabetes mellitus (T2DM) patients with different stages of diabetic kidney disease (DKD). Urine from 60 T2DM patients was collected: 22 normal (stage A1), 18 moderately increased (stage A2) and 20 severely increased (stage A3) albuminuria. A total of 1080 naturally occurring peptides were detected, which resulted in the identification of a total of 100 proteins, irrespective of the patients’ renal status. The classification accuracy showed that the most severe DKD (A3) presented a distinct urinary peptidomic pattern. Estimates for peptide importance assessed during RF model training included multiple fragments of collagen and alpha-1 antitrypsin, previously associated to DKD. Proteasix tool predicted 48 proteases potentially involved in the generation of the 60 most important peptides identified in the urine of DM patients, including metallopeptidases, cathepsins, and calpains. Collectively, our study lightened some biomarkers possibly involved in the pathogenic mechanisms of DKD, suggesting that peptidomics is a valuable tool for identifying the molecular mechanisms underpinning the disease and thus novel therapeutic targets.
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16
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Ren X, Li X. Advances in Research on Diabetes by Human Nutriomics. Int J Mol Sci 2019; 20:ijms20215375. [PMID: 31671732 PMCID: PMC6861882 DOI: 10.3390/ijms20215375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/12/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022] Open
Abstract
The incidence and prevalence of diabetes mellitus (DM) have increased rapidly worldwide over the last two decades. Because the pathogenic factors of DM are heterogeneous, determining clinically effective treatments for DM patients is difficult. Applying various nutrient analyses has yielded new insight and potential treatments for DM patients. In this review, we summarized the omics analysis methods, including nutrigenomics, nutritional-metabolomics, and foodomics. The list of the new targets of SNPs, genes, proteins, and gut microbiota associated with DM has been obtained by the analysis of nutrigenomics and microbiomics within last few years, which provides a reference for the diagnosis of DM. The use of nutrient metabolomics analysis can obtain new targets of amino acids, lipids, and metal elements, which provides a reference for the treatment of DM. Foodomics analysis can provide targeted dietary strategies for DM patients. This review summarizes the DM-associated molecular biomarkers in current applied omics analyses and may provide guidance for diagnosing and treating DM.
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Affiliation(s)
- Xinmin Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China.
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Xiangdong Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China.
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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17
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Xiang AS, Ekinci EI, MacIsaac RJ. Inflammatory proteins in diabetic kidney disease-potential as biomarkers and therapeutic targets. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S243. [PMID: 31656822 DOI: 10.21037/atm.2019.08.20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Angie S Xiang
- Central Clinical School, Monash University, Victoria, Australia
| | - Elif I Ekinci
- Endocrine Center, Austin Health, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard J MacIsaac
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia.,Department of Endocrinology & Diabetes, St Vincent's Hospital Melbourne, Victoria, Australia
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18
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Elsheikh M, Elhefnawy KA, Emad G, Ismail M, Borai M. Zinc alpha 2 glycoprotein as an early biomarker of diabetic nephropathy in patients with type 2 diabetes mellitus. ACTA ACUST UNITED AC 2019; 41:509-517. [PMID: 30897192 PMCID: PMC6979576 DOI: 10.1590/2175-8239-jbn-2018-0200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/11/2019] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Although microalbuminuria remains the gold standard for early detection of diabetic nephropathy (DN), it is not a sufficiently accurate predictor of DN risk. Thus, new biomarkers that would help to predict DN risk earlier and possibly prevent the occurrence of end-stage kidney disease are being investigated. OBJECTIVE To investigate the role of zinc-alpha-2-glycoprotein (ZAG) as an early marker of DN in type 2 diabetic (T2DM) patients. METHODS 88 persons were included and classified into 4 groups: Control group (group I), composed of normal healthy volunteers, and three patient groups with type 2 diabetes mellitus divided into: normo-albuminuria group (group II), subdivided into normal eGFR subgroup and increased eGFR subgroup > 120 mL/min/1.73m2), microalbuminuria group (group III), and macroalbuminuria group (group IV). All subjects were submitted to urine analysis, blood glucose levels, HbA1c, liver function tests, serum creatinine, uric acid, lipid profile and calculation of eGFR, urinary albumin creatinine ratio (UACR), and measurement of urinary and serum ZAG. RESULTS The levels of serum and urine ZAG were higher in patients with T2DM compared to control subjects and a statistically significant difference among studied groups regarding serum and urinary ZAG was found. Urine ZAG levels were positively correlated with UACR. Both ZAG levels were negatively correlated with eGFR. Urine ZAG levels in the eGFR ˃ 120 mL/min/1.73m2 subgroup were higher than that in the normal eGFR subgroup. CONCLUSION These findings suggest that urine and serum ZAG might be useful as early biomarkers for detection of DN in T2DM patients, detectable earlier than microalbuminuria.
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Affiliation(s)
- Mohamed Elsheikh
- Faculty of Medicine, Internal Medicine Department, Zagazig University, Egypt
| | - Khaled A Elhefnawy
- Faculty of Medicine, Internal Medicine Department, Zagazig University, Egypt
| | - George Emad
- Faculty of Medicine, Internal Medicine Department, Zagazig University, Egypt
| | - Mabrouk Ismail
- Faculty of Medicine, Internal Medicine Department, Zagazig University, Egypt
| | - Maher Borai
- Faculty of Medicine, Clinical Pathology Department, Zagazig University, Egypt
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19
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Cañadas-Garre M, Anderson K, McGoldrick J, Maxwell AP, McKnight AJ. Proteomic and metabolomic approaches in the search for biomarkers in chronic kidney disease. J Proteomics 2019; 193:93-122. [PMID: 30292816 DOI: 10.1016/j.jprot.2018.09.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/20/2018] [Accepted: 09/30/2018] [Indexed: 12/15/2022]
Abstract
Chronic kidney disease (CKD) is an aging-related disorder that represents a major global public health burden. Current biochemical biomarkers, such as serum creatinine and urinary albumin, have important limitations when used to identify the earliest indication of CKD or in tracking the progression to more advanced CKD. These issues underline the importance of finding and testing new molecular biomarkers that are capable of successfully meeting this clinical need. The measurement of changes in nature and/or levels of proteins and metabolites in biological samples from patients provide insights into pathophysiological processes. Proteomic and metabolomic techniques provide opportunities to record dynamic chemical signatures in patients over time. This review article presents an overview of the recent developments in the fields of metabolomics and proteomics in relation to CKD. Among the many different proteomic biomarkers proposed, there is particular interest in the CKD273 classifier, a urinary proteome biomarker reported to predict CKD progression and with implementation potential. Other individual non-invasive peptidomic biomarkers that are potentially relevant for CKD detection include type 1 collagen, uromodulin and mucin-1. Despite the limited sample sizes and variability of the metabolomics studies, some metabolites such as trimethylamine N-oxide, kynurenine and citrulline stand out as potential biomarkers in CKD.
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Affiliation(s)
- M Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, United Kingdom; Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom.
| | - K Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, United Kingdom; Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom.
| | - J McGoldrick
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, United Kingdom; Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom.
| | - A P Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, United Kingdom; Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom.
| | - A J McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, United Kingdom; Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom.
