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Elguoshy A, Yamamoto K, Hirao Y, Uchimoto T, Yanagita K, Yamamoto T. Investigating and Annotating the Human Peptidome Profile from Urine under Normal Physiological Conditions. Proteomes 2024; 12:18. [PMID: 39051237 PMCID: PMC11270373 DOI: 10.3390/proteomes12030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Examining the composition of the typical urinary peptidome and identifying the enzymes responsible for its formation holds significant importance, as it mirrors the normal physiological state of the human body. Any deviation from this normal profile could serve as an indicator of pathological processes occurring in vivo. Consequently, this study focuses on characterizing the normal urinary peptidome and investigating the various catalytic enzymes that are involved in generating these native peptides in urine. Our findings reveal that 1503 endogenous peptides, corresponding to 436 precursor proteins, were consistently identified robustly in at least 10 samples out of a total of 19 samples. Notably, the liver and kidneys exhibited the highest number of tissue-enriched or enhanced genes in the analyzed urinary peptidome. Furthermore, among the catalytic types, CTSD (cathepsin D) and MMP2 (matrix metalloproteinase-2) emerged as the most prominent peptidases in the aspartic and metallopeptidases categories, respectively. A comparison of our dataset with two of the most comprehensive urine peptidome datasets to date indicates a consistent relative abundance of core endogenous peptides for different proteins across all three datasets. These findings can serve as a foundational reference for the discovery of biomarkers in various human diseases.
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Affiliation(s)
- Amr Elguoshy
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Keiko Yamamoto
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Yoshitoshi Hirao
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Tomohiro Uchimoto
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Kengo Yanagita
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Tadashi Yamamoto
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
- Department of Clinical Laboratory, Shinrakuen Hospital, Niigata 950-2087, Japan
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2
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Zakharova NV, Bugrova AE, Indeykina MI, Brzhozovskiy AG, Nikolaev EN, Kononikhin AS. The Strategy for Peptidomic LC-MS/MS Data Analysis: The Case of Urinary Peptidome Study. Methods Mol Biol 2024; 2758:389-399. [PMID: 38549026 DOI: 10.1007/978-1-0716-3646-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The study of urinary peptidome is an important area of research, which concerns the characterization of endogenous peptides, as well as the identification of biomarkers for a wide range of socially significant diseases. First of all, this relates to renal and genitourinary pathologies and/or pathologies associated with proteinuria, such as kidney diseases, bladder, prostate and ovarian cancers, diabetic nephropathy, and pre-eclampsia. Unlike proteins, peptides do not require proteolytic hydrolysis, can be analyzed in their native form and can provide certain information about occurring (patho)physiological processes. Mass spectrometry (MS)-based approaches are the most unbiased and sensitive instruments with high multiplexing capacity and provided most of the current information about endogenous urine peptides. However, despite the large number of urine peptidomic studies, there are certain issues related to the insufficient comparability of their results due to the lack of consistent approaches to their interpretation. Also the development of a custom project-specific protein library for endogenous peptides search and identification is another important point that should be noted in the context of high-throughput peptidomic analysis. Here we propose the custom-specific urinary protein database and the grouping of endogenous urinary peptides with overlapping sequences as useful tools, which can facilitate the acquisition and analysis of LC-MS peptidomic data, as well as the comparison of results of different studies, which should facilitate their more efficient further application.
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Affiliation(s)
- Natalia V Zakharova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Moscow, Russia
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of the Ministry of Health, Moscow, Russia
| | - Maria I Indeykina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Emanuel Institute for Biochemical Physics, Russian Academy of Science, Moscow, Russia
| | - Alexander G Brzhozovskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of the Ministry of Health, Moscow, Russia
| | - Evgeny N Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - Alexey S Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia.
