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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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2
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Jung S, Kim J. Biomarker discovery and beyond for diagnosis of bladder diseases. Bladder (San Franc) 2020; 7:e40. [PMID: 32775482 PMCID: PMC7401981 DOI: 10.14440/bladder.2020.813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 01/15/2023] Open
Abstract
Molecular biosignatures of altered cellular landscapes and functions have been casually linked with pathological conditions, which imply the promise of biomarkers specific to bladder diseases, such as bladder cancer and other dysfunctions. Urinary biomarkers are particularly attractive due to costs, time, and the minimal and noninvasive efforts acquiring urine. The evolution of omics platforms and bioinformatics for analyzing the genome, epigenome, transcriptome, proteome, lipidome, metabolome, etc., have enabled us to develop more sensitive and disease-specific biomarkers. These discoveries broaden our understanding of the complex biology and pathophysiology of bladder diseases, which can ultimately be translated into the clinical setting. In this short review, we will discuss current efforts on identification of promising urinary biomarkers of bladder diseases and their roles in diagnosis and monitoring. With these considerations, we also aim to provide a prospective view of how we can further utilize these bladder biomarkers in developing ideal and smart medical devices that would be applied in the clinic.
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Affiliation(s)
- Sungyong Jung
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jayoung Kim
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Medicine, University of California Los Angeles, CA 90095, USA
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3
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Gargan S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Identification of marker proteins of muscular dystrophy in the urine proteome from the mdx-4cv model of dystrophinopathy. Mol Omics 2020; 16:268-278. [PMID: 32211681 DOI: 10.1039/c9mo00182d] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the protein constituents of urine present a dynamic proteome that can reflect a variety of disease-related alterations in the body, the mass spectrometric survey of proteome-wide changes in urine promises new insights into pathogenic mechanisms. Urine can be investigated in a completely non-invasive way and provides valuable biomedical information on body-wide changes. In this report, we have focused on the urine proteome in X-linked muscular dystrophy using the established mdx-4cv mouse model of dystrophinopathy. In order to avoid potential artefacts due to the manipulation of the biofluid proteome prior to mass spectrometry, crude urine specimens were analyzed without the prior usage of centrifugation steps or concentration procedures. Comparative proteomics revealed 21 increased and 8 decreased proteins out of 870 identified urinary proteoforms using 50 μl of biofluid per investigated sample, i.e. 14 wild type versus 14 mdx-4cv specimens. Promising marker proteins that were almost exclusively found in mdx-4cv urine included nidogen, parvalbumin and titin. Interestingly, the mass spectrometric identification of urine-associated titin revealed a wide spread of peptides over the sequence of this giant muscle protein. The newly established urinomic signature of dystrophinopathy might be helpful for the design of non-invasive assays to improve diagnosis, prognosis, therapy-monitoring and evaluation of potential harmful side effects of novel treatments in the field of muscular dystrophy research.
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Affiliation(s)
- Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth W23F2H6, Co. Kildare, Ireland.
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4
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Watanabe Y, Hirao Y, Kasuga K, Tokutake T, Semizu Y, Kitamura K, Ikeuchi T, Nakamura K, Yamamoto T. Molecular Network Analysis of the Urinary Proteome of Alzheimer's Disease Patients. Dement Geriatr Cogn Dis Extra 2019; 9:53-65. [PMID: 31043964 PMCID: PMC6477484 DOI: 10.1159/000496100] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022] Open
Abstract
Background/Aims The identification of predictive biomarkers for Alzheimer's disease (AD) from urine would aid in screening for the disease, but information about biological and pathophysiological changes in the urine of AD patients is limited. This study aimed to explore the comprehensive profile and molecular network relations of urinary proteins in AD patients. Methods Urine samples collected from 18 AD patients and 18 age- and sex-matched cognitively normal controls were analyzed by mass spectrometry and semiquantified with the normalized spectral index method. Bioinformatics analyses were performed on proteins which significantly increased by more than 2-fold or decreased by less than 0.5-fold compared to the control (p < 0.05) using DAVID bioinformatics resources and KeyMolnet software. Results The levels of 109 proteins significantly differed between AD patients and controls. Among these, annotation clusters related to lysosomes, complement activation, and gluconeogenesis were significantly enriched. The molecular relation networks derived from these proteins were mainly associated with pathways of lipoprotein metabolism, heat shock protein 90 signaling, matrix metalloproteinase signaling, and redox regulation by thioredoxin. Conclusion Our findings suggest that changes in the urinary proteome of AD patients reflect systemic changes related to AD pathophysiology.