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20
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Overview of genomics and post-genomics research on type 2 diabetes mellitus: Future perspectives and a framework for further studies. J Biosci 2019. [DOI: 10.1007/s12038-018-9818-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Patel DN, Kalia K. Characterization of low molecular weight urinary proteins at varying time intervals in type 2 diabetes mellitus and diabetic nephropathy patients. Diabetol Metab Syndr 2019; 11:39. [PMID: 31131043 PMCID: PMC6525442 DOI: 10.1186/s13098-019-0430-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/20/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND To identify low molecular weight urinary proteins capable of detecting diabetic nephropathy patients which may predict renal alterations at early stages and prevent it from worsening further. METHOD Three hundred ninety (390) age-matched subjects were divided into 8 groups depending upon duration of diabetes and the severity of renal damage. Urinary proteome profile of all subjects was determined with the help of microfluidic array. Participants with similar profile were further selected to study proteome map of urinary low molecular weight proteins with the help of 2 dimensional gel electrophoresis. RESULTS Out of 390 total patients 268 patients showed a similar one dimensional proteomic pattern. Further, two-dimensional urinary proteomic pattern of these patients with molecular weight < 50 kDa was studied. Eight proteins with molecular weight 11, 15, 17, 23, 34, 38 and 46 kDa were identified with MALDI-QTOF. These low molecular weight proteins showed gradual increase in urinary excretion along with the duration of diabetes and severity of renal damage. CONCLUSION The study concludes that proteomic analysis might be a useful tool for detecting some novel markers capable of detecting patients susceptible to diabetic nephropathy in the early phase.
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Affiliation(s)
- Dhara N. Patel
- Department of Medical Laboratory Technology, Charotar Institute of Paramedical Sciences, CHARUSAT, CHARUSAT-Campus, Highway 139, Off, Nadiad-Petlad Road, Changa, Gujarat 388421 India
| | - Kiran Kalia
- Present Address: National Institute of Pharmaceutical Education and Research (NIPER-G), Gandhinagar Opposite Air Force Station, Palaj, Gandhinagar, Gujarat 382355 India
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22
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Pang L, Duan N, Xu D, Jiao L, Huang C, Du J, Guo Q, Li H. Urine afamin and afamin-creatinine ratio as biomarkers for kidney injury. Biomark Med 2018; 12:1241-1249. [PMID: 30433819 DOI: 10.2217/bmm-2018-0126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIM The aim of this study was to evaluate the urine afamin (uAFM) and afamin-creatinine ratio (AfCR) levels in patients with glomerulonephritis. PATIENTS & METHODS We determined uAFM and AfCR of 247 healthy volunteers and 129 biopsy-proven glomerulonephritis patients. RESULTS Analytical evaluation study revealed the assay is a reliable and robust test for measuring uAFM. For reference intervals, uAFM and AfCR values were different significantly between males and females. uAFM and AfCR levels were significantly increased in patients with primary membranous nephropathy, IgA nephropathy and minimal change disease compared with healthy volunteers. uAFM and AfCR were positively correlated with urine albumin and albumin-creatinine ratio, respectively. CONCLUSION Our study suggested that uAFM and AfCR may be attractive biomarkers for kidney injury.
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Affiliation(s)
- Lu Pang
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Nan Duan
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Dong Xu
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Lili Jiao
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Chenwei Huang
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Jialin Du
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Qi Guo
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
| | - Haixia Li
- Department of Clinical Laboratory, Peking University First Hospital, 100034, Beijing, PR China
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23
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Wang N, Zhu F, Chen L, Chen K. Proteomics, metabolomics and metagenomics for type 2 diabetes and its complications. Life Sci 2018; 212:194-202. [DOI: 10.1016/j.lfs.2018.09.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/18/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023]
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24
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Cheng CW, Chang CC, Chen HW, Lin CY, Chen JS. Serum ApoA4 levels predicted the progression of renal impairment in T2DM. Eur J Clin Invest 2018; 48:e12937. [PMID: 29675916 DOI: 10.1111/eci.12937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/12/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Among multiple causes, diabetic nephropathy (DN) is the major underlying renal disease that leads to end-stage renal disease (ESRD), and early diagnosis can effectively prevent or delay the progression to ESRD. Therefore, the current study aimed to develop noninvasive, accurate detection markers. MATERIALS & METHODS For this study, 62 diabetes mellitus (DM) patients, 59 DN patients and 21 healthy controls (HCs) were recruited. All participants' serum samples were subjected to concavanalin (Con) A affinity chromatography, which utilizes glycoproteins to discover potential markers. RESULTS From nano LC-MS and Western blot analysis, apolipoprotein A-IV (ApoA4) was selected which featured a gradual, almost twofold increase in the order of HC, DM and DN. In the Con A-based ELISA, the DM group was 1.91-fold higher than the HC group, while the DN group was 2.56-fold higher than the HCs and 1.33-fold higher than the DM group. In addition, significant positive correlations were observed between ApoA4 and blood urea nitrogen levels and between ApoA4 and creatine levels, while significant negative correlations were seen between serum protein levels and between serum albumin levels in comparisons of DM and DN samples. CONCLUSIONS Serum Con A-bound ApoA4 levels were higher in the DM group than in HCs, and further increased in the DN group. Levels of ApoA4 were positively correlated with blood urea nitrogen and creatine, but negatively correlated with serum protein and albumin. This evidence supports serum Con A-bound ApoA4 as a circulating marker for predicting the progression of renal impairment in DM patients.
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Affiliation(s)
- Chao-Wen Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Che-Chang Chang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hsiu-Wen Chen
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ching-Yu Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Department of Biotechnology and Animal Science, National Ilan University, Ilan, Taiwan.,PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jin-Shuen Chen
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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25
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Grove KJ, Lareau NM, Voziyan PA, Zeng F, Harris RC, Hudson BG, Caprioli RM. Imaging mass spectrometry reveals direct albumin fragmentation within the diabetic kidney. Kidney Int 2018; 94:292-302. [PMID: 29779708 DOI: 10.1016/j.kint.2018.01.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/26/2022]
Abstract
Albumin degradation in the renal tubules is impaired in diabetic nephropathy such that levels of the resulting albumin fragments increase with the degree of renal injury. However, the mechanism of albumin degradation is unknown. In particular, fragmentation of the endogenous native albumin has not been demonstrated in the kidney and the enzymes that may contribute to fragmentation have not been identified. To explore this we utilized matrix-assisted laser desorption/ionization imaging mass spectrometry for molecular profiling of specific renal regions without disturbing distinct tissue morphology. Changes in protein expression were measured in kidney sections of eNOS-/-db/db mice, a model of diabetic nephropathy, by high spatial resolution imaging allowing molecular localizations at the level of single glomeruli and tubules. Significant increases were found in the relative abundances of several albumin fragments in the kidney of the mice with diabetic nephropathy compared with control nondiabetic mice. The relative abundance of fragments detected correlated positively with the degree of nephropathy. Furthermore, specific albumin fragments accumulating in the lumen of diabetic renal tubules were identified and predicted the enzymatic action of cathepsin D based on cleavage specificity and in vitro digestions. Importantly, this was demonstrated directly in the renal tissue with the endogenous nonlabeled murine albumin. Thus, our results provide molecular insights into the mechanism of albumin degradation in diabetic nephropathy.
