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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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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Liu W, Zhu X, Li L, Wang S, Li CZ, Liang T. Reining in Cas13a activity with N-terminal removable tags expands Cas13a based molecular sensing and enables precise gene interference. Biosens Bioelectron 2023; 227:115138. [PMID: 36809733 DOI: 10.1016/j.bios.2023.115138] [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: 11/18/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Activation of Cas13 is exclusively dependent on crRNA-target RNA hybridization according to the canonical mode of Cas13 action. Upon activation Cas13 can cleave both target RNA and any surrounding RNA. The latter has been well adopted by therapeutic gene interference and biosensor development. This work for the first time, rationale designs and validates a multi-component controlled activation system of Cas13 by N-terminus tagging. A composite SUMO tag comprised of His, Twinstrep, and Smt3 tags fully suppresses target dependent activation of Cas13a by interfering with crRNA docking. The suppression releases upon proteases mediated proteolytic cleavage. The modular composition of the composite tag can be altered to fulfill customized response to alternative proteases. The biosensor SUMO-Cas13a is able to resolve a broad concentration range of protease Ulp1 with a calculated LOD of 48.8pg/μL in aqueous buffer. Further, in accordance with this finding Cas13a was successfully programmed to exert target gene knock down preferentially in SUMO protease high cell types. In summary the discovered regulatory component not only fulfills Cas13a based protease detection for the first time, but also delivers a novel strategy for multi-component controlled activation of Cas13a toward temporal and spacial precision.
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Affiliation(s)
- Wenjun Liu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, 310003, China.
| | - Xuena Zhu
- Department of Pathology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Ling Li
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shanshan Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen-Zhong Li
- Biomedical Engineering Program, The Chinese University of Hong Kong School of Medicine, Shenzhen, 518172, China
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, 310003, China.
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Salivary peptidome analysis and protease prediction during orthodontic treatment with fixed appliances. Sci Rep 2023; 13:677. [PMID: 36635354 PMCID: PMC9837200 DOI: 10.1038/s41598-022-26969-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Orthodontic tooth movement (OTM) occurs through proteolytic remodelling within the periodontium following the application of external force to the tooth. This study describes the first characterization of the salivary peptidome and protease profile during the alignment stage of fixed appliance orthodontic treatment. Unstimulated whole mouth saliva from 16 orthodontic patients (10 males, 6 females, mean (SD) age 15.2 (1.6) years) was collected prior to fixed appliance placement (T1), 1-h (T2), 1-week (T3) following fixed appliance placement and on completion of mandibular arch alignment (T4). Salivary peptides were extracted using filtration followed by mass spectrometry to identify amino acid sequences. Protease prediction was carried out in silico using Proteasix and validated with gelatin zymography and enzyme-linked immunosorbent assay. A total of 2852 naturally-occurring peptides were detected, originating from 436 different proteins. Both collagen and statherin-derived peptide levels were increased at T2. Proteasix predicted 73 proteases potentially involved in generating these peptides, including metalloproteinases, calpains and cathepsins. Changes in predicted activity of proteases over time were also observed, with most metalloproteinases showing increased predicted activity at T2-T3. Increased gelatinolytic activity and MMP8/MMP9 levels were detected at T3. Collectively, multiple protein targets and changes in protease-predicted activity during OTM have been identified.
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Limonte CP, Valo E, Drel V, Natarajan L, Darshi M, Forsblom C, Henderson CM, Hoofnagle AN, Ju W, Kretzler M, Montemayor D, Nair V, Nelson RG, O’Toole JF, Toto RD, Rosas SE, Ruzinski J, Sandholm N, Schmidt IM, Vaisar T, Waikar SS, Zhang J, Rossing P, Ahluwalia TS, Groop PH, Pennathur S, Snell-Bergeon JK, Costacou T, Orchard TJ, Sharma K, de Boer IH. Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes. Diabetes Care 2022; 45:1416-1427. [PMID: 35377940 PMCID: PMC9210873 DOI: 10.2337/dc21-2204] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/04/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Understanding mechanisms underlying rapid estimated glomerular filtration rate (eGFR) decline is important to predict and treat kidney disease in type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS We performed a case-control study nested within four T1D cohorts to identify urinary proteins associated with rapid eGFR decline. Case and control subjects were categorized based on eGFR decline ≥3 and <1 mL/min/1.73 m2/year, respectively. We used targeted liquid chromatography-tandem mass spectrometry to measure 38 peptides from 20 proteins implicated in diabetic kidney disease. Significant proteins were investigated in complementary human cohorts and in mouse proximal tubular epithelial cell cultures. RESULTS The cohort study included 1,270 participants followed a median 8 years. In the discovery set, only cathepsin D peptide and protein were significant on full adjustment for clinical and laboratory variables. In the validation set, associations of cathepsin D with eGFR decline were replicated in minimally adjusted models but lost significance with adjustment for albuminuria. In a meta-analysis with combination of discovery and validation sets, the odds ratio for the association of cathepsin D with rapid eGFR decline was 1.29 per SD (95% CI 1.07-1.55). In complementary human cohorts, urine cathepsin D was associated with tubulointerstitial injury and tubulointerstitial cathepsin D expression was associated with increased cortical interstitial fractional volume. In mouse proximal tubular epithelial cell cultures, advanced glycation end product-BSA increased cathepsin D activity and inflammatory and tubular injury markers, which were further increased with cathepsin D siRNA. CONCLUSIONS Urine cathepsin D is associated with rapid eGFR decline in T1D and reflects kidney tubulointerstitial injury.
