scholarly journals Application of Preparative Electrophoresis for Clinical Proteomics in Urine: Is it Feasible?

2009 ◽  
Vol 28 (4) ◽  
pp. 268-273 ◽  
Author(s):  
Jérôme Zoidakis ◽  
Ploumisti Dimitraki ◽  
Panagiotis Zerefos ◽  
Antonia Vlahou
Keyword(s):  
Protein Separation ◽  
Biomarker Discovery ◽  
Clinical Proteomics ◽  
Urinary Proteins ◽  
Preparative Electrophoresis ◽  
Disease Biomarkers ◽  
Electrophoretic Techniques ◽  
Biomarker Research ◽  
Low Molecular Weight Proteins ◽  
Proteins And Peptides

Application of Preparative Electrophoresis for Clinical Proteomics in Urine: Is it Feasible?Urine samples are easily attainable which makes them ideal substrates for biomarker research. Various techniques have been employed to unravel the urine proteome and identify disease biomarkers. Even though the presence of high abundance proteins in urine is not so pronounced as in the case of plasma, the presence of proteolytic products, many of which at low abundance, along with numerous frequently random chemical modifications, makes the analysis of urinary proteins challenging. To facilitate the detection of low abundance urinary proteins, in the study presented herein we applied two different electrophoretic techniques, preparative Lithium Dodecyl Sulfate (LDS)-PAGE in combination with 2-DE for urinary protein separation and enrichment. Our results indicate the effectiveness of this approach for the enrichment of low abundance and low molecular weight proteins and peptides in urine, and contribute towards the establishment of a urinary proteomic database. The application of this technique as a biomarker discovery tool faces several challenges: these include down-scaling of the technique, possible recompensation for the consequent expected decrease in protein resolution, by optimizing steps of the experimental workflow as well as getting a good understanding of the technical variability of the technique. Under these conditions, preparative electrophoresis can become an effective tool for clinical proteomics applications.

scholarly journals Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases

2015 ◽  
Vol 2015 ◽  
pp. 1-17 ◽  
Author(s):  
Shiva Kalantari ◽  
Ameneh Jafari ◽  
Raheleh Moradpoor ◽  
Elmira Ghasemi ◽  
Ensieh Khalkhal
Keyword(s):  
Biomarker Discovery ◽  
Immunoglobulin A ◽  
Kidney Injury ◽  
Analytical Techniques ◽  
Clinical Applications ◽  
Clinical Proteomics ◽  
Renal Diseases ◽  
The Past ◽  
Urinary Proteomics ◽  
Proteins And Peptides

Urine has been in the center of attention among scientists of clinical proteomics in the past decade, because it is valuable source of proteins and peptides with a relative stable composition and easy to collect in large and repeated quantities with a noninvasive procedure. In this review, we discuss technical aspects of urinary proteomics in detail, including sample preparation, proteomic technologies, and their advantage and disadvantages. Several recent experiments are presented which applied urinary proteome for biomarker discovery in renal diseases including diabetic nephropathy, immunoglobulin A (IgA) nephropathy, focal segmental glomerulosclerosis, lupus nephritis, membranous nephropathy, and acute kidney injury. In addition, several available databases in urinary proteomics are also briefly introduced.

scholarly journals Effects of the glucocorticoid drug prednisone on urinary proteome and candidate biomarkers

2017 ◽  
Author(s):  
Jianqiang Wu ◽  
Xundou Li ◽  
Manxia An ◽  
Youhe Gao
Keyword(s):  
Drug Efficacy ◽  
Clinical Proteomics ◽  
Label Free ◽  
Urinary Proteins ◽  
Rat Urine ◽  
Urine Proteome ◽  
Disease Biomarkers ◽  
Urinary Proteome ◽  
Prednisone Treatment ◽  
Human Orthologs

AbstractUrine is a good source of biomarkers for clinical proteomics studies. However, one challenge in the use of urine biomarkers is that outside factors can affect the urine proteome. Prednisone is a commonly prescribed glucocorticoid used to treat various diseases in the clinic. To evaluate the possible impact of glucocorticoid drugs on the urine proteome, specifically disease biomarkers, this study investigated the effects of prednisone on the rat urine proteome. Urine samples were collected from control rats and prednisone-treated rats after drug administration. The urinary proteome was analyzed using liquid chromatography–tandem mass spectrometry (LC-MS/MS), and proteins were identified using label-free proteome quantification. Differentially expressed proteins and their human orthologs were analyzed with bioinformatics methods. A total of 523 urinary proteins were identified in rat urine. Using label-free quantification, 27 urinary proteins showed expression changes after prednisone treatment. A total of 16 proteins and/or their human orthologs have been previously annotated as disease biomarkers. After functional analysis, we found that the pharmacological effects of prednisone were reflected in the urine proteome. Thus, urinary proteomics has the potential to be a powerful drug efficacy monitoring tool in the clinic. Meanwhile, alteration of the urine proteome due to prednisone treatment should be considered in future disease biomarker studies.