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Affiliation(s)
- Kerri J Grove
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nichole M Lareau
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Paul A Voziyan
- Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Fenghua Zeng
- Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Raymond C Harris
- Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Billy G Hudson
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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26
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27
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Abdella NA, Mojiminiyi OA. Vitamin D-Binding Protein Clearance Ratio Is Significantly Associated with Glycemic Status and Diabetes Complications in a Predominantly Vitamin D-Deficient Population. J Diabetes Res 2018; 2018:6239158. [PMID: 29888290 PMCID: PMC5985098 DOI: 10.1155/2018/6239158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Studies have shown increased urine excretion of vitamin D-binding protein (VDBP) in patients with diabetic nephropathy (DN) resulting from postulated mechanisms linked to renal tubular damage. In this study, we evaluate the utility of VDBP clearance ratio as a novel determinant of glycemic status, DN, and other diabetes-associated complications. METHODS Levels of vitamin D, HbA1c, serum, urine concentrations of VDBP, and creatinine were measured in 309 subjects. The ratio of urine microalbumin to creatinine was determined to categorize subjects as normoalbuminuric (NAO), microalbuminuric (MIA), and macroalbuminuric (MAA). The VDBP clearance ratio was calculated. RESULTS Mean VDBP clearance ratios in NAO, MIA, and MAA were 0.7, 4, and 15, respectively. Significant positive correlations of VDBP clearance ratio were found with age, WC, SBP, DBP, TG, glucose, HbA1c, urine VDBP, urine microalbumin, and urine microalbumin/creatinine, and a significant negative correlation was found with the steady-state estimate of beta cell function (B%). Receiver operating curve (ROC) analyses of the use of VDBP clearance ratio for detection of albumin status shows a value of 0.81 for the area under the curve. CONCLUSIONS The strong associations of VDBP clearance ratio with glycemic control and diabetes-associated complications suggest that this index could play a wider role in detection and/or pathogenesis and complications of diabetes.
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Affiliation(s)
- Nabila A. Abdella
- Department of Medicine, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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28
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Fawzy MS, Abu AlSel BT. Assessment of Vitamin D-Binding Protein and Early Prediction of Nephropathy in Type 2 Saudi Diabetic Patients. J Diabetes Res 2018; 2018:8517929. [PMID: 29850609 PMCID: PMC5903345 DOI: 10.1155/2018/8517929] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/04/2018] [Indexed: 12/20/2022] Open
Abstract
Early detection of diabetic nephropathy (DN) represents a great challenge in an attempt to reduce the burden of chronic kidney diseases in diabetic patients. This study aimed to investigate the potential early prediction role of urinary vitamin D-binding protein (uVDBP) for the diagnosis of DN and to examine the possible correlation to serum VDBP, high-sensitivity C-reactive protein (hs-CRP), and insulin resistance in these patients. Serum and urine samples were obtained from 40 healthy volunteers and 120 patients with type 2 diabetes divided into 3 groups: normoalbuminuria, microalbuminuria, and macroalbuminuria (urinary albumin excretion rate < 30, 30-300, and >300 μg/mg, resp.); n = 40/group. Serum and urinary VDBP levels were quantified by ELISA. Insulin resistance has been assessed by homeostasis model assessment index (HOMAI). Correction for urine creatinine concentration was applied for urinary quantitative measurements. uVDBP levels were significantly elevated in micro- and macroalbuminuria patient groups compared with those of the normoalbuminuria patient group and controls (820.4 ± 402.8 and 1458.1 ± 210.0 compared with 193.1 ± 141.0 and 127.7 ± 21.9 ng/mg, resp.) (P < 0.001). There was significant correlation between serum and urinary levels of VDBP in total patient group. Receiver operating characteristic analysis of uVDBP levels showed optimum cut-off value of 216.0 ng/mg corresponding to 98.8% sensitivity and 80.0% specificity and an area under the curve of 0.973 to discriminate the normoalbuminuria from the microalbuminuria groups. In multivariate analysis, ordination plot showed obvious demarcation between the study groups caused by the higher levels of uVDBP and albumin/creatinine ratio among other variables. The study findings suggested a possible clinical application of uVDPB as an early and a good marker for the detection of early renal disease in type 2 DM Saudi patients. Large-scale validation studies are warranted to confirm the results before including uVDBP with the available list of other conventional biomarkers.
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Affiliation(s)
- Manal S. Fawzy
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Baraah T. Abu AlSel
- Department of Microbiology, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
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Guillén-Gómez E, Bardají-de-Quixano B, Ferrer S, Brotons C, Knepper MA, Carrascal M, Abian J, Mas JM, Calero F, Ballarín JA, Fernández-Llama P. Urinary Proteome Analysis Identified Neprilysin and VCAM as Proteins Involved in Diabetic Nephropathy. J Diabetes Res 2018; 2018:6165303. [PMID: 29854824 PMCID: PMC5949160 DOI: 10.1155/2018/6165303] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/12/2018] [Accepted: 04/04/2018] [Indexed: 01/13/2023] Open
Abstract
Urinary proteome was analyzed and quantified by tandem mass tag (TMT) labeling followed by bioinformatics analysis to study diabetic nephropathy (DN) pathophysiology and to identify biomarkers of a clinical outcome. We included type 2 diabetic normotensive non-obese males with (n = 9) and without (n = 11) incipient DN (microalbuminuria). Sample collection included blood and urine at baseline (control and DN basal) and, in DN patients, after 3 months of losartan treatment (DN treated). Urinary proteome analysis identified 166 differentially abundant proteins between controls and DN patients, 27 comparing DN-treated and DN-basal patients, and 182 between DN-treated patients and controls. The mathematical modeling analysis predicted 80 key proteins involved in DN pathophysiology and 15 in losartan effect, a total of 95 proteins. Out of these 95, 7 are involved in both processes. VCAM-1 and neprilysin stand out of these 7 for being differentially expressed in the urinary proteome. We observed an increase of VCAM-1 urine levels in DN-basal patients compared to diabetic controls and an increase of urinary neprilysin in DN-treated patients with persistent albuminuria; the latter was confirmed by ELISA. Our results point to neprilysin and VCAM-1 as potential candidates in DN pathology and treatment.
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Affiliation(s)
- Elena Guillén-Gómez
- Molecular Biology Laboratory, Fundació Puigvert, Barcelona, Spain
- Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Beatriz Bardají-de-Quixano
- Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Renal Transplantation Unit, Nephrology Department, Fundació Puigvert, Barcelona, Spain
| | - Sílvia Ferrer
- Maragall Primary Health Care Center, Barcelona, Spain
| | - Carlos Brotons
- Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Sardenya Primary Health Care Center, Barcelona, Spain
| | - Mark A. Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute (NIH), Bethesda, MD, USA
| | - Montserrat Carrascal
- Proteomics Laboratory CSIC/UAB, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC-IDIBAPS), Barcelona, Spain
| | - Joaquin Abian
- Proteomics Laboratory CSIC/UAB, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC-IDIBAPS), Barcelona, Spain
| | | | - Francesca Calero
- Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Hypertension Unit, Nephrology Department, Fundació Puigvert, Barcelona, Spain
| | - José A. Ballarín
- Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Hypertension Unit, Nephrology Department, Fundació Puigvert, Barcelona, Spain
| | - Patricia Fernández-Llama
- Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
- Hypertension Unit, Nephrology Department, Fundació Puigvert, Barcelona, Spain
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Soboleva A, Schmidt R, Vikhnina M, Grishina T, Frolov A. Maillard Proteomics: Opening New Pages. Int J Mol Sci 2017; 18:E2677. [PMID: 29231845 PMCID: PMC5751279 DOI: 10.3390/ijms18122677] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs) represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer's disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus), proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.