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Affiliation(s)
- Christine P. Limonte
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Viktor Drel
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and Moores Cancer Center at UC San Diego Health, La Jolla, CA
| | - Manjula Darshi
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Clark M. Henderson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Andrew N. Hoofnagle
- Kidney Research Institute, University of Washington, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
- Division of Metabolism, Endocrinology, and Nutrition, UW Medicine Diabetes Institute, University of Washington, Seattle, WA
| | - Wenjun Ju
- Division of Nephrology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Matthias Kretzler
- Division of Nephrology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Daniel Montemayor
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Viji Nair
- Division of Nephrology, University of Michigan, Ann Arbor, MI
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - John F. O’Toole
- Department of Nephrology and Hypertension, Cleveland Clinic, Cleveland, OH
| | - Robert D. Toto
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX
| | | | - John Ruzinski
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Insa M. Schmidt
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA
| | - Tomas Vaisar
- Division of Metabolism, Endocrinology, and Nutrition, UW Medicine Diabetes Institute, University of Washington, Seattle, WA
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA
| | - Jing Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and Moores Cancer Center at UC San Diego Health, La Jolla, CA
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tarunveer S. Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | - Janet K. Snell-Bergeon
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | | | - Kumar Sharma
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Ian H. de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
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Novel Markers in Diabetic Kidney Disease—Current State and Perspectives. Diagnostics (Basel) 2022; 12:diagnostics12051205. [PMID: 35626360 PMCID: PMC9140176 DOI: 10.3390/diagnostics12051205] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/01/2022] [Accepted: 05/07/2022] [Indexed: 02/05/2023] Open
Abstract
Diabetic kidney disease (DKD) is a leading cause of end-stage renal disease. Along with the increasing prevalence of diabetes, DKD is expected to affect a higher number of patients. Despite the major progress in the therapy of DKD and diabetes mellitus (DM), the classic clinical diagnostic tools in DKD remain insufficient, delaying proper diagnosis and therapeutic interventions. We put forward a thesis that there is a need for novel markers that will be early, specific, and non-invasively obtained. The ongoing investigations uncover new molecules that may potentially become new markers of DKD—among those are: soluble α-Klotho and proteases (ADAM10, ADAM17, cathepsin, dipeptidyl peptidase 4, caspase, thrombin, and circulating microRNAs). This review summarizes the current clinical state-of-the-art in the diagnosis of DKD and a selection of potential novel markers, based on up-to-date literature.
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Petra E, Siwy J, Vlahou A, Jankowski J. Urine peptidome in combination with transcriptomics analysis highlights MMP7, MMP14 and PCSK5 for further investigation in chronic kidney disease. PLoS One 2022; 17:e0262667. [PMID: 35045102 PMCID: PMC8769332 DOI: 10.1371/journal.pone.0262667] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/03/2022] [Indexed: 11/21/2022] Open
Abstract
Chronic kidney disease (CKD) is characterized by the loss of kidney function. The molecular mechanisms underlying the development and progression of CKD are still not fully understood. Among others, the urinary peptidome has been extensively studied, with several urinary peptides effectively detecting disease progression. However, their link to proteolytic events has not been made yet. This study aimed to predict the proteases involved in the generation of CKD-associated urinary excreted peptides in a well-matched (for age, sex, lack of heart disease) case-control study. The urinary peptide profiles from CKD (n = 241) and controls (n = 240) were compared and statistically analyzed. The in-silico analysis of the involved proteases was performed using Proteasix and proteases activity was predicted based on the abundance changes of the associated peptides. Predictions were cross-correlated to transcriptomics datasets by using the Nephroseq database. Information on the respective protease inhibitors was also retrieved from the MEROPS database. Totally, 303 urinary peptides were significantly associated with CKD. Among the most frequently observed were fragments of collagen types I, II and III, uromodulin, albumin and beta-2-microglobulin. Proteasix predicted 16 proteases involved in their generation. Through investigating CKD-associated transcriptomics datasets, several proteases are highlighted including members of matrix metalloproteinases (MMP7, MMP14) and serine proteases (PCSK5); laying the foundation for further studies towards elucidating their role in CKD pathophysiology.