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Affiliation(s)
- Yumi Watanabe
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Kensaku Kasuga
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Takayoshi Tokutake
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuka Semizu
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaori Kitamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kazutoshi Nakamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Jedinak A, Loughlin KR, Moses MA. Approaches to the discovery of non-invasive urinary biomarkers of prostate cancer. Oncotarget 2018; 9:32534-32550. [PMID: 30197761 PMCID: PMC6126692 DOI: 10.18632/oncotarget.25946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) continues to be one of the most common cancers in men worldwide. Prostate specific antigen (PSA) measured in blood has been used for decades as an aid for physicians to detect the presence of prostate cancer. However, the PSA test has limited sensitivity and specificity, leading to unnecessary biopsies, overdiagnosis and overtreatment of patients. For these reasons, there is an urgent need for more accurate PCa biomarkers that can detect PCa with high sensitivity and specificity. Urine is a unique source of potential protein biomarkers that can be measured in a non-invasive way. This review comprehensively summarizes state of the art approaches used in the discovery and validation of urinary biomarkers for PCa. Numerous strategies are currently being used in the discovery of urinary biomarkers for prostate cancer including gel-based separation techniques, mass spectrometry, activity-based proteomic assays and software approaches. Antibody-based approaches remain preferred method for validation of candidate biomarkers with rapidly advancing multiplex immunoassays and MS-based targeted approaches. In the last decade, there has been a dramatic acceleration in the development of new techniques and approaches in the discovery of protein biomarkers for prostate cancer including computational, statistical and data mining methods. Many urinary-based protein biomarkers have been identified and have shown significant promise in initial studies. Examples of these potential biomarkers and the methods utilized in their discovery are also discussed in this review.
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Affiliation(s)
- Andrej Jedinak
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kevin R Loughlin
- Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marsha A Moses
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
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Integration of 24 Feature Types to Accurately Detect and Predict Seizures Using Scalp EEG Signals. SENSORS 2018; 18:s18051372. [PMID: 29710763 PMCID: PMC5982573 DOI: 10.3390/s18051372] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 01/22/2023]
Abstract
The neurological disorder epilepsy causes substantial problems to the patients with uncontrolled seizures or even sudden deaths. Accurate detection and prediction of epileptic seizures will significantly improve the life quality of epileptic patients. Various feature extraction algorithms were proposed to describe the EEG signals in frequency or time domains. Both invasive intracranial and non-invasive scalp EEG signals have been screened for the epileptic seizure patterns. This study extracted a comprehensive list of 24 feature types from the scalp EEG signals and found 170 out of the 2794 features for an accurate classification of epileptic seizures. An accuracy (Acc) of 99.40% was optimized for detecting epileptic seizures from the scalp EEG signals. A balanced accuracy (bAcc) was calculated as the average of sensitivity and specificity and our seizure detection model achieved 99.61% in bAcc. The same experimental procedure was applied to predict epileptic seizures in advance, and the model achieved Acc = 99.17% for predicting epileptic seizures 10 s before happening.