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Affiliation(s)
- Alena Soboleva
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Rico Schmidt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther Universität Halle-Wittenberg, 06108 Halle, Germany.
| | - Maria Vikhnina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Tatiana Grishina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
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Markoska K, Pejchinovski M, Pontillo C, Zürbig P, Jacobs L, Smith A, Masin-Spasovska J, Stojceva-Taneva O, Polenakovic M, Magni F, Mischak H, Spasovski G. Urinary peptide biomarker panel associated with an improvement in estimated glomerular filtration rate in chronic kidney disease patients. Nephrol Dial Transplant 2017; 33:751-759. [DOI: 10.1093/ndt/gfx263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/09/2017] [Indexed: 01/21/2023] Open
Affiliation(s)
| | | | - Claudia Pontillo
- Department of Clinical Proteomics, Mosaiques Diagnostics, Hanover, Germany
| | - Petra Zürbig
- Department of Clinical Proteomics, Mosaiques Diagnostics, Hanover, Germany
| | - Lotte Jacobs
- Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Andrew Smith
- Unit of Proteomics, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | | | | | - Fulvio Magni
- Unit of Proteomics, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Harald Mischak
- Department of Clinical Proteomics, Mosaiques Diagnostics, Hanover, Germany
| | - Goce Spasovski
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
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An M, Ni Y, Li X, Gao Y. Effects of arginine vasopressin on the urine proteome in rats. PeerJ 2017; 5:e3350. [PMID: 28560103 PMCID: PMC5444365 DOI: 10.7717/peerj.3350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
Biomarkers are the measurable changes associated with a physiological or pathophysiological process. The content of urine frequently changes because it is not controlled by homeostatic mechanisms, and these alterations can be a source of biomarkers. However, urine is affected by many factors. In this study, vasoconstrictor and antidiuretic arginine vasopressin (AVP) were infused into rats using an osmotic pump. The rats’ urinary proteome after one week of infusion was analyzed by label-free LC-MS/MS. A total of 408 proteins were identified; among these proteins, eight and 10 proteins had significantly altered expression in the low and high dose groups, respectively, compared with the control group using the one-way ANOVA analysis followed by post hoc analysis with the least significant difference (LSD) test or Dunnett’s T3 test. Three differential proteins were described in prior studies as related to AVP physiological processes, and nine differential proteins are known disease biomarkers. Sixteen of the 17 differential proteins have human orthologs. These results suggest that we should consider the effects of AVP on urinary proteins in future urinary disease biomarker researches. The study data provide clues regarding underlying mechanisms associated with AVP for future physiological researches on AVP. This study provide a sensitive changes associated with AVP. However, the limitation of this result is that the candidate biomarkers should be further verified and filtered. Large clinical samples must be examined to verify the differential proteins identified in this study before these proteins are used as biomarkers for pathological AVP increased diseases, such as syndrome of inappropriate antidiuretic hormone secretion (SIADH).
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Affiliation(s)
- Manxia An
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanying Ni
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xundou Li
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Youhe Gao
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing, China
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Li Z, Xu Y, Liu X, Nie Y, Zhao Z. Urinary heme oxygenase-1 as a potential biomarker for early diabetic nephropathy. Nephrology (Carlton) 2017; 22:58-64. [PMID: 26733347 DOI: 10.1111/nep.12719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/24/2015] [Accepted: 12/31/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Our previous study showed that increases of urinary heme oxygenase-1 (uHO-1) could be a potential biomarker indicating evaluating intrarenal oxidative damage in obstructive nephropathy. Activation of oxidative stress is an important mediator of diabetic nephropathy (DN). The aim of this study was to investigate the clinical implications of uHO-1 levels in patients with type 2 diabetes. METHODS Eighty-four type 2 diabetic patients with normoalbuminuria (n=28), microalbuminuria (n=28), and macroalbuminuria (n=28) were included in this study. Control samples were collected from healthy volunteers (n=28) who had normal albuminuria and renal function. Urine HO-1 levels were evaluated by enzyme-linked immunosorbent assay. RESULTS Urinary HO-1/creatinine (cr.) levels were significantly elevated in diabetic patients with microalbuminuria and macroalbuminuria compared to those in diabetic patients with normoalbuminuria (P<0.001) and control subjects (all P<0.001). In diabetic patients with normoalbuminuria, uHO-1/cr. levels were also higher than those in controls (P<0.001). Multivariate regression analyses revealed that uHO-1/cr. levels were positively correlated to urinary albumin/creatinine ratio and inversely correlated to glomerular filtration rate. Receiver operating characteristic (ROC) curve analysis of uHO-1/cr. levels for early diagnosis and detection of DN revealed that the cut-off value of uHO-1/cr. was 4.59 ng/mg (sensitivity 75%, specificity 78.6%). CONCLUSIONS The findings of this study indicate that increases of urine HO-1 levels can be detected in patients with type 2 diabetes before the onset of significant albuminuria, and associated with renal derangement in patients with established diabetic nephropathy. Urinary HO-1 may be used as an early biomarker for diabetic renal injury.
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Affiliation(s)
- Zhenzhen Li
- Institute of Clinical Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuliang Xu
- Department of Nephrology, the People's Hospital of Hebi, Hebi, China
| | - Xianghua Liu
- Center for Experimental Pathology, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Yali Nie
- Department of Pharmacology, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhanzheng Zhao
- Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Van JAD, Scholey JW, Konvalinka A. Insights into Diabetic Kidney Disease Using Urinary Proteomics and Bioinformatics. J Am Soc Nephrol 2017; 28:1050-1061. [PMID: 28159781 DOI: 10.1681/asn.2016091018] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A number of proteomic and peptidomic analyses of urine from diabetic subjects have been published in the quest for a biomarker that predicts progression of nephropathy. Less attention has been paid to the relationships between urinary proteins and the underlying biological processes revealed by the analyses. In this review, we focus on the biological processes identified by studying urinary proteins and protein-protein interactions at each stage of diabetic nephropathy to provide an overview of the events underlying progression of kidney disease reflected in the urine. In uncomplicated diabetes, proteomic/peptidomic analyses indicate that early activation of fibrotic pathways in the kidney occurs before the onset of microalbuminuria. In incipient nephropathy, when albumin excretion rates are abnormal, proteomic/peptidomic analyses suggest that changes in glomerular permselectivity and tubular reabsorption account, at least in part, for the proteins and peptides that appear in the urine. Finally, overt nephropathy is characterized by proteins involved in wound healing, ongoing fibrosis, and inflammation. These findings suggest that there is a spectrum of biological processes in the diabetic kidney and that assessing protein networks may be more informative than individual markers with respect to the stage of disease and the risk of progression.