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3
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Ma W, Zhang C, Zhang W, Sheng P, Xu M, Ni Y, Chen M, Cheng B, Zhang X. TMT-Based Comparative Peptidomics Analysis of Rice Seedlings under Salt Stress: An Accessible Method to Explore Plant Stress-Tolerance Processing. J Proteome Res 2022; 21:2905-2919. [PMID: 36351196 DOI: 10.1021/acs.jproteome.2c00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rice (Oryza sativa L.) is an important staple crop, particularly in Asia, and abiotic stress conditions easily reduce its yields. Salt stress is one of the critical factors affecting rice growth and yield. In this study, a tandem mass tag (TMT)-based comparative peptidomics analysis of rice seedlings under salt stress was conducted. Rice seedlings were exposed to 50 and 150 mM NaCl for 24 and 72 h, respectively, and the root and shoot tissues of different treatment groups were collected separately for peptidomics analysis. A total of 911 and 1263 nonredundant peptides were identified in two pooled shoot tissue samples, while there were 770 and 672 nonredundant peptides in two pooled root tissue samples, respectively. Compared with the control groups, dozens to hundreds of differentially expressed peptides (DEPs) were characterized in all treatment groups. To explore the potential functions of these DEPs, we analyzed the basic characteristics of DEPs and further analyzed the annotated Gene Ontology terms according to their precursor proteins. Several DEP precursor proteins were closely related to the response to salt stress, and some were derived from the functional domains of their corresponding precursors. The germination rate and cotyledon greening rate of transgenic Arabidopsis expressing two DEPs, OsSTPE2 and OsSTPE3, were significantly enhanced under salt stress. The described workflow enables the discovery of a functional pipeline for the characterization of the plant peptidome and reveals two new plant peptides that confer salinity tolerance to plants. Data are available via ProteomeXchange with identifier PXD037574.
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Affiliation(s)
- Wanlu Ma
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Chenchen Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Wei Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Pijie Sheng
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Minyan Xu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Ying Ni
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Meng Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Beijiu Cheng
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China.,Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Xin Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China.,Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, P. R. China
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4
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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5
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Han T, Cong H, Yu B, Shen Y. Application of peptide biomarkers in life analysis based on liquid chromatography-mass spectrometry technology. Biofactors 2022; 48:725-743. [PMID: 35816279 DOI: 10.1002/biof.1875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/18/2022] [Indexed: 12/11/2022]
Abstract
Biomedicine is developing rapidly in the 21st century. Among them, the qualitative and quantitative analysis of peptide biomarkers is of considerable importance for the diagnosis and therapy of diseases and the quality evaluation of drugs and food. The identification and quantitative analysis of peptides have been going on for decades. Traditionally, immunoassays or biological assays are generally used to quantify peptides in biological matrices. However, the selectivity and sensitivity of these methods cannot meet the requirements of the application. The separation and analysis technique of liquid chromatography-mass spectrometry (LC-MS) supplies a reliable alternative. In contrast to immunoassays, LC-MS methods are capable of providing the analytical prowess necessary to satisfy the demands of peptide biomarker research in the life sciences arena. This review article provides a historical account of the in-roads made by LC-MS technology for the detection of peptide biomarkers in the past 10 years, with the focus on the qualification/quantification developments and their applications.
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Affiliation(s)
- Tingting Han
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
| | - Hailin Cong
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, China
| | - Bing Yu
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, China
| | - Youqing Shen
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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6
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Galvan DL, Mise K, Danesh FR. Mitochondrial Regulation of Diabetic Kidney Disease. Front Med (Lausanne) 2021; 8:745279. [PMID: 34646847 PMCID: PMC8502854 DOI: 10.3389/fmed.2021.745279] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
The role and nature of mitochondrial dysfunction in diabetic kidney disease (DKD) has been extensively studied. Yet, the molecular drivers of mitochondrial remodeling in DKD are poorly understood. Diabetic kidney cells exhibit a cascade of mitochondrial dysfunction ranging from changes in mitochondrial morphology to significant alterations in mitochondrial biogenesis, biosynthetic, bioenergetics and production of reactive oxygen species (ROS). How these changes individually or in aggregate contribute to progression of DKD remain to be fully elucidated. Nevertheless, because of the remarkable progress in our basic understanding of the role of mitochondrial biology and its dysfunction in DKD, there is great excitement on future targeted therapies based on improving mitochondrial function in DKD. This review will highlight the latest advances in understanding the nature of mitochondria dysfunction and its role in progression of DKD, and the development of mitochondrial targets that could be potentially used to prevent its progression.