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7
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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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8
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Bastos P, Trindade F, Ferreira R, Leite-Moreira A, Falcão-Pires I, Manadas B, Daniel-da-Silva AL, Vitorino R. EDTA-functionalized magnetic nanoparticles: A suitable platform for the analysis of low abundance urinary proteins. Talanta 2017; 170:81-88. [PMID: 28501217 DOI: 10.1016/j.talanta.2017.03.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 12/24/2022]
Abstract
Urine is a highly attractive source of biological information and disease biomarkers, whose proteome characterization is ongoing. To that end, depletion/enrichment strategies for protein analysis can be of great convenience. We have thus developed a method based on the use of EDTA-functionalized magnetic nanoparticles (NPs@EDTA), to fractionate urine samples before liquid chromatography-mass spectrometry analysis and compared the identified proteins with those obtained from ultrafiltrated/unfractionated (UF) urine samples. NPs@EDTA allowed larger urine volumes to be processed, resulting in a greater number of protein identifications (~2-fold) at a lower cost when compared to UF samples. Proteins of greater abundance (such as albumin and uromodulin) were, at least partially, depleted with NPs@EDTA while those of lower abundance were enriched. Bioinformatics analysis showed that approximately 27% of NPs@EDTA-enriched proteins were annotated as displaying enzymatic activity, most of these being hydrolytic enzymes (56%), particularly proteases/peptidases (48%). Also, post-translational modifications were prominently predicted across NPs@EDTA-enriched proteins (90%), particularly glycosylation (52%), phosphorylation (47%) and acetylation (30%). NPs@EDTA allowed the identification of 109 proteins in urine for the first time, showing high potential as a platform for urine's fractionation prior to proteomic analysis.
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Affiliation(s)
- Paulo Bastos
- iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Fábio Trindade
- iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Portugal.
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Portugal
| | - Adelino Leite-Moreira
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Portugal
| | - Inês Falcão-Pires
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ana L Daniel-da-Silva
- Department of Chemistry, CICECO Aveiro Institute of Materials, University of Aveiro, Portugal
| | - Rui Vitorino
- iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Portugal
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9
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Pejchinovski M, Siwy J, Mullen W, Mischak H, Petri MA, Burkly LC, Wei R. Urine peptidomic biomarkers for diagnosis of patients with systematic lupus erythematosus. Lupus 2017; 27:6-16. [PMID: 28474961 DOI: 10.1177/0961203317707827] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Systematic lupus erythematosus (SLE) is characterized with various complications which can cause serious organ damage in the human body. Despite the significant improvements in disease management of SLE patients, the non-invasive diagnosis is entirely missing. In this study, we used urinary peptidomic biomarkers for early diagnosis of disease onset to improve patient risk stratification, vital for effective drug treatment. Methods Urine samples from patients with SLE, lupus nephritis (LN) and healthy controls (HCs) were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS) for state-of-the-art biomarker discovery. Results A biomarker panel made up of 65 urinary peptides was developed that accurately discriminated SLE without renal involvement from HC patients. The performance of the SLE-specific panel was validated in a multicentric independent cohort consisting of patients without SLE but with different renal disease and LN. This resulted in an area under the receiver operating characteristic (ROC) curve (AUC) of 0.80 ( p < 0.0001, 95% confidence interval (CI) 0.65-0.90) corresponding to a sensitivity and a specificity of 83% and 73%, respectively. Based on the end terminal amino acid sequences of the biomarker peptides, an in silico methodology was used to identify the proteases that were up or down-regulated. This identified matrix metalloproteinases (MMPs) as being mainly responsible for the peptides fragmentation. Conclusions A laboratory-based urine test was successfully established for early diagnosis of SLE patients. Our approach determined the activity of several proteases and provided novel molecular information that could potentially influence treatment efficacy.
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Affiliation(s)
| | - J Siwy
- 1 Mosaiques Diagnostics GmbH, Hannover, Germany
| | - W Mullen
- 2 BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - H Mischak
- 1 Mosaiques Diagnostics GmbH, Hannover, Germany.,2 BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - M A Petri
- 3 Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - L C Burkly
- 4 Biogen Inc, Cambridge, Cambridge, MA, USA
| | - R Wei
- 4 Biogen Inc, Cambridge, Cambridge, MA, USA
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Abstract
Research efforts targeting the identification of bladder cancer biomarkers have been extensive during the past decade. Investigations have been performed at the genome, transcriptome, proteome, and metabolome levels and outputs have started appearing including the sketching of disease molecular subtypes. Proteins are directly linked to cell phenotype hence they accumulate special interest as both biomarkers and therapeutic targets. Multiple technical challenges exist, of the main, being the protein concentration vast dynamic range and presence of proteins in modified forms. The scope of this review is to summarize the contribution of proteomics research in this quest of bladder cancer biomarkers. To obtain an unbiased and comprehensive overview, the scientific literature was searched for manuscripts describing proteomic studies on urothelial cancer from the last ten years and those including independent verification studies in urine, tissue and blood are briefly presented. General observations include: a) in most cases, suboptimal experimental design including healthy controls in biomarker discovery and frequently biomarker verification, is followed; b) variability in protein findings between studies can be observed, to some extent reflecting complexity of experimental approaches and proteome itself; c) consistently reported biomarkers include mainly plasma proteins and d) compilation of protein markers into diagnostic panels appears the most promising way forward. Two main avenues of research can now be foreseen: targeting integration of the existing disparate data with proteomic findings being placed in the context of existing knowledge on bladder cancer subtypes and in parallel, accumulation of clinical samples to support proper validation studies of promising marker combinations.