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Affiliation(s)
- Julie A D Van
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; and
| | - James W Scholey
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; and.,Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; and.,Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada
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Xu L, Yu W, Niu M, Zheng C, Qu B, Li Y, Wang J, Huang P, Wang O, Gong F. Serum ZAG Levels Were Associated with eGFR Mild Decrease in T2DM Patients with Diabetic Nephropathy. Int J Endocrinol 2017; 2017:5372625. [PMID: 28352283 PMCID: PMC5352973 DOI: 10.1155/2017/5372625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/07/2016] [Accepted: 12/26/2016] [Indexed: 12/26/2022] Open
Abstract
Objective. To investigate the changes of serum zinc-α2-glycoprotein (ZAG) in type 2 diabetes mellitus (T2DM) with eGFR mild decrease. Subjects and Methods. A total of 438 T2DM patients (61.3 ± 4.0 y) were recruited and the demographic, anthropometric, and biochemical parameters were all collected. Serum ZAG levels were determined by commercially available ELISA kits. Results. The proportion of T2DM patients with the high tertile ZAG levels was 11.9% higher in patients with mildly decreased estimated glomerular filtration rate (eGFR) (<90 mL/min/1.73 m2) than those with the low tertile ZAG levels (P = 0.038). The probability of the eGFR < 90 mL/min/1.73 m2 in patients with the high ZAG levels was 94% higher than those with the low serum ZAG levels after adjusting for age, gender, and education [OR = 1.94, 95% CI (1.17-3.23), P = 0.0094]. This phenomenon was more likely to be observed in the condition of uACR ≥ 2.7 mg/mmol, WC ≥ 90 cm for men, or WC ≥ 85 cm for women. Conclusion. Serum ZAG levels were firstly found to be related with eGFR in T2DM patients. The patients with the high tertile ZAG levels were more likely to have mildly eGFR decrease, especially for female patients with higher uACR and bigger WC.
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Affiliation(s)
- Lingling Xu
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Weihong Yu
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Meng Niu
- Department of Endocrinology, Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Caixia Zheng
- Department of Ophthalmology, Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Bin Qu
- Department of Ophthalmology, Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Yan Li
- Department of Ophthalmology, Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Jing Wang
- Department of Ophthalmology, Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Ping Huang
- Department of Ophthalmology, Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - O. Wang
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Fengying Gong
- Key Laboratory of Endocrinology of National Health and Family Planning Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
- *Fengying Gong:
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Tomato Juice Consumption Modifies the Urinary Peptide Profile in Sprague-Dawley Rats with Induced Hepatic Steatosis. Int J Mol Sci 2016; 17:ijms17111789. [PMID: 27792191 PMCID: PMC5133790 DOI: 10.3390/ijms17111789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disorder in Western countries, with a high prevalence, and has been shown to increase the risk of type 2 diabetes, cardiovascular disease (CVD), etc. Tomato products contain several natural antioxidants, including lycopene—which has displayed a preventive effect on the development of steatosis and CVD. Accordingly, the aim of the present work was to evaluate the effect of tomato juice consumption on the urinary peptide profile in rats with NAFLD induced by an atherogenic diet and to identify potential peptide biomarkers for diagnosis. Urine samples, collected weekly for four weeks, were analyzed by capillary electrophoresis (CE) coupled to a mass spectrometer (MS). A partial least squares-discriminant analysis (PLS-DA) was carried out to explore the association between differential peptides and treatments. Among the 888 peptides initially identified, a total of 55 were obtained as potential biomarkers. Rats with steatosis after tomato juice intake showed a profile intermediate between that of healthy rats and that of rats with induced hepatic steatosis. Accordingly, tomato products could be considered as a dietary strategy for the impairment of NAFLD, although further research should be carried out to develop a specific biomarkers panel for NAFLD.
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37
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Zhao M, Wu J, Gao Y. The Specific α1-Adrenergic Receptor Antagonist Prazosin Influences the Urine Proteome. PLoS One 2016; 11:e0164796. [PMID: 27780262 PMCID: PMC5079574 DOI: 10.1371/journal.pone.0164796] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/30/2016] [Indexed: 11/19/2022] Open
Abstract
Urine, reflecting many changes in the body, is a better source than blood for biomarker discovery. However, even under physiological conditions, the urine proteome often varies. Understanding how various regulating factors affect urine proteome helps link changes to urine proteome with urinary biomarkers of physiological conditions as well as corresponding diseases. To evaluate the possible impact of α1-adrenergic receptor on urine proteome, this study investigated effects of the specific inhibitor prazosin on the urine proteome in a rat model by using tandem mass tagging and two-dimensional liquid chromatography-tandem mass spectrometry. A total of 775 proteins were identified, approximately half of which were influenced by prazosin treatment, indicating that the sympathetic nervous system exerts a significant impact on urine proteome. Eight significantly changed proteins were previously annotated as urinary candidate biomarkers. Angiotensinogen, haptoglobin, and beta-2 microglobulin, which were reported to be associated with blood pressure, were validated via Western blot. Prazosin is widely used in clinical practice; thus, these protein changes should be considered when studying corresponding diseases such as hypertension, post-traumatic stress disorder and benign prostatic hyperplasia. The related physiological activities of α1-receptors, controlling blood pressure and fear response might significantly affect the urine proteome and warrant further biomarker studies.
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Affiliation(s)
- Mindi Zhao
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jianqiang Wu
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Youhe Gao
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing, China
- * E-mail:
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38
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Gonzalez-Calero L, Martin-Lorenzo M, de la Cuesta F, Maroto AS, Baldan-Martin M, Ruiz-Hurtado G, Pulido-Olmo H, Segura J, Barderas MG, Ruilope LM, Vivanco F, Alvarez-Llamas G. Urinary alpha-1 antitrypsin and CD59 glycoprotein predict albuminuria development in hypertensive patients under chronic renin-angiotensin system suppression. Cardiovasc Diabetol 2016; 15:8. [PMID: 26772976 PMCID: PMC4715311 DOI: 10.1186/s12933-016-0331-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hypertension is a multi-factorial disease of increasing prevalence and a major risk factor for cardiovascular mortality even in the presence of adequate treatment. Progression of cardiovascular disease (CVD) occurs frequently during chronic renin-angiotensin-system (RAS) suppression, and albuminuria is a marker of CV risk. High prevalence of albuminuria in treated hypertensive patients has been demonstrated, but there are no available markers able to predict evolution. The aim of this study was the identification of novel indicators of albuminuria progression measurable in urine of diabetic and non-diabetic patients. METHODS 1143 hypertensive patients under chronic treatment were followed for a minimum period of 3 years. Among them, 105 diabetic and non-diabetic patients were selected and classified in three groups according to albuminuria development during follow-up: (a) patients with persistent normoalbuminuria; (b) patients developing de novo albuminuria; (c) patients with maintained albuminuria. Differential urine analysis was performed by 2D gel electrophoresis (2D-DIGE) and further confirmed by liquid chromatography-mass spectrometry. Non-parametric statistical tests were applied. RESULTS CD59 glycoprotein and alpha-1 antitrypsin (AAT) resulted already altered in patients developing albuminuria de novo, with a similar response in those with maintained albuminuria. A prospective study in a sub-group of normoalbuminuric patients who were clinically followed up for at least 1 year from urine sampling, revealed CD59 and AAT proteins significantly varied in the urine collected from normoalbuminurics who will negatively progress, serving as predictors of future albuminuria development. CONCLUSIONS CD59 and AAT proteins are significantly altered in hypertensive patients developing albuminuria. Interestingly, CD59 and AAT are able to predict, in normoalbuminuric individuals, who will develop albuminuria in the future, being potential predictors of vascular damage and CV risk. These findings contribute to early identify patients at risk of developing albuminuria even when this classical predictor is still in the normal range, constituting a novel strategy towards a prompt and more efficient therapeutic intervention with better outcome.