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Affiliation(s)
- Daniel L Galvan
- Section of Nephrology, The University of Texas at MD Anderson Cancer Center, Houston, TX, United States
| | - Koki Mise
- Section of Nephrology, The University of Texas at MD Anderson Cancer Center, Houston, TX, United States.,Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Farhad R Danesh
- Section of Nephrology, The University of Texas at MD Anderson Cancer Center, Houston, TX, United States.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, United States
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7
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Abstract
Peptides play a crucial role in many vitally important functions of living organisms. The goal of peptidomics is the identification of the "peptidome," the whole peptide content of a cell, organ, tissue, body fluid, or organism. In peptidomic or proteomic studies, capillary electrophoresis (CE) is an alternative technique for liquid chromatography. It is a highly efficient and fast separation method requiring extremely low amounts of sample. In peptidomic approaches, CE is commonly combined with mass spectrometric (MS) detection. Most often, CE is coupled with electrospray ionization MS and less frequently with matrix-assisted laser desorption/ionization MS. CE-MS has been employed in numerous studies dealing with determination of peptide biomarkers in different body fluids for various diseases, or in food peptidomic research for the analysis and identification of peptides with special biological activities. In addition to the above topics, sample preparation techniques commonly applied in peptidomics before CE separation and possibilities for peptide identification and quantification by CE-MS or CE-MS/MS methods are discussed in this chapter.
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Paats J, Adoberg A, Arund J, Fridolin I, Lauri K, Leis L, Luman M, Tanner R. Optical Method and Biochemical Source for the Assessment of the Middle-Molecule Uremic Toxin β2-Microglobulin in Spent Dialysate. Toxins (Basel) 2021; 13:toxins13040255. [PMID: 33807387 PMCID: PMC8067283 DOI: 10.3390/toxins13040255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Optical monitoring of spent dialysate has been used to estimate the removal of water-soluble low molecular weight as well as protein-bound uremic toxins from the blood of end stage kidney disease (ESKD) patients. The aim of this work was to develop an optical method to estimate the removal of β2-microglobulin (β2M), a marker of middle molecule (MM) uremic toxins, during hemodialysis (HD) treatment. Ultraviolet (UV) and fluorescence spectra of dialysate samples were recorded from 88 dialysis sessions of 22 ESKD patients, receiving four different settings of dialysis treatments. Stepwise regression was used to obtain the best model for the assessment of β2M concentration in the spent dialysate. The correlation coefficient 0.958 and an accuracy of 0.000 ± 0.304 mg/L was achieved between laboratory and optically estimated β2M concentrations in spent dialysate for the entire cohort. Optically and laboratory estimated reduction ratio (RR) and total removed solute (TRS) of β2M were not statistically different (p > 0.35). Dialytic elimination of MM uremic toxin β2M can be followed optically during dialysis treatment of ESKD patients. The main contributors to the optical signal of the MM fraction in the spent dialysate were provisionally identified as tryptophan (Trp) in small peptides and proteins, and advanced glycation end-products.
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Affiliation(s)
- Joosep Paats
- Department of Health Technologies, Tallinn University of Technology, 19086 Tallinn, Estonia; (J.A.); (I.F.); (K.L.); (M.L.); (R.T.)
- Correspondence:
| | - Annika Adoberg
- Centre of Nephrology, North Estonia Medical Centre, 13419 Tallinn, Estonia; (A.A.); (L.L.)
| | - Jürgen Arund
- Department of Health Technologies, Tallinn University of Technology, 19086 Tallinn, Estonia; (J.A.); (I.F.); (K.L.); (M.L.); (R.T.)
| | - Ivo Fridolin
- Department of Health Technologies, Tallinn University of Technology, 19086 Tallinn, Estonia; (J.A.); (I.F.); (K.L.); (M.L.); (R.T.)
| | - Kai Lauri
- Department of Health Technologies, Tallinn University of Technology, 19086 Tallinn, Estonia; (J.A.); (I.F.); (K.L.); (M.L.); (R.T.)
- SYNLAB Eesti OÜ, 10138 Tallinn, Estonia
| | - Liisi Leis
- Centre of Nephrology, North Estonia Medical Centre, 13419 Tallinn, Estonia; (A.A.); (L.L.)
| | - Merike Luman
- Department of Health Technologies, Tallinn University of Technology, 19086 Tallinn, Estonia; (J.A.); (I.F.); (K.L.); (M.L.); (R.T.)