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Affiliation(s)
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens , Biotechnology Division, Athens, Greece
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11
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Krochmal M, Fernandes M, Filip S, Pontillo C, Husi H, Zoidakis J, Mischak H, Vlahou A, Jankowski J. PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw128. [PMID: 27589965 PMCID: PMC5009324 DOI: 10.1093/database/baw128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/17/2016] [Indexed: 01/11/2023]
Abstract
The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated. Extracted datasets include information about the experimental setup, clinical study design, discovery-validation sample sizes and list of differentially expressed proteins (P-value < 0.05). A dedicated interactive web interface, equipped with multiparametric search engine, data export and visualization tools, enables easy browsing of the data and comprehensive analysis. In conclusion, this repository might serve as a source of data for integrative analysis or a knowledgebase for scientists seeking confirmation of their findings and as such, is expected to facilitate the modeling of molecular mechanisms underlying CKD and identification of biologically relevant biomarkers. Database URL:www.peptickddb.com
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Affiliation(s)
- Magdalena Krochmal
- Biomedical Research Foundation Academy of Athens, Center of Basic Research, Athens, Greece University Hospital RWTH Aachen University, Institute for Molecular Cardiovascular Research, Aachen, Germany
| | - Marco Fernandes
- University of Glasgow, BHF Glasgow Cardiovascular Research Centre, Glasgow, United Kingdom
| | - Szymon Filip
- Biomedical Research Foundation Academy of Athens, Center of Basic Research, Athens, Greece Experimental Nephrology and Hypertension, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Pontillo
- Experimental Nephrology and Hypertension, Charité-Universitätsmedizin Berlin, Berlin, Germany Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Holger Husi
- University of Glasgow, BHF Glasgow Cardiovascular Research Centre, Glasgow, United Kingdom
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Center of Basic Research, Athens, Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany University of Glasgow, Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Center of Basic Research, Athens, Greece
| | - Joachim Jankowski
- University Hospital RWTH Aachen University, Institute for Molecular Cardiovascular Research, Aachen, Germany University of Maastricht, CARIM School for Cardiovascular Diseases, Maastricht, The Netherlands
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12
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Abstract
As our knowledge of the mechanisms underlying cancer development and progression has increased, so too have more effective, less toxic, and targeted therapies begun to reach the clinic. However, the full impact of these clinical advances and the practical success of the emerging field of precision medicine are dependent on the discovery and validation of sensitive and accurate biomarkers that can enable appropriate and rigorous sample type and patient selection, reliable longitudinal monitoring of therapeutic efficacy, and even risk assessment and early detection. Within the context of this review, we examine state-of-the-art approaches to the discovery and validation of noninvasive cancer biomarkers, with a specific emphasis on those that are protein or protein-associated ones. We also review sample selection strategies, currently utilized proteomic approaches for both discovery and validation requirements, and data analysis standards. Finally, we provide examples of these elements of biomarker discovery and validation from our own biomarker research.
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13
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Chen Z, Kim J. Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. BMC Urol 2016; 16:11. [PMID: 27000794 PMCID: PMC4802825 DOI: 10.1186/s12894-016-0129-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
Background Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism. Discussion We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition. Conclusion Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.