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Affiliation(s)
- Laura Gonzalez-Calero
- Departamento de Inmunologia, Laboratorio de Inmunoalergia y Proteomica, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avda Reyes Catolicos 2, 28040, Madrid, Spain.
| | - Marta Martin-Lorenzo
- Departamento de Inmunologia, Laboratorio de Inmunoalergia y Proteomica, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avda Reyes Catolicos 2, 28040, Madrid, Spain.
| | - Fernando de la Cuesta
- Laboratorio de Fisiopatologia Vascular, Hospital Nacional de Paraplejicos SESCAM, Toledo, Spain.
| | - Aroa S Maroto
- Departamento de Inmunologia, Laboratorio de Inmunoalergia y Proteomica, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avda Reyes Catolicos 2, 28040, Madrid, Spain.
| | - Montserrat Baldan-Martin
- Laboratorio de Fisiopatologia Vascular, Hospital Nacional de Paraplejicos SESCAM, Toledo, Spain.
| | - Gema Ruiz-Hurtado
- Unidad de Hipertension, Instituto de Investigacion i + 12, Hospital Universitario 12 de Octubre, Avenida de Córdoba s/n, 28041, Madrid, Spain.
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Madrid, Spain.
| | - Helena Pulido-Olmo
- Unidad de Hipertension, Instituto de Investigacion i + 12, Hospital Universitario 12 de Octubre, Avenida de Córdoba s/n, 28041, Madrid, Spain.
| | - Julian Segura
- Unidad de Hipertension, Instituto de Investigacion i + 12, Hospital Universitario 12 de Octubre, Avenida de Córdoba s/n, 28041, Madrid, Spain.
| | - Maria G Barderas
- Laboratorio de Fisiopatologia Vascular, Hospital Nacional de Paraplejicos SESCAM, Toledo, Spain.
| | - Luis M Ruilope
- Unidad de Hipertension, Instituto de Investigacion i + 12, Hospital Universitario 12 de Octubre, Avenida de Córdoba s/n, 28041, Madrid, Spain.
| | - Fernando Vivanco
- Departamento de Inmunologia, Laboratorio de Inmunoalergia y Proteomica, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avda Reyes Catolicos 2, 28040, Madrid, Spain.
- Departamento de Bioquimica y Biologia Molecular I, Universidad Complutense de Madrid, Madrid, Spain.
| | - Gloria Alvarez-Llamas
- Departamento de Inmunologia, Laboratorio de Inmunoalergia y Proteomica, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avda Reyes Catolicos 2, 28040, Madrid, Spain.
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Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
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Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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40
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Marikanty RK, Gupta MK, Cherukuvada SVB, Kompella SSS, Prayaga AK, Konda S, Polisetty RV, Idris MM, Rao PV, Chandak GR, Dakshinamurty KV. Identification of urinary proteins potentially associated with diabetic kidney disease. Indian J Nephrol 2016; 26:434-445. [PMID: 27942176 PMCID: PMC5131383 DOI: 10.4103/0971-4065.176144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diabetic nephropathy (DN) is the most common cause of chronic kidney disease. Although several parameters are used to evaluate renal damage, in many instances, there is no pathological change until damage is already advanced. Mass spectrometry-based proteomics is a novel tool to identify newer diagnostic markers. To identify urinary proteins associated with renal complications in diabetes, we collected urine samples from 10 type 2 diabetes patients each with normoalbuminuria, micro- and macro-albuminuria and compared their urinary proteome with that of 10 healthy individuals. Urinary proteins were concentrated, depleted of albumin and five other abundant plasma proteins and in-gel trypsin digested after prefractionation on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The peptides were analyzed using a nanoflow reverse phase liquid chromatography system coupled to linear trap quadrupole-Orbitrap mass spectrometer. We identified large number of proteins in each group, of which many were exclusively present in individual patient groups. A total of 53 proteins were common in all patients but were absent in the controls. The majority of the proteins were functionally binding, biologically involved in metabolic processes, and showed enrichment of alternative complement and blood coagulation pathways. In addition to identifying reported proteins such as α2-HS-glycoprotein and Vitamin D binding protein, we detected novel proteins such as CD59, extracellular matrix protein 1 (ECM1), factor H, and myoglobin in the urine of macroalbuminuria patients. ECM1 and factor H are known to influence mesangial cell proliferation, and CD59 causes microvascular damage by influencing membrane attack complex deposition, suggestive their biological relevance to DN. Thus, we have developed a proteome database where various proteins exclusively present in the patients may be further investigated for their role as stage-specific markers and possible therapeutic targets.
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Affiliation(s)
- R K Marikanty
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - M K Gupta
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India; Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - S V B Cherukuvada
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - S S S Kompella
- Department of Biochemistry, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - A K Prayaga
- Department of Pathology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - S Konda
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - R V Polisetty
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - M M Idris
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - P V Rao
- Department of Endocrinology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - G R Chandak
- CSIR-Centre for Cellular and Molecular Biology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - K V Dakshinamurty
- Department of Nephrology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
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The eye and the kidney: twin targets in diabetes. Int J Diabetes Dev Ctries 2015. [DOI: 10.1007/s13410-015-0461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Guo Z, Liu X, Li M, Shao C, Tao J, Sun W, Li M. Differential urinary glycoproteome analysis of type 2 diabetic nephropathy using 2D-LC-MS/MS and iTRAQ quantification. J Transl Med 2015; 13:371. [PMID: 26608305 PMCID: PMC4660682 DOI: 10.1186/s12967-015-0712-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/23/2015] [Indexed: 01/20/2023] Open
Abstract
Background Diabetic nephropathy (DN) is the leading cause of chronic kidney failure and end-stage kidney disease. More accurate and non-invasive test for the diagnosis and monitoring the progression of DN is urgently needed for the better care of such patients. Methods In this study we utilized urinary glycoproteome to discover the differential proteins during the course of type 2 DN. The urinary glycoproteins from normal controls, normalbuminuira, microalbuminura, and macroalbuminuria patients were enriched by concanavalin A (ConA) and analyzed by 2DLC/MS/MS and isobaric tags for relative and absolute quantitation quantification. Results A total of 478 proteins were identified and 408 were annotated as N-linked glycoproteins. A total of 72, 107 and 123 differential proteins were identified in normalbuminuria, microalbuminuria and macroalbuminuria, respectively. By bioinformatics analysis, in normalbuminruia state, cell proliferation and cell movement were activated, which might reflect the compensatory phase during the disease development. In micro- and macro-albuminuria, cell death and apoptosis was activated, which might reflect the de-compensatory phase. Pathway analysis showed acute phase proteins, the member of high density lipoprotein and low density lipoprotein proteins were changed, indicating the role of the inflammatory response and lipid metabolism abnormality in the pathogenesis of DN. Six selected differential proteins were validated by Western Blot. Alpha-1-antitrypsin (SERPINA1) and Ceruloplasmin are the two markers with excellent area under curve values (0.929 and 1.000 respectively) to distinguish the microalbuminuria and normalbuminuria. For the first time, we found pro-epidermal growth factor and prolactin-inducible protein were decreased in macroalbuminuria stage, which might reflect the inhibition of cell viability and the activation of cell death in kidney. Conclusions Above data indicated that urinary glycoproteome could be useful to distinguish the differences in protein profiles in different stages in DN, which will help better individualized care of patients in DN. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0712-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhengguang Guo
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China.
| | - Xuejiao Liu
- Department of Nephrology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyan, Wangfujing Street, Beijing, China.
| | - Menglin Li
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China.
| | - Chen Shao
- The Center for Biomedical Information, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China.
| | - Jianling Tao
- Department of Nephrology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyan, Wangfujing Street, Beijing, China.
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China.
| | - Mingxi Li
- Department of Nephrology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyan, Wangfujing Street, Beijing, China.
