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Akshintala VS, Moore MG, Cruz-Monserrate Z, Nathan JD, Searle BC, Abu-El-Haija M. Urine Proteomics Profiling Identifies Novel Acute Pancreatitis Diagnostic Biomarkers in a Pediatric Population. Gastroenterology 2024; 167:1019-1021.e2. [PMID: 38797238 PMCID: PMC11416306 DOI: 10.1053/j.gastro.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/12/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Venkata S Akshintala
- Division of Gastroenterology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Madalyn G Moore
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology and Nutrition and, The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jaimie D Nathan
- Department of Pediatric Abdominal Transplant and Hepatopancreatobiliary Surgery, Nationwide Children's Hospital, Columbus, Ohio; Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Brian C Searle
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.
| | - Maisam Abu-El-Haija
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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Zhen K, Hou W, Bai L, Wang M, Yue Z, Xu Z, Xiong D, Gao L, Ying W. An effective urobilin clearance strategy based on paramagnetic beads facilitates microscale proteomic analysis of urine. Analyst 2024; 149:3625-3635. [PMID: 38775334 DOI: 10.1039/d4an00312h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Urine provides an ideal source for disease biomarker discovery. High-adhesion contaminants such as urobilin, which are difficult to remove from urine, can severely interfere with urinary proteomic analysis. Here, we aimed to establish a strategy based on single-pot, solid-phase-enhanced sample preparation (SP3) technology to prepare samples for urinary proteomics analysis that almost completely eliminates the impact of urobilin. A systematic evaluation of the effects of two urinary protein precipitation methods, two types of protein lysis buffers, and different ratios of magnetic digestion beads on the identification and quantification of the microscale urinary proteome was conducted. Our results indicate that methanol-chloroform precipitation, coupled with efficient lysis facilitated by urea, and subsequent enzymatic digestion using a mix of hydrophilic and hydrophobic magnetic beads offers the best performance. Further applying this strategy to the urine of patients with benign prostatic hyperplasia, prostate cancer and healthy individuals, combined with a narrow window of data-independent acquisition, FGFR4, MYLK, ORM2, GOLM1, SPP1, CD55, CSF1, DLD and TIMP3 were identified as potential biomarkers to discriminate benign prostatic hyperplasia and prostate cancer patients.
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Affiliation(s)
- Kemiao Zhen
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Wenhao Hou
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Lu Bai
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Mingchao Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Zhan Yue
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Zanxin Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Deyun Xiong
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Li Gao
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Wantao Ying
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Wong CHM, Ko ICH, Ng CF. Liquid biomarkers in prostate cancer: recent advancements and future directions. Curr Opin Urol 2024:00042307-990000000-00158. [PMID: 38712633 DOI: 10.1097/mou.0000000000001188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
PURPOSE OF REVIEW Traditional diagnostic approaches of prostate cancer like PSA are limited by high false-positive rates and insufficient capture of tumour heterogeneity, necessitating the development of more precise tools. This review examines the latest advancements in liquid biomarkers for prostate cancer, focusing on their potential to refine diagnostic accuracy and monitor disease progression. RECENT FINDINGS Liquid biomarkers have gained prominence because of their minimally invasive nature and ability to reflect the molecular characteristics of prostate cancer. Circulating tumour cells provide insight into tumour cell dissemination and are indicative of aggressive disease phenotypes, with single-cell analyses revealing genomic instability and treatment resistance. Circulating tumour DNA offers real-time tumour genomic information, aiding in treatment decision-making in advanced prostate cancer, where it has been associated with clinical progression. MicroRNAs act as oncogenes or tumour suppressors and exhibit diagnostic and prognostic potential; however, their clinical utility is constrained by the lack of consistent validation. Extracellular vesicles contain tumour-derived biomolecules, with specific proteins demonstrating prognostic relevance. Applications of these markers to urinary testing have been demonstrated. SUMMARY Liquid biomarkers show potential in refining prostate cancer management. Future research should aim to integrate these biomarkers into a cohesive framework in line with precision medicine principles.
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Affiliation(s)
- Chris Ho-Ming Wong
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
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Repetto O, Vettori R, Steffan A, Cannizzaro R, De Re V. Circulating Proteins as Diagnostic Markers in Gastric Cancer. Int J Mol Sci 2023; 24:16931. [PMID: 38069253 PMCID: PMC10706891 DOI: 10.3390/ijms242316931] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has a poor prognosis. Most GC cases are detected at advanced stages due to the cancer lacking early detectable symptoms. Therefore, there is great interest in improving early diagnosis by implementing targeted prevention strategies. Markers are necessary for early detection and to guide clinicians to the best personalized treatment. The current semi-invasive endoscopic methods to detect GC are invasive, costly, and time-consuming. Recent advances in proteomics technologies have enabled the screening of many samples and the detection of novel biomarkers and disease-related signature signaling networks. These biomarkers include circulating proteins from different fluids (e.g., plasma, serum, urine, and saliva) and extracellular vesicles. We review relevant published studies on circulating protein biomarkers in GC and detail their application as potential biomarkers for GC diagnosis. Identifying highly sensitive and highly specific diagnostic markers for GC may improve patient survival rates and contribute to advancing precision/personalized medicine.