scholarly journals Recent Advances in Chiral Analysis of Proteins and Peptides

Separations ◽  
2021 ◽  
Vol 8 (8) ◽  
pp. 112
Author(s):  
Marine Morvan ◽  
Ivan Mikšík
Keyword(s):  
Amino Acids ◽  
Stationary Phases ◽  
Enzymatic Digestion ◽  
Chiral Separations ◽  
Biological Compounds ◽  
Health And Disease ◽  
Electrophoretic Techniques ◽  
A Site ◽  
Future Work ◽  
Proteins And Peptides

Like many biological compounds, proteins are found primarily in their homochiral form. However, homochirality is not guaranteed throughout life. Determining their chiral proteinogenic sequence is a complex analytical challenge. This is because certain D-amino acids contained in proteins play a role in human health and disease. This is the case, for example, with D-Asp in elastin, β-amyloid and α-crystallin which, respectively, have an action on arteriosclerosis, Alzheimer's disease and cataracts. Sequence-dependent and sequence-independent are the two strategies for detecting the presence and position of D-amino acids in proteins. These methods rely on enzymatic digestion by a site-specific enzyme and acid hydrolysis in a deuterium or tritium environment to limit the natural racemization of amino acids. In this review, chromatographic and electrophoretic techniques, such as LC, SFC, GC and CE, will be recently developed (2018–2020) for the enantioseparation of amino acids and peptides. For future work, the discovery and development of new chiral stationary phases and derivatization reagents could increase the resolution of chiral separations.

scholarly journals Methodology and Applications of Disease Biomarker Identification in Human Serum

2007 ◽  
Vol 2 ◽  
pp. 117727190700200 ◽  
Author(s):  
Ziad J. Sahab ◽  
Suzan M. Semaan ◽  
Qing-Xiang Amy Sang
Keyword(s):  
Human Serum ◽  
Protein Separation ◽  
High Sensitivity ◽  
Disease Diagnosis ◽  
Plasma Lipoproteins ◽  
Great Promise ◽  
Protein Biomarkers ◽  
Serum Samples ◽  
Disease Biomarkers ◽  
Diagnosis And Prognosis

Biomarkers are biomolecules that serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Because of the high abundance of albumin and heterogeneity of plasma lipoproteins and glycoproteins, biomarkers are difficult to identify in human serum. Due to the clinical significance the identification of disease biomarkers in serum holds great promise for personalized medicine, especially for disease diagnosis and prognosis. This review summarizes some common and emerging proteomics techniques utilized in the separation of serum samples and identification of disease signatures. The practical application of each protein separation or identification technique is analyzed using specific examples. Biomarkers of cancers of prostate, breast, ovary, and lung in human serum have been reviewed, as well as those of heart disease, arthritis, asthma, and cystic fibrosis. Despite the advancement of technology few biomarkers have been approved by the Food and Drug Administration for disease diagnosis and prognosis due to the complexity of structure and function of protein biomarkers and lack of high sensitivity, specificity, and reproducibility for those putative biomarkers. The combination of different types of technologies and statistical analysis may provide more effective methods to identify and validate new disease biomarkers in blood.

scholarly journals Potential urinary aging markers of 20-month-old rats

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2058 ◽  
Author(s):  
Xundou Li ◽  
Youhe Gao
Keyword(s):  
Biomarker Discovery ◽  
The Body ◽  
Disease Biomarkers ◽  
Urinary Proteome ◽  
Human Orthologs ◽  
Human Protein Atlas ◽  
Aging Conditions ◽  
Old Rats ◽  
Spectral Counts ◽  
Altered Proteins

Urine is a very good source for biomarker discovery because it accumulates changes in the body. However, a major challenge in urinary biomarker discovery is the fact that the urinary proteome is influenced by various elements. To circumvent these problems, simpler systems, such as animal models, can be used to establish associations between physiological or pathological conditions and alterations in the urinary proteome. In this study, the urinary proteomes of young (two months old) and old rats (20 months old; nine in each group) were analyzed using LC-MS/MS and quantified using the Progenesis LC-MS software. A total of 371 proteins were identified, 194 of which were shared between the young and old rats. Based on criteria of a fold change ≥2,P< 0.05 and identification in each rat of the high-abundance group, 33 proteins were found to be changed (15 increased and 18 decreased in old rats). By adding a more stringent standard (protein spectral counts from every rat in the higher group greater than those in the lower group), eight proteins showed consistent changes in all rats of the groups; two of these proteins are also altered in the urinary proteome of aging humans. However, no shared proteins between our results and the previous aging plasma proteome were identified. Twenty of the 33 (60%) altered proteins have been reported to be disease biomarkers, suggesting that aging may share similar urinary changes with some diseases. The 33 proteins corresponded to 28 human orthologs which, according to the Human Protein Atlas, are strongly expressed in the kidney, intestine, cerebellum and lung. Therefore, the urinary proteome may reflect aging conditions in these organs.