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Pietrzyk AJ, Bujacz A, Mak P, Potempa B, Niedziela T. Structural studies of Helix aspersa agglutinin complexed with GalNAc: A lectin that serves as a diagnostic tool. Int J Biol Macromol 2015; 81:1059-68. [PMID: 26416237 DOI: 10.1016/j.ijbiomac.2015.09.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 02/07/2023]
Abstract
Lectins belong to a differentiated group of proteins known to possess sugar-binding properties. Due to this fact, they are interesting research targets in medical diagnostics. Helix aspersa agglutinin (HAA) is a lectin that recognizes the epitopes containing α-d-N-acetylgalactosamine (GalNAc), which is present at the surface of metastatic cancer cells. Although several reports have already described the use of HAA as a diagnostic tool, this protein was not characterized on the molecular level. Here, we present for the first time the structural information about lectin isolated from mucus of Helix aspersa (garden snail). The amino acid sequence of this agglutinin was determined by Edman degradation and tertiary as well as quaternary structure by X-ray crystallography. The high resolution crystal structure (1.38Å) and MALDI-TOF mass spectrometry analysis provide the detailed information about a large part of the HAA natural glycan chain. The topology of the GalNAc binding cleft and interaction with lectin are very well defined in the structure and fully confirmed by STD HSQC NMR spectroscopy. Together, this provides structural clues regarding HAA specificity and opens possibilities to rational modifications of this important diagnostic tool.
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Affiliation(s)
- Agnieszka J Pietrzyk
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, Lodz 90-924, Poland
| | - Anna Bujacz
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, Lodz 90-924, Poland.
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Barbara Potempa
- University of Louisville School of Dentistry, Department of Oral Immunology and Infectious Diseases, 501 South Preston Street, Louisville, KY 40202, USA
| | - Tomasz Niedziela
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, Wrocław 53-114, Poland
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Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJM, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R. Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes. J Proteome Res 2015; 14:3123-35. [PMID: 26143644 DOI: 10.1021/acs.jproteome.5b00052] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Individuals with type 1 diabetes (T1D) often have higher than normal blood glucose levels, causing advanced glycation end product formation and inflammation and increasing the risk of vascular complications years or decades later. To examine the urinary proteome in juveniles with T1D for signatures indicative of inflammatory consequences of hyperglycemia, we profiled the proteome of 40 T1D patients with an average of 6.3 years after disease onset and normal or elevated HbA1C levels, in comparison with a cohort of 41 healthy siblings. Using shotgun proteomics, 1036 proteins were identified, on average, per experiment, and 50 proteins showed significant abundance differences using a Wilcoxon signed-rank test (FDR q-value ≤ 0.05). Thirteen lysosomal proteins were increased in abundance in the T1D versus control cohort. Fifteen proteins with functional roles in vascular permeability and adhesion were quantitatively changed, including CD166 antigen and angiotensin-converting enzyme 2. α-N-Acetyl-galactosaminidase and α-fucosidase 2, two differentially abundant lysosomal enzymes, were detected in western blots with often elevated quantities in the T1D versus control cohort. Increased release of proteins derived from lysosomes and vascular epithelium into urine may result from hyperglycemia-associated inflammation in the kidney vasculature.
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Affiliation(s)
- Moo-Jin Suh
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Andrey Tovchigrechko
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Vishal Thovarai
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Melanie A Rolfe
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Manolito G Torralba
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Junmin Wang
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Joshua N Adkins
- ‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Bobbie-Jo M Webb-Robertson
- ‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Whitney Osborne
- §Children's National Medical Center, 111 Michigan Avenue North West, Washington, DC 20010, United States
| | - Fran R Cogen
- §Children's National Medical Center, 111 Michigan Avenue North West, Washington, DC 20010, United States
| | - Paul B Kaplowitz
- §Children's National Medical Center, 111 Michigan Avenue North West, Washington, DC 20010, United States
| | - Thomas O Metz
- ‡Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Karen E Nelson
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ramana Madupu
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rembert Pieper
- †J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
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Urinary monocyte chemoattractant protein-1 and vitamin D-binding protein as biomarkers for early detection of diabetic nephropathy in type 2 diabetes mellitus. Mol Cell Biochem 2015; 408:25-35. [PMID: 26104579 DOI: 10.1007/s11010-015-2479-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 06/13/2015] [Indexed: 01/15/2023]
Abstract
Diabetic nephropathy is a serious complication of both type 1 and type 2 diabetes and, unless arrested, leads to end-stage renal disease. Therefore, early prediction and detection of DN would greatly benefit the disease management and delay its progression. The aim of this study is to evaluate the levels of urinary monocyte chemoattractant protein-1 (uMCP-1) and urinary vitamin D-binding protein (uVDBP) in type 2 diabetic patients with different degrees of diabetic nephropathy (DN) and to assess the value of uMCP-1 and uVDBP in the early detection of DN. Seventy-five type 2 diabetic patients with normoalbuminuria (n = 25), microalbuminuria (n = 25), macroalbuminuria (n = 25), and 25 healthy controls were included in this study. Urinary MCP-1 and VDBP levels were evaluated by enzyme-linked immunosorbent assay. A significant elevation in the uMCP-1 and uVDBP levels was found in macroalbuminuric (p < 0.001) and microalbuminuric (p < 0.01) diabetic patients compared to that in normoalbuminuric diabetic patients and control subjects (p < 0.001). Correlation study revealed that both uMCP-1 and uVDBP were significantly positively correlated to urinary albumin/creatinine ratio (r = 0.968, p < 0.001 and r = 0.973, p < 0.001, respectively), serum urea (r = 0.461, p = 0.001 and r = 0.456, p = 0.002, respectively), and serum creatinine (r = 0.475, p = 0.001 and r = 0.448, p = 0.004, respectively) and significantly inversely correlated to glomerular filtration rate (r = -0.983, p < 0.001 and r = -0.988, p < 0.001, respectively). Receiver operating characteristic (ROC) curve analysis of uMCP-1 and uVDBP levels for early diagnosis and detection of DN revealed that the cut-off value of uMCP-1 was 110 pg/mg with 92% sensitivity and 100% specificity; whereas, the cut-off value of uVDBP was 550 ng/mg with 96% sensitivity and 84% specificity. The findings of the present study suggest that uMCP-1 and uVDBP may be considered as novel potential diagnostic biomarkers for the early detection of diabetic nephropathy.
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Zhang M, Fu G, Lei T. Two urinary peptides associated closely with type 2 diabetes mellitus. PLoS One 2015; 10:e0122950. [PMID: 25902048 PMCID: PMC4406586 DOI: 10.1371/journal.pone.0122950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/16/2015] [Indexed: 12/18/2022] Open
Abstract
Objective To monitor of type 2 diabetes more simply, conveniently and noninvasively, we are trying to identify the potential urinary peptides that associated with different stages of glucose control in type 2 diabetes mellitus. Methods Firstly, we collected urine samples from type 2 diabetic patients and normal controls. These type 2 diabetic patients were divided into two groups according to fasting plasma glucose (FPG) and hemoglobin A1c% (HbA1c), respectively. Magnetic beads based weak cation exchange chromatography (MB-WCX) was used to condense urinary peptides. The eluates were then analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Subsequently, ClinProt was used to profile and screen the polypeptide patterns based on different methods of grouping in diabetic patients and normal controls. Finally, the amino acid sequences of differentially expressed peptides were identified by nano-liquid chromatography-tandem mass spectrometry and the protein sources of the corresponding peptide were matched in IPI Human database. Results Proteomics analysis found two up-regulated peptide (m/z 2756.1 and m/z 3223.2) representations in diabetic subjects, and the two peptides increased with increases in the amount of glycosylated hemoglobin. Further, the parallelism between m/z 3223.2 and glycosylated hemoglobin was better than the parallelism between m/z 2756.1 and glycosylated hemoglobin. Area under the receiver operating characteristic of the two peptides was 0.722 and 0.661, respectively. The above-mentioned peptide m/z 2756.1 was further identified as fragment of fibrinogen alpha chain precursor and m/z 3223.2 was fragment of prothrombin precursor. Conclusion These results suggested the two urinary biomarkers enable monitor of type 2 diabetes patients with different stages of glucose control.