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Affiliation(s)
- Eleni Petra
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Antonia Vlahou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany
- Experimental Vascular Pathology, Cardiovascular Research Institute Maastricht (CARIM), University of Maastricht, Maastricht, The Netherlands
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Lin B, Liu J, Zhang Y, Wu Y, Chen S, Bai Y, Liu Q, Qin X. Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy. BMC Genomics 2021; 22:852. [PMID: 34819020 PMCID: PMC8613922 DOI: 10.1186/s12864-021-08155-3] [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] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic membranous nephropathy (IMN) is a cause of nephrotic syndrome that is increasing in incidence but has unclear pathogenesis. Urinary peptidomics is a promising technology for elucidating molecular mechanisms underlying diseases. Dysregulation of the proteolytic system is implicated in various diseases. Here, we aimed to conduct urinary peptidomics to identify IMN-related proteases. RESULTS Peptide fingerprints indicated differences in naturally produced urinary peptide components among 20 healthy individuals, 22 patients with IMN, and 15 patients with other kidney diseases. In total, 1,080 peptide-matched proteins were identified, 279 proteins differentially expressed in the urine of IMN patients were screened, and 32 proteases were predicted; 55 of the matched proteins were also differentially expressed in the kidney tissues of IMN patients, and these were mainly involved in the regulation of proteasome-, lysosome-, and actin cytoskeleton-related signaling pathways. The 32 predicted proteases showed abnormal expression in the glomeruli of IMN patients based on Gene Expression Omnibus databases. Western blot revealed abnormal expression of calpain, matrix metalloproteinase 14, and cathepsin S in kidney tissues of patients with IMN. CONCLUSIONS This work shown the calpain/matrix metalloproteinase/cathepsin axis might be dysregulated in IMN. Our study is the first to systematically explore the role of proteases in IMN by urinary peptidomics, which are expected to facilitate discovery of better biomarkers for IMN.
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Affiliation(s)
- Baoxu Lin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Jianhua Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Yue Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Yabin Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Shixiao Chen
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Yibo Bai
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Qiuying Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, 110004, Shenyang, P. R. China.
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Simple urine storage protocol for extracellular vesicle proteomics compatible with at-home self-sampling. Sci Rep 2021; 11:20760. [PMID: 34675268 PMCID: PMC8531010 DOI: 10.1038/s41598-021-00289-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
Urinary extracellular vesicles (EVs) have gained increased interest as a biomarker source. Clinical implementation on a daily basis requires protocols that inevitably includes short-term storage of the clinical samples, especially when collected at home. However, little is known about the effect of delayed processing on the urinary EVs concentration and proteome. We evaluated two storage protocols. First, urine stored at 4 °C. Secondly a protocol compatible with at-home collection, in which urine was stored with the preservative EDTA at room temperature (RT). EVs were isolated using the ME-kit (VN96-peptide). For both conditions we explored the effect of storage duration (0, 2, 4 and 8 days) on EV concentration and proteome using EVQuant and data-independent acquisition mass spectrometry, respectively. The urinary EV concentration and proteome was highly stable using both protocols, in terms of protein number and quantitative changes. Furthermore, EDTA does not affect the urinary EV concentration or global proteome. In conclusion, urine can be stored either at 4 °C or with EDTA at RT for up to 8 days without any significant decay in EV concentration or a notable effect on the EV-proteome. These findings open up biomarker studies in urine collected via self-sampling at home.
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10
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Al-Essa MK, Alzayadneh E, Al-Hadidi K. Assessment of Proteolysis by Pyrylium and Other Fluorogenic Reagents. Protein Pept Lett 2021; 28:809-816. [PMID: 33390107 PMCID: PMC9175085 DOI: 10.2174/0929866528999201231214954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 11/22/2022]
Abstract
Aims We aim to evaluate the potential application of amine reactive fluorogenic reagents for estimating enzymatic proteolysis. Background Proteolytic enzymes play important roles in regulating many physiological processes in living organisms. Objectives
Assessment of protein degradation by using reagents for protein assay techniques. Methods We have assayed samples at the start and after 30-60 minutes incubation with trypsin by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents and NanoOrange as non-amine reactive dye. Results All BSA prepared samples with trypsin have shown significantly higher fluorescence intensity (FI) versus controls (which reflects proteolysis) when assayed by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents. However, same samples assayed with NanoOrange as non-amine reactive reagent did not show any significant variation between samples containing trypsin and controls. Conclusion These results are confirming reliability of highly sensitive protein assays utilizing amine reactive fluorogenic reagents for general estimation of proteolysis.