scholarly journals Novel Synthesis of Core-Shell Silica Nanoparticles for the Capture of Low Molecular Weight Proteins and Peptides

Molecules ◽  
2017 ◽  
Vol 22 (10) ◽  
pp. 1712 ◽  
Author(s):  
Sergio Hernandez-Leon ◽  
Jose Sarabia-Sainz ◽  
Gabriela Montfort ◽  
Ana Guzman-Partida ◽  
Maria Robles-Burgueño ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Silica Nanoparticles ◽  
Core Shell ◽  
Low Molecular Weight ◽  
Novel Synthesis ◽  
Low Molecular Weight Proteins ◽  
Proteins And Peptides

scholarly journals Heart Disease, Clinical Proteomics and Mass Spectrometry

2004 ◽  
Vol 20 (3) ◽  
pp. 167-178 ◽  
Author(s):  
Brian A. Stanley ◽  
Rebekah L. Gundry ◽  
Robert J. Cotter ◽  
Jennifer E. Van Eyk
Keyword(s):  
Heart Disease ◽  
Troponin I ◽  
Biomarker Discovery ◽  
Clinical Proteomics ◽  
Acute Injury ◽  
Therapeutic Monitoring ◽  
Post Translational Modification ◽  
Cardiac Biomarker ◽  
Mortality And Morbidity ◽  
Surface Enhanced

Heart disease is the leading cause of mortality and morbidity in the world. As such, biomarkers are needed for the diagnosis, prognosis, therapeutic monitoring and risk stratification of acute injury (acute myocardial infarction (AMI)) and chronic disease (heart failure). The procedure for biomarker development involves the discovery, validation, and translation into clinical practice of a panel of candidate proteins to monitor risk of heart disease. Two types of biomarkers are possible; heart-specific and cardiovascular pulmonary system monitoring markers. Here we review the use of MS in the process of cardiac biomarker discovery and validation by proteomic analysis of cardiac myocytes/tissue or serum/plasma. An example of the use of MS in biomarker discovery is given in which the albumin binding protein sub-proteome was examined using MALDI-TOF MS/MS. Additionally, an example of MS in protein validation is given using affinity surface enhanced laser desorption ionization (SELDI) to monitor the disease-induced post-translational modification and the ternary status of myoctye-originating protein, cardiac troponin I in serum.

Pattern of urinary proteins and peptides in patients with rheumatoid arthritis investigated with the Iso-Dalt technique.

1980 ◽  
Vol 26 (2) ◽  
pp. 201-204 ◽  
Author(s):  
P M Clark ◽  
L J Kricka ◽  
T P Whitehead
Keyword(s):  
Rheumatoid Arthritis ◽  
Gel Electrophoresis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Rheumatoid Arthritis Group ◽  
Control Group ◽  
Urinary Proteins ◽  
Composite Pattern ◽  
The Individual ◽  
Proteins And Peptides

Abstract Characteristic differences in the pattern of urinary proteins and peptides have been found in patients with rheumatoid arthritis, compared with patterns from healthy controls. These differences have been demonstrated with a two-dimensional gel electrophoretic technique (Iso-Dalt) involving isoelectric focusing in the first dimension, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. Using simple photographic techniques, one can obtain a composite pattern of the individual protein-stained gels for each group. Comparison of the composite patterns from the rheumatoid arthritis group and the control group revealed several proteins in the urine of the rheumatoid arthritis patients not found in the control group. Two groupings of these proteins were identified: acidic, high-Mr proteins and more basic, low-Mr proteins.

How Clinical Trial Data Sharing Platforms Can Advance the Study of Biomarkers

2019 ◽  
Vol 47 (3) ◽  
pp. 369-373 ◽  
Author(s):  
Rebecca Li ◽  
Ida Sim
Keyword(s):  
Clinical Trial ◽  
Data Sharing ◽  
Biomarker Discovery ◽  
Clinical Trial Data ◽  
Trial Data ◽  
Data Types ◽  
Current State ◽  
Biomarker Research ◽  
Diverse Data

Although data sharing platforms host diverse data types the features of these platforms are well-suited to facilitating biomarker research. Given the current state of biomarker discovery, an innovative paradigm to accelerate biomarker discovery is to utilize platforms such as Vivli to leverage researchers' abilities to integrate certain classes of biomarkers.

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