- Centre of Nephrology, North Estonia Medical Centre, 13419 Tallinn, Estonia; (A.A.); (L.L.)
| | - Risto Tanner
- Department of Health Technologies, Tallinn University of Technology, 19086 Tallinn, Estonia; (J.A.); (I.F.); (K.L.); (M.L.); (R.T.)
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9
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Latosinska A, Siwy J, Faguer S, Beige J, Mischak H, Schanstra JP. Value of Urine Peptides in Assessing Kidney and Cardiovascular Disease. Proteomics Clin Appl 2021; 15:e2000027. [PMID: 32710812 DOI: 10.1002/prca.202000027] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/18/2020] [Indexed: 12/14/2022]
Abstract
Urinary peptides gained significant attention as potential biomarkers especially in the context of kidney and cardiovascular disease. In this manuscript the recent literature since 2015 on urinary peptide investigation in human kidney and cardiovascular disease is reviewed. The technology most commonly used in this context is capillary electrophoresis coupled mass spectrometry, in part owed to the large database available and the well-defined dataspace. Several studies based on over 1000 subjects are reported in the recent past, especially examining CKD273, a classifier for assessment of chronic kidney disease based on 273 urine peptides. Interestingly, the most abundant urinary peptides are generally collagen fragments, which may have gone undetected for some time as they are typically modified via proline hydroxylation. The data available suggest that urinary peptides specifically depict inflammation and fibrosis, and may serve as a non-invasive tool to assess fibrosis, which appears to be a key driver in kidney and cardiovascular disease. The recent successful completion of the first urinary peptide guided intervention trial, PRIORITY, is expected to further spur clinical application of urinary peptidomics, aiming especially at early detection of chronic diseases, prediction of progression, and prognosis of drug response.
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Affiliation(s)
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Stanislas Faguer
- Département de Néphrologie et Transplantation d'organes, Centre de référence des maladies rénales rares, Centre Hospitalier Universitaire de Toulouse, 1, Avenue Jean Poulhes, Toulouse, 31059, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France
- Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
| | - Joachim Beige
- Department of Nephrology and Kuratorium for Dialysis and Transplantation Renal Unit, Hospital St Georg, Delitzscher Str. 141, 04129, Leipzig, Germany
- Department of Nephrology, Martin-Luther-University Halle/Wittenberg, Universitätsplatz 10, 06108, Halle (Saale), Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France
- Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
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10
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Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nat Rev Nephrol 2020; 17:205-219. [PMID: 33028957 DOI: 10.1038/s41581-020-00348-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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11
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Sirolli V, Pieroni L, Di Liberato L, Urbani A, Bonomini M. Urinary Peptidomic Biomarkers in Kidney Diseases. Int J Mol Sci 2019; 21:E96. [PMID: 31877774 PMCID: PMC6982248 DOI: 10.3390/ijms21010096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
In order to effectively develop personalized medicine for kidney diseases we urgently need to develop highly accurate biomarkers for use in the clinic, since current biomarkers of kidney damage (changes in serum creatinine and/or urine albumin excretion) apply to a later stage of disease, lack accuracy, and are not connected with molecular pathophysiology. Analysis of urine peptide content (urinary peptidomics) has emerged as one of the most attractive areas in disease biomarker discovery. Urinary peptidome analysis allows the detection of short and long-term physiological or pathological changes occurring within the kidney. Urinary peptidomics has been applied extensively for several years now in renal patients, and may greatly improve kidney disease management by supporting earlier and more accurate detection, prognostic assessment, and prediction of response to treatment. It also promises better understanding of kidney disease pathophysiology, and has been proposed as a "liquid biopsy" to discriminate various types of renal disorders. Furthermore, proteins being the major drug targets, peptidome analysis may allow one to evaluate the effects of therapies at the protein signaling pathway level. We here review the most recent findings on urinary peptidomics in the setting of the most common kidney diseases.
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Affiliation(s)
- Vittorio Sirolli
- Nephrology and Dialysis Unit, Department of Medicine, G. d’Annunzio University, Chieti-Pescara, SS.Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy; (V.S.); (L.D.L.)
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy;
| | - Lorenzo Di Liberato
- Nephrology and Dialysis Unit, Department of Medicine, G. d’Annunzio University, Chieti-Pescara, SS.Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy; (V.S.); (L.D.L.)
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Mario Bonomini
- Nephrology and Dialysis Unit, Department of Medicine, G. d’Annunzio University, Chieti-Pescara, SS.Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy; (V.S.); (L.D.L.)