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Affiliation(s)
- Man Zhang
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing, China
- Department of Clinical Laboratory, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- * E-mail:
| | - Guangzhen Fu
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing, China
| | - Ting Lei
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing, China
- Department of Clinical Laboratory, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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Dynamic changes of urinary proteins in focal segmental glomerulosclerosis model. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 845:167-73. [PMID: 25355579 DOI: 10.1007/978-94-017-9523-4_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Compare to blood, which has mechanisms to maintain homeostasis, urine is more likely to reflect changes in the body. As urine accumulates all types of changes, identifying the precise cause of changes in the urine proteome is challenging and crucial in biomarker discovery. To reduce the confounding factors to minimal, some studies used animal model resembling human diseases. This chapter highlights the importance of animal models and introduces a strategic research which focused on adriamycin-induced nephropathy. In this study, urine samples were collected at before adriamycin administration and days 3, 7, 11, 15, and 23 after, urinary proteins were profiled by LC-MS/MS. Of 23 changed proteins with disease development, 13 proteins were identified as stable in normal human urine, meaning that changes in these proteins are more likely to reflect disease. We think this stage-dependent dynamic changes of urine proteome in animal models will help to support the role of urine as key source in biomarker discovery especially in kidney diseases and help to identify corresponding biomarkers for clinical validation.
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Nagalla SR, Snyder CK, Michaels JE, Laughlin MJ, Roberts CT, Balaji M, Balaji V, Seshiah V, Rao PV. Maternal serum biomarkers for risk assessment in gestational diabetes. A potential universal screening test to predict GDM status. Indian J Endocrinol Metab 2015; 19:155-159. [PMID: 25593844 PMCID: PMC4287761 DOI: 10.4103/2230-8210.140226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The prevalence of gestational diabetes mellitus (GDM) is increasing because of the worldwide obesity/diabetes epidemic. The complications of untreated GDM affect both the mother and baby and include complications during pregnancy as well as increased risk of subsequent type-2 diabetes in mothers and offspring. Standard tests for hyperglycemia in diabetes, such as fasting glucose and hemoglobin (HbA1c), are currently not recommended for GDM screening. Instead, an oral glucose tolerance test is specified, which is invasive, time-consuming, and not easily accessible to many at-risk populations. In this study, we describe a multi-analyte maternal serum profile test that incorporates novel glycoprotein biomarkers and previously described GDM-associated markers. In screening for GDM by multi-analyte panel, the detection rate was 87% at a false-positive rate of 1%.
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Affiliation(s)
| | | | | | | | | | - Madhuri Balaji
- Dr. V. Seshiah Diabetes Care and Research Institute, Chennai, Tamil Nadu, India
| | - V. Balaji
- Dr. V. Seshiah Diabetes Care and Research Institute, Chennai, Tamil Nadu, India
| | - V. Seshiah
- Dr. V. Seshiah Diabetes Care and Research Institute, Chennai, Tamil Nadu, India
| | - Paturi V. Rao
- Department of Endocrinology and Metabolism, Nizam's Institute of Medical Sciences University, Hyderabad, Telangana, India
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Pei F, Li BY, Zhang Z, Yu F, Li XL, Lu WD, Cai Q, Gao HQ, Shen L. Beneficial effects of phlorizin on diabetic nephropathy in diabetic db/db mice. J Diabetes Complications 2014; 28:596-603. [PMID: 24927646 DOI: 10.1016/j.jdiacomp.2014.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/18/2014] [Accepted: 04/16/2014] [Indexed: 11/23/2022]
Abstract
AIMS This study observes the effects of phlorizin on diabetic nephrology in db/db diabetic mice and explores possible underlying mechanisms. METHODS Sixteen diabetic db/db mice and eight age-matched db/m mice were divided into three groups: vehicle-treated diabetic group (DM group), diabetic group treated with phlorizin (DMT group) and normal control group (CC group). Phlorizin was given in normal saline solution by intragastric administration for 10 weeks. Differentially expressed proteins in three groups were identified using iTRAQ quantitative proteomics and the data were further analyzed with ingenuity pathway analysis. RESULTS The body weight and serum concentrations of fasting blood glucose (FBG), advanced glycation end products (AGEs), total cholesterol, triglycerides, blood urea nitrogen, creatinine and 24-h urine albumin were increased in the DM group compared to those of the CC group (P<0.05), and they were decreased by treatment with phlorizin (P<0.05). Morphologic observations showed phlorizin markedly attenuated renal injury. Phlorizin prevented diabetic nephropathy by regulating the expression of a series of proteins involved in renal and urological disease, molecular transport, free radical scavenging, and lipid metabolism. CONCLUSIONS Phlorizin protects mice from diabetic nephrology and thus may be a novel therapeutic approach for the treatment of diabetic nephrology.
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Affiliation(s)
- Fei Pei
- Department of Nephrology, Qi-Lu Hospital of Shandong University, Shandong Province 250012, People's Republic of China
| | - Bao-Ying Li
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
| | - Zhen Zhang
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
| | - Fei Yu
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
| | - Xiao-Li Li
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
| | - Wei-da Lu
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
| | - Qian Cai
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
| | - Hai-Qing Gao
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China.
| | - Lin Shen
- Department of Geriatrics, Qi-Lu Hospital of Shandong University, Key Laboratory of Cardiovascular Proteomics of Shandong Province, Shandong Province 250012, People's Republic of China
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50
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Dynamic changes of urinary proteins in a focal segmental glomerulosclerosis rat model. Proteome Sci 2014; 12:42. [PMID: 25061428 PMCID: PMC4109389 DOI: 10.1186/1477-5956-12-42] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/14/2014] [Indexed: 12/20/2022] Open
Abstract
Background In contrast to blood, which has mechanisms to maintain a homeostatic internal environment, urine is more likely to reflect changes in the body. As urine accumulates all types of changes, identifying the precise cause of changes in the urine proteome is challenging and crucial in biomarker discovery. To reduce the effects of both genetic and environmental factors on the urinary proteome, this study used a rat model of adriamycin-induced nephropathy resembling human focal segmental glomerulosclerosis (FSGS) development. Results Urine samples were collected at before adriamycin administration and day3, 7, 11, 15 and 23 after. Urinary proteins were profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Of 23 changed proteins with disease development, 20 have human orthologs, and 13 proteins were identified as stable in normal human urine, meaning that changes in these proteins are more likely to reflect disease. Fifteen of the identified proteins have not been established to function in FSGS development. Seven proteins were selected for verification in ten more rats as markers closely associated with disease severity by western blot. Conclusion We identified proteins changed in different stages of FSGS in rat models, which may aid in biomarker development and the understanding of FSGS pathogenesis.
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