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Affiliation(s)
- Mohamed K Al-Essa
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Ebaa Alzayadneh
- Department of Physiology and Biochemistry, School of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Kamal Al-Hadidi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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Boder P, Mary S, Mark PB, Leiper J, Dominiczak AF, Padmanabhan S, Rampoldi L, Delles C. Mechanistic interactions of uromodulin with the thick ascending limb: perspectives in physiology and hypertension. J Hypertens 2021; 39:1490-1504. [PMID: 34187999 PMCID: PMC7611110 DOI: 10.1097/hjh.0000000000002861] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hypertension is a significant risk factor for cardiovascular disease and mortality worldwide. The kidney is a major regulator of blood pressure and electrolyte homeostasis, with monogenic disorders indicating a link between abnormal ion transport and salt-sensitive hypertension. However, the association between salt and hypertension remains controversial. Thus, there is continued interest in deciphering the molecular mechanisms behind these processes. Uromodulin (UMOD) is the most abundant protein in the normal urine and is primarily synthesized by the thick ascending limb epithelial cells of the kidney. Genome-wide association studies have linked common UMOD variants with kidney function, susceptibility to chronic kidney disease and hypertension independent of renal excretory function. This review will discuss and provide predictions on the role of the UMOD protein in renal ion transport and hypertension based on current observational, biochemical, genetic, pharmacological and clinical evidence.
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Affiliation(s)
- Philipp Boder
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sheon Mary
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick B. Mark
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - James Leiper
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christian Delles
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
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12
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Trindade F, Barros AS, Silva J, Vlahou A, Falcão-Pires I, Guedes S, Vitorino C, Ferreira R, Leite-Moreira A, Amado F, Vitorino R. Mining the Biomarker Potential of the Urine Peptidome: From Amino Acids Properties to Proteases. Int J Mol Sci 2021; 22:5940. [PMID: 34073067 PMCID: PMC8197949 DOI: 10.3390/ijms22115940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
Native biofluid peptides offer important information about diseases, holding promise as biomarkers. Particularly, the non-invasive nature of urine sampling, and its high peptide concentration, make urine peptidomics a useful strategy to study the pathogenesis of renal conditions. Moreover, the high number of detectable peptides as well as their specificity set the ground for the expansion of urine peptidomics to the identification of surrogate biomarkers for extra-renal diseases. Peptidomics further allows the prediction of proteases (degradomics), frequently dysregulated in disease, providing a complimentary source of information on disease pathogenesis and biomarkers. Then, what does urine peptidomics tell us so far? In this paper, we appraise the value of urine peptidomics in biomarker research through a comprehensive analysis of all datasets available to date. We have mined > 50 papers, addressing > 30 different conditions, comprising > 4700 unique peptides. Bioinformatic tools were used to reanalyze peptide profiles aiming at identifying disease fingerprints, to uncover hidden disease-specific peptides physicochemical properties and to predict the most active proteases associated with their generation. The molecular patterns found in this study may be further validated in the future as disease biomarker not only for kidney diseases but also for extra-renal conditions, as a step forward towards the implementation of a paradigm of predictive, preventive and personalized (3P) medicine.
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Affiliation(s)
- Fábio Trindade
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - António S. Barros
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - Jéssica Silva
- iBiMED—Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece;
| | - Inês Falcão-Pires
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - Sofia Guedes
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
| | - Carla Vitorino
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Center for Neurosciences and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Rita Ferreira
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
| | - Adelino Leite-Moreira
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - Francisco Amado
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
| | - Rui Vitorino
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
- iBiMED—Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal;
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
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13
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Klein O. Proteomics in Kidney and Cardiovascular Clinical Research. Proteomics Clin Appl 2021; 15:e1900132. [PMID: 33458964 DOI: 10.1002/prca.201900132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Oliver Klein
- Berlin Institute of Health Center for Regenerative Therapies and Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Augustenburger Platz 1, Berlin, 13353, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, Germany
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14
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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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15
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Insights into predicting diabetic nephropathy using urinary biomarkers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140475. [DOI: 10.1016/j.bbapap.2020.140475] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/27/2020] [Accepted: 06/14/2020] [Indexed: 12/20/2022]
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16
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He T, Siwy J, Metzger J, Mullen W, Mischak H, Schanstra JP, Zürbig P, Jankowski V. Associations of urinary polymeric immunoglobulin receptor peptides in the context of cardio-renal syndrome. Sci Rep 2020; 10:8291. [PMID: 32427855 PMCID: PMC7237418 DOI: 10.1038/s41598-020-65154-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/24/2020] [Indexed: 11/09/2022] Open
Abstract
The polymeric immunoglobulin receptor (pIgR) transports immunoglobulins from the basolateral to the apical surface of epithelial cells. PIgR was recently shown to be associated with kidney dysfunction. The immune defense is initiated at the apical surface of epithelial cells where the N-terminal domain of pIgR, termed secretory component (SC), is proteolytically cleaved and released either unbound (free SC) or bound to immunoglobulins. The aim of our study was to evaluate the association of pIgR peptides with the cardio-renal syndrome in a large cohort and to obtain information on how the SC is released. We investigated urinary peptides of 2964 individuals available in the Human Urine Proteome Database generated using capillary electrophoresis coupled to mass spectrometry. The mean amplitude of 23 different pIgR peptides correlated negatively with the estimated glomerular filtration rate (eGFR, rho = −0.309, p < 0.0001). Furthermore, pIgR peptides were significantly increased in cardiovascular disease (coronary artery disease and heart failure) after adjustment for eGFR. We further predicted potential proteases involved in urinary peptide generation using the Proteasix algorithm. Peptide cleavage site analysis suggested that several, and not one, proteases are involved in the generation of the SC. In this large cohort, we could demonstrate that pIgR is associated with the cardio-renal syndrome and provided a more detailed insight on how pIgR can be potentially cleaved to release the SC.