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Affiliation(s)
- Zhaohui Chen
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Medicine, University of California, Los Angeles, CA, USA.
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14
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Chatziharalambous D, Lygirou V, Latosinska A, Stravodimos K, Vlahou A, Jankowski V, Zoidakis J. Analytical Performance of ELISA Assays in Urine: One More Bottleneck towards Biomarker Validation and Clinical Implementation. PLoS One 2016; 11:e0149471. [PMID: 26889680 PMCID: PMC4758723 DOI: 10.1371/journal.pone.0149471] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/31/2016] [Indexed: 01/04/2023] Open
Abstract
ELISA is the main approach for the sensitive quantification of protein biomarkers in body fluids and is currently employed in clinical laboratories for the measurement of clinical markers. As such, it also constitutes the main methodological approach for biomarker validation and further qualification. For the latter, specific assay performance requirements have to be met, as described in respective guidelines of regulatory agencies. Even though many clinical ELISA assays in serum are regularly used, ELISA clinical applications in urine are significantly less. The scope of our study was to evaluate ELISA assay analytical performance in urine for a series of potential biomarkers for bladder cancer, as a first step towards their large scale clinical validation. Seven biomarkers (Secreted protein acidic and rich in cysteine, Survivin, Slit homolog 2 protein, NRC-Interacting Factor 1, Histone 2B, Proteinase-3 and Profilin-1) previously described in the literature as having differential expression in bladder cancer were included in the study. A total of 11 commercially available ELISA tests for these markers were tested by standard curve analysis, assay reproducibility, linearity and spiking experiments. The results show disappointing performance with coefficients of variation>20% for the vast majority of the tests performed. Only 3 assays (for Secreted protein acidic and rich in cysteine, Survivin and Slit homolog 2 protein) passed the accuracy thresholds and were found suitable for further application in marker quantification. These results collectively reflect the difficulties in developing urine-based ELISA assays of sufficient analytical performance for clinical application, presumably attributed to the urine matrix itself and/or presence of markers in various isoforms.
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Affiliation(s)
- Despina Chatziharalambous
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Agnieszka Latosinska
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantinos Stravodimos
- Department of Urology, Laikon Hospital, University of Athens, School of Medicine, Athens, Greece
| | - Antonia Vlahou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vera Jankowski
- RWTH-Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | - Jerome Zoidakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- * E-mail:
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15
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Iadarola P, Fumagalli M, Bardoni AM, Salvini R, Viglio S. Recent applications of CE- and HPLC-MS in the analysis of human fluids. Electrophoresis 2015; 37:212-30. [PMID: 26426542 DOI: 10.1002/elps.201500272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/06/2015] [Accepted: 09/11/2015] [Indexed: 01/08/2023]
Abstract
The present review intends to cover the literature on the use of CE-/LC-MS for the analysis of human fluids, from 2010 until present. It has been planned to provide an overview of the most recent practical applications of these techniques to less extensively used human body fluids, including, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate, tear fluid, breast fluid, amniotic fluid, and cerumen. Potential pitfalls related to fluid collection and sample preparation, with particular attention to sample clean-up procedures, and methods of analysis, from the research laboratory to a clinical setting will also be addressed. While being apparent that proteomics/metabolomics represent the most prominent approaches for global identification/quantification of putative biomarkers for a variety of human diseases, evidence is also provided of the suitability of these sophisticated techniques for the detection of heterogeneous components carried by these fluids.
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Affiliation(s)
- Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Maria Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
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Filip S, Vougas K, Zoidakis J, Latosinska A, Mullen W, Spasovski G, Mischak H, Vlahou A, Jankowski J. Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine. PLoS One 2015. [PMID: 26208298 PMCID: PMC4514849 DOI: 10.1371/journal.pone.0133773] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.
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Affiliation(s)
- Szymon Filip
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantinos Vougas
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Agnieszka Latosinska
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - William Mullen
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - Goce Spasovski
- Ss. Cyril and Methodius University in Skopje, Nephrology Department, Skopje, Former Yugoslav Republic of Macedonia
| | - Harald Mischak
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Joachim Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research, Aachen, Germany
- * E-mail:
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