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2017–mid 2019). Electrophoresis 2019; 41:10-35. [DOI: 10.1002/elps.201900269] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/08/2019] [Accepted: 10/19/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Prague 6 Czechia
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Manole E, E. Bastian A, D. Popescu I, Constantin C, Mihai S, F. Gaina G, Codrici E, T. Neagu M. Immunoassay Techniques Highlighting Biomarkers in Immunogenetic Diseases. Immunogenetics 2019. [DOI: 10.5772/intechopen.75951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Wu Y, Han M, Wang Y, Gao Y, Cui X, Xu P, Ji C, Zhong T, You L, Zeng Y. A Comparative Peptidomic Characterization of Cultured Skeletal Muscle Tissues Derived From db/db Mice. Front Endocrinol (Lausanne) 2019; 10:741. [PMID: 31736878 PMCID: PMC6828820 DOI: 10.3389/fendo.2019.00741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
As an important secretory organ, skeletal muscle has drawn attention as a potential target tissue for type 2 diabetic mellitus (T2DM). Recent peptidomics approaches have been applied to identify secreted peptides with potential bioactive. However, comprehensive analysis of the secreted peptides from skeletal muscle tissues of db/db mice and elucidation of their possible roles in insulin resistance remains poorly characterized. Here, we adopted a label-free discovery using liquid chromatography tandem mass spectrometry (LC-MS/MS) technology and identified 63 peptides (42 up-regulated peptides and 21 down-regulated peptides) differentially secreted from cultured skeletal muscle tissues of db/db mice. Analysis of relative molecular mass (Mr), isoelectric point (pI) and distribution of Mr vs pI of differentially secreted peptides presented the general feature. Furthermore, Gene ontology (GO) and pathway analyses for the parent proteins made a comprehensive functional assessment of these differential peptides, indicating the enrichment in glycolysis/gluconeogenesis and striated muscle contraction processes. Intercellular location analysis pointed out most precursor proteins of peptides were cytoplasmic or cytoskeletal. Additionally, cleavage site analysis revealed that Lysine (N-terminal)-Alanine (C-terminal) and Lysine (N-terminal)-Leucine (C-terminal) represents the preferred cleavage sites for identified peptides and proceeding peptides respectively. Mapped to the precursors' sequences, most identified peptides were observed cleaved from creatine kinase m-type (KCRM) and fructose-bisphosphate aldolase A (Aldo A). Based on UniProt and Pfam database for specific domain structure or motif, 44 peptides out of total were positioned in the functional motif or domain from their parent proteins. Using C2C12 myotubes as cell model in vitro, we found several candidate peptides displayed promotive or inhibitory effects on insulin and mitochondrial-related pathways by an autocrine manner. Taken together, this study will encourage us to investigate the biologic functions and the potential regulatory mechanism of these secreted peptides from skeletal muscle tissues, thus representing a promising strategy to treat insulin resistance as well as the associated metabolic disorders.
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Affiliation(s)
- Yanting Wu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Affiliated Maternity and Child Health Care Hospital of Nantong University, NanTong, China
| | - Mei Han
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yan Wang
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yao Gao
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xianwei Cui
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Chenbo Ji
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tianying Zhong
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lianghui You
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- *Correspondence: Lianghui You
| | - Yu Zeng
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Yu Zeng
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Magalhães P, Pontillo C, Pejchinovski M, Siwy J, Krochmal M, Makridakis M, Carrick E, Klein J, Mullen W, Jankowski J, Vlahou A, Mischak H, Schanstra JP, Zürbig P, Pape L. Comparison of Urine and Plasma Peptidome Indicates Selectivity in Renal Peptide Handling. Proteomics Clin Appl 2018; 12:e1700163. [DOI: 10.1002/prca.201700163] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Pedro Magalhães
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
| | - Claudia Pontillo
- Department of Toxicology and Pharmacology; Hannover Medical School; 30625 Hannover Germany
| | | | - Justyna Siwy
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | | | - Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Emma Carrick
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Julie Klein
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joachim Jankowski
- RWTH Aachen University Hospital; 52074 Aachen Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht; University of Maastricht; 6211 Maastricht The Netherlands
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joost P. Schanstra
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - Petra Zürbig
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | - Lars Pape
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
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