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Affiliation(s)
- Tianlin He
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH Aachen, Aachen, Germany
| | | | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Joost P Schanstra
- INSERM U1048, Institute of Cardiovascular and Metabolic Diseases, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Toulouse, France.
| | | | - Vera Jankowski
- Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH Aachen, Aachen, Germany
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17
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Wang W, Shen J, Qi C, Pu J, Chen H, Zuo Z. The key candidate genes in tubulointerstitial injury of chronic kidney diseases patients as determined by bioinformatic analysis. Cell Biochem Funct 2020; 38:761-772. [PMID: 32340064 DOI: 10.1002/cbf.3545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/19/2020] [Accepted: 04/11/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Wanpeng Wang
- Department of Nephrology, Lianshui County People's HospitalKangda College of Nanjing Medical University Huai'an China
- Department of Central LaboratoryLianshui County People's Hospital Huai'an China
| | - Jianxiao Shen
- Department of Nephrology, Renji Hospital, School of MedicineShanghai Jiaotong University Shanghai China
| | - Chaojun Qi
- Department of Nephrology, Renji Hospital, School of MedicineShanghai Jiaotong University Shanghai China
| | - Juan Pu
- Department of Central LaboratoryLianshui County People's Hospital Huai'an China
| | - Haoyu Chen
- Department of Central LaboratoryLianshui County People's Hospital Huai'an China
| | - Zhi Zuo
- Department of Cardiology, Zhongda HospitalMedical School of Southeast University Nanjing China
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18
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Audzeyenka I, Rachubik P, Rogacka D, Typiak M, Kulesza T, Angielski S, Rychłowski M, Wysocka M, Gruba N, Lesner A, Saleem MA, Piwkowska A. Cathepsin C is a novel mediator of podocyte and renal injury induced by hyperglycemia. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118723. [PMID: 32302668 DOI: 10.1016/j.bbamcr.2020.118723] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023]
Abstract
A growing body of evidence suggests a role of proteolytic enzymes in the development of diabetic nephropathy. Cathepsin C (CatC) is a well-known regulator of inflammatory responses, but its involvement in podocyte and renal injury remains obscure. We used Zucker rats, a genetic model of metabolic syndrome and insulin resistance, to determine the presence, quantity, and activity of CatC in the urine. In addition to the animal study, we used two cellular models, immortalized human podocytes and primary rat podocytes, to determine mRNA and protein expression levels via RT-PCR, Western blot, and confocal microscopy, and to evaluate CatC activity. The role of CatC was analyzed in CatC-depleted podocytes using siRNA and glycolytic flux parameters were obtained from extracellular acidification rate (ECAR) measurements. In functional analyses, podocyte and glomerular permeability to albumin was determined. We found that podocytes express and secrete CatC, and a hyperglycemic environment increases CatC levels and activity. Both high glucose and non-specific activator of CatC phorbol 12-myristate 13-acetate (PMA) diminished nephrin, cofilin, and GLUT4 levels and induced cytoskeletal rearrangements, increasing albumin permeability in podocytes. These negative effects were completely reversed in CatC-depleted podocytes. Moreover, PMA, but not high glucose, increased glycolytic flux in podocytes. Finally, we demonstrated that CatC expression and activity are increased in the urine of diabetic Zucker rats. We propose a novel mechanism of podocyte injury in diabetes, providing deeper insight into the role of CatC in podocyte biology.
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Affiliation(s)
- Irena Audzeyenka
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland; Faculty of Chemistry, University of Gdansk, Poland.
| | - Patrycja Rachubik
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland
| | - Dorota Rogacka
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland; Faculty of Chemistry, University of Gdansk, Poland
| | - Marlena Typiak
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland
| | - Tomasz Kulesza
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland
| | - Stefan Angielski
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland
| | - Michał Rychłowski
- Intercollegiate Faculty of Biotechnology, University of Gdansk - Medical University of Gdansk, Poland
| | | | | | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Poland
| | - Moin A Saleem
- Bristol Renal, University of Bristol, United Kingdom
| | - Agnieszka Piwkowska
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Gdansk, Poland; Faculty of Chemistry, University of Gdansk, Poland
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19
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Massolini BD, Contieri SSG, Lazarini GS, Bellacosa PA, Dobre M, Petroianu G, Brateanu A, Campos LA, Baltatu OC. Therapeutic Renin Inhibition in Diabetic Nephropathy-A Review of the Physiological Evidence. Front Physiol 2020; 11:190. [PMID: 32231590 PMCID: PMC7082742 DOI: 10.3389/fphys.2020.00190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/19/2020] [Indexed: 11/13/2022] Open
Abstract
The purpose of this systematic review was to investigate the scientific evidence to support the use of direct renin inhibitors (DRIs) in diabetic nephropathy (DN). MEDLINE was searched for articles reported until 2018. A standardized dataset was extracted from articles describing the effects of DRIs on plasma renin activity (PRA) in DN. A total of three clinical articles studying PRA as an outcome measure for DRIs use in DN were identified. These clinical studies were randomized controlled trials (RCTs): one double-blind crossover, one post hoc of a double-blind and placebo-controlled study, and one open-label and parallel-controlled study. Two studies reported a significant decrease of albuminuria associated with PRA reduction. One study had a DRI as monotherapy compared with placebo, and two studies had DRI as add-in to an angiotensin II (Ang II) receptor blocker (ARB). Of 10,393 patients with DN enrolled in five studies with DRI, 370 (3.6%) patients had PRA measured. Only one preclinical study was identified that determined PRA when investigating the effects of aliskiren in DN. Moreover, most of observational preclinical and clinical studies identified report on a low PRA or hyporeninemic hypoaldosteronism in DM. Renin inhibition has been suggested for DN, but proof-of-concept studies for this are scant. A small number of clinical and preclinical studies assessed the PRA effects of DRIs in DN. For a more successful translational research for DRIs, specific patient population responsive to the treatment should be identified, and PRA may remain a biomarker of choice for patient stratification.
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Affiliation(s)
- Bianca Domingues Massolini
- Center of Innovation, Technology and Education-CITÉ, São José dos Campos Technology Park, São José dos Campos, São Paulo, Brazil.,Institute of Biomedical Engineering, Anhembi Morumbi University, Laureate International Universities, São José dos Campos, São Paulo, Brazil
| | - Stephanie San Gregorio Contieri
- Center of Innovation, Technology and Education-CITÉ, São José dos Campos Technology Park, São José dos Campos, São Paulo, Brazil.,Institute of Biomedical Engineering, Anhembi Morumbi University, Laureate International Universities, São José dos Campos, São Paulo, Brazil
| | - Giulia Severini Lazarini
- Center of Innovation, Technology and Education-CITÉ, São José dos Campos Technology Park, São José dos Campos, São Paulo, Brazil.,Institute of Biomedical Engineering, Anhembi Morumbi University, Laureate International Universities, São José dos Campos, São Paulo, Brazil
| | - Paula Antoun Bellacosa
- Center of Innovation, Technology and Education-CITÉ, São José dos Campos Technology Park, São José dos Campos, São Paulo, Brazil.,Institute of Biomedical Engineering, Anhembi Morumbi University, Laureate International Universities, São José dos Campos, São Paulo, Brazil
| | - Mirela Dobre
- Division of Nephrology and Hypertension, University Hospitals, Cleveland, OH, United States
| | - Georg Petroianu
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Andrei Brateanu
- Medicine Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Luciana Aparecida Campos
- Center of Innovation, Technology and Education-CITÉ, São José dos Campos Technology Park, São José dos Campos, São Paulo, Brazil.,Institute of Biomedical Engineering, Anhembi Morumbi University, Laureate International Universities, São José dos Campos, São Paulo, Brazil.,College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Ovidiu Constantin Baltatu
- Center of Innovation, Technology and Education-CITÉ, São José dos Campos Technology Park, São José dos Campos, São Paulo, Brazil.,Institute of Biomedical Engineering, Anhembi Morumbi University, Laureate International Universities, São José dos Campos, São Paulo, Brazil.,College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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20
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Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud FH, Sochett E, Diamandis EP, Scholey JW, Konvalinka A. Peptidomic Analysis of Urine from Youths with Early Type 1 Diabetes Reveals Novel Bioactivity of Uromodulin Peptides In Vitro. Mol Cell Proteomics 2020; 19:501-517. [PMID: 31879271 PMCID: PMC7050109 DOI: 10.1074/mcp.ra119.001858] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/20/2019] [Indexed: 12/17/2022] Open
Abstract
Chronic hyperglycemia is known to disrupt the proteolytic milieu, initiating compensatory and maladaptive pathways in the diabetic kidney. Such changes in intrarenal proteolysis are captured by the urinary peptidome. To elucidate the early kidney response to chronic hyperglycemia, we conducted a peptidomic investigation into urines from otherwise healthy youths with type 1 diabetes and their non-diabetic peers using unbiased and targeted mass spectrometry-based techniques. This cross-sectional study included two separate cohorts for the discovery (n = 30) and internal validation (n = 30) of differential peptide excretion. Peptide bioactivity was predicted using PeptideRanker and subsequently verified in vitro Proteasix and the Nephroseq database were used to identify putative proteases responsible for peptide generation and examine their expression in diabetic nephropathy. A total of 6550 urinary peptides were identified in the discovery analysis. We further examined the subset of 162 peptides, which were quantified across all thirty samples. Of the 15 differentially excreted peptides (p < 0.05), seven derived from a C-terminal region (589SGSVIDQSRVLNLGPITRK607) of uromodulin, a kidney-specific protein. Increased excretion of five uromodulin peptides was replicated in the validation cohort using parallel reaction monitoring (p < 0.05). One of the validated peptides (SGSVIDQSRVLNLGPI) activated NFκB and AP-1 signaling, stimulated cytokine release, and enhanced neutrophil migration in vitro. In silico analyses highlighted several potential proteases such as hepsin, meprin A, and cathepsin B to be responsible for generating these peptides. In summary, we identified a urinary signature of uromodulin peptides associated with early type 1 diabetes before clinical manifestations of kidney disease and discovered novel bioactivity of uromodulin peptides in vitro Our present findings lay the groundwork for future studies to validate peptide excretion in larger and broader populations, to investigate the role of bioactive uromodulin peptides in high glucose conditions, and to examine proteases that cleave uromodulin.
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Affiliation(s)
- Julie A D Van
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada.
| | - Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Joyce Zhou
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Chunxiang Sun
- Faculty of Dentistry, University of Toronto, Toronto, Canada
| | | | - Luca Rampoldi
- Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | | | | | | | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, University of Toronto, Toronto, Canada
| | - James W Scholey
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Medicine, Division of Nephrology, University Health Network, Toronto, Canada
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Medicine, Division of Nephrology, University Health Network, Toronto, Canada
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21
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de Oliveira TM, de Lacerda JTJG, Leite GGF, Dias M, Mendes MA, Kassab P, E Silva CGS, Juliano MA, Forones NM. Label-free peptide quantification coupled with in silico mapping of proteases for identification of potential serum biomarkers in gastric adenocarcinoma patients. Clin Biochem 2020; 79:61-69. [PMID: 32097616 DOI: 10.1016/j.clinbiochem.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/31/2020] [Accepted: 02/18/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVES We aimed to identify serum level variations in protein-derived peptides between patients diagnosed with gastric adenocarcinoma (GAC) and non-cancer persons (control) to detect the activity changes of proteases and explore the auxiliary diagnostic value in the context of GAC physiopathology. METHODS The label-free quantitative peptidome approach was applied to identify variants in serum levels of peptides that can differentiate GAC patients from the control group. Peptide sequences were submitted against Proteasix tool predicting proteases potentially involved in their generation. The activity change of proteases was subsequently estimated based on the peptides with significantly altered relative abundance. In turn, activity change prediction of proteases was correlated with relevant protease expression data from the literature. RESULTS A total of 191 peptide sequences generated by the cleavage of 36 precursor proteins were identified. Using the label-free quantification approach, 33 peptides were differentially quantified (adjusted fold change ≥ 1.5 and p-value < 0.05) in which 19 were up-regulated and 14 were down-regulated in GAC samples. Of these peptides, fibrinopeptide A was significantly decreased and its phosphorylated form ADpSGEGDFLAEGGGVR was upregulated in GAC samples. Activity change prediction yielded 10 proteases including 6 Matrix Metalloproteinases (MMPs), Thrombin, Plasmin, and kallikreins 4 and 14. Among predicted proteases in our analysis, MMP-7 was presented as a more promising biomarker associated with useful assays of clinical practice for GAC diagnosis. CONCLUSION Our experimental results demonstrate that the serum levels of peptides were significantly differentiated in GAC physiopathology. The hypotheses built on protease regulation could be used for further investigations to measure proteases and their activity levels that have been poorly studied for GAC diagnosis.
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Affiliation(s)
- Talita Mendes de Oliveira
- Department of Medicine, Division of Gastroenterology, Oncology Group, Federal University of São Paulo, São Paulo, SP, Brazil.
| | | | | | - Meriellen Dias
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil
| | - Maria Anita Mendes
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil
| | - Paulo Kassab
- Digestive Surgical Oncology Division, Santa Casa of São Paulo Medical School, São Paulo, SP, Brazil
| | | | | | - Nora Manoukian Forones
- Department of Medicine, Division of Gastroenterology, Oncology Group, Federal University of São Paulo, São Paulo, SP, Brazil
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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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Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
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Dong Z, Sun Y, Wei G, Li S, Zhao Z. Ergosterol Ameliorates Diabetic Nephropathy by Attenuating Mesangial Cell Proliferation and Extracellular Matrix Deposition via the TGF-β1/Smad2 Signaling Pathway. Nutrients 2019; 11:nu11020483. [PMID: 30823598 PMCID: PMC6412245 DOI: 10.3390/nu11020483] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 01/18/2023] Open
Abstract
(1) Background: Diabetic nephropathy, a microvascular complication of diabetes, is one of the principal causes of end-stage renal disease worldwide. The aim of this study was to explore the therapeutic effects of ergosterol on diabetic nephropathy. (2) Methods: Streptozotocin (STZ)-induced C57BL/6 diabetic mice were treated with ergosterol (10, 20, 40 mg/kg/day) for 8 weeks by oral gavage. The in vitro study employed rat mesangial cells exposed to 30 mM glucose for 48 h in the presence of 10 or 20 μM ergosterol. (3) Results: Ergosterol treatment improved body weights, ameliorated the majority of biochemical and renal functional parameters and histopathological changes, and reduced extracellular matrix (ECM) deposition in diabetic mice. In vitro, ergosterol suppressed proliferation, reduced the levels of ECM proteins, and increased the expression of matrix metalloproteinase-2 and -9 in high glucose-induced mesangial cells; Furthermore, ergosterol markedly improved transforming growth factor-β1 (TGF-β1) expression, enhanced phosphorylation levels of drosophila mothers against decapentaplegic 2 (Smad2), and regulated the downstream factors in vivo and in vitro. (4) Conclusions: Ergosterol alleviated mesangial cell proliferation and the subsequent ECM deposition by regulating the TGF-β1/Smad2 signaling pathway.
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Affiliation(s)
- Zhonghua Dong
- School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan 250012, Shandong, China.
| | - Yueyue Sun
- School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan 250012, Shandong, China.
| | - Guangwei Wei
- School of Basic Medical Sciences, Shandong University, 44 West Wenhua Road, Jinan 250012, Shandong, China.
| | - Siying Li
- School of Basic Medical Sciences, Shandong University, 44 West Wenhua Road, Jinan 250012, Shandong, China.
| | - Zhongxi Zhao
- School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan 250012, Shandong, China.
- Shandong Engineering & Technology Research Center for Jujube Food and Drug, 44 West Wenhua Road, Jinan 250012, Shandong, China.
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Frantzi M, Latosinska A, Kontostathi G, Mischak H. Clinical Proteomics: Closing the Gap from Discovery to Implementation. Proteomics 2018; 18:e1700463. [PMID: 29785737 DOI: 10.1002/pmic.201700463] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/10/2018] [Indexed: 12/15/2022]
Abstract
Clinical proteomics, the application of proteome analysis to serve a clinical purpose, represents a major field in the area of proteome research. Over 1000 manuscripts on this topic are published each year, with numbers continuously increasing. However, the anticipated outcome, the transformation of the reported findings into improvements in patient management, is not immediately evident. In this article, the value and validity of selected clinical proteomics findings are investigated, and it is assessed how far implementation has progressed. A main conclusion from this assessment is that to achieve implementation, well-powered clinical studies are required in the appropriate population, addressing a specific clinical need and with a clear context-of-use. Efforts toward implementation, to be feasible, must be supported by the key players in science: publishers and funders. The authors propose a change on objectives, from additional discovery studies toward studies aiming at validation of the plethora of potential biomarkers that have been described, to demonstrate practical value of clinical proteomics. All elements required, potential biomarkers, technologies, and bio-banked samples are available (based on today's literature), hence a change in focus from discovery toward validation and application is not only urgently necessary, but also possible based on resources available today.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Hannover, 30659, Germany
| | | | - Georgia Kontostathi
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, 11527, Greece
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Krochmal M, Schanstra JP, Mischak H. Urinary peptidomics in kidney disease and drug research. Expert Opin Drug Discov 2017; 13:259-268. [DOI: 10.1080/17460441.2018.1418320] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Magdalena Krochmal
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, Greece
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Joost P Schanstra
- Institut of Cardiovascular and Metabolic Disease, Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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