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Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Roberto Vettori
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Renato Cannizzaro
- Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy;
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
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Govender IS, Mokoena R, Stoychev S, Naicker P. Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics. Proteomes 2023; 11:29. [PMID: 37873871 PMCID: PMC10594433 DOI: 10.3390/proteomes11040029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Urine provides a diverse source of information related to a patient's health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at ≥8.35-fold change in abundance, ≥2 unique peptides and ≤1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.
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Affiliation(s)
- Ireshyn Selvan Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- ReSyn Biosciences, Edenvale 1610, South Africa
| | - Rethabile Mokoena
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- School of Molecular and Cellular Biology, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
- ReSyn Biosciences, Edenvale 1610, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0001, South Africa
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Keller F, Beige J, Siwy J, Mebazaa A, An D, Mischak H, Schanstra JP, Mokou M, Perco P, Staessen JA, Vlahou A, Latosinska A. Urinary peptides provide information about the risk of mortality across a spectrum of diseases and scenarios. J Transl Med 2023; 21:663. [PMID: 37741989 PMCID: PMC10518109 DOI: 10.1186/s12967-023-04508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/07/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND There is evidence of pre-established vulnerability in individuals that increases the risk of their progression to severe disease or death, although the mechanisms causing this are still not fully understood. Previous research has demonstrated that a urinary peptide classifier (COV50) predicts disease progression and death from SARS-CoV-2 at an early stage, indicating that the outcome prediction may be partly due to vulnerabilities that are already present. The aim of this study is to examine the ability of COV50 to predict future non-COVID-19-related mortality, and evaluate whether the pre-established vulnerability can be generic and explained on a molecular level by urinary peptides. METHODS Urinary proteomic data from 9193 patients (1719 patients sampled at intensive care unit (ICU) admission and 7474 patients with other diseases (non-ICU)) were extracted from the Human Urinary Proteome Database. The previously developed COV50 classifier, a urinary proteomics biomarker panel consisting of 50 peptides, was applied to all datasets. The association of COV50 scoring with mortality was evaluated. RESULTS In the ICU group, an increase in the COV50 score of one unit resulted in a 20% higher relative risk of death [adjusted HR 1.2 (95% CI 1.17-1.24)]. The same increase in COV50 in non-ICU patients resulted in a higher relative risk of 61% [adjusted HR 1.61 (95% CI 1.47-1.76)], consistent with adjusted meta-analytic HR estimate of 1.55 [95% CI 1.39-1.73]. The most notable and significant changes associated with future fatal events were reductions of specific collagen fragments, most of collagen alpha I (I). CONCLUSION The COV50 classifier is predictive of death in the absence of SARS-CoV-2 infection, suggesting that it detects pre-existing vulnerability. This prediction is mainly based on collagen fragments, possibly reflecting disturbances in the integrity of the extracellular matrix. These data may serve as a basis for proteomics-guided intervention aiming towards manipulating/ improving collagen turnover, thereby reducing the risk of death.
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Affiliation(s)
- Felix Keller
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Joachim Beige
- Martin-Luther-University Halle-Wittenberg, 06108, Halle (Saale), Germany
- Kuratorium for Dialysis and Transplantation, 04129, Leipzig, Germany
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, 30659, Hannover, Germany
| | - Alexandre Mebazaa
- Department of Anaesthesiology and Critical Care, Hôpital Lariboisière, AP-HP, 75010, Paris, France
| | - Dewei An
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine, 2800, Mechelen, Belgium
| | | | - Joost P Schanstra
- Institute of Cardiovascular and Metabolic Disease, U1297, Institut National de la Santé et de la Recherche Médicale, 31432, Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062, Toulouse, France
| | - Marika Mokou
- Mosaiques Diagnostics GmbH, 30659, Hannover, Germany
| | - Paul Perco
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020, Innsbruck, Austria
| | - Jan A Staessen
- Non-Profit Research Association Alliance for the Promotion of Preventive Medicine, 2800, Mechelen, Belgium
| | - Antonia Vlahou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
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Joshi N, Bhat F, Bellad A, Sathe G, Jain A, Chavan S, Sirdeshmukh R, Pandey A. Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:361-371. [PMID: 37579183 PMCID: PMC10625469 DOI: 10.1089/omi.2023.0077] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
For precision in clinical oncology practice, detection of tumor-derived peptides and proteins in urine offers an attractive and noninvasive alternative for diagnostic or screening purposes. In this study, we report comparative quantitative proteomic profiling of urine samples from patients with gastric cancer and healthy controls using tandem mass tags-based multiplexed mass spectrometry approach. We identified 1504 proteins, of which 246 were differentially expressed in gastric cancer cases. Notably, ephrin A1 (EFNA1), pepsinogen A3 (PGA3), sortilin 1 (SORT1), and vitronectin (VTN) were among the upregulated proteins, which are known to play crucial roles in the progression of gastric cancer. We also found other overexpressed proteins, including shisa family member 5 (SHISA5), mucin like 1 (MUCL1), and leukocyte cell derived chemotaxin 2 (LECT2), which had not previously been linked to gastric cancer. Using a novel approach for targeted proteomics, SureQuant, we validated changes in abundance of a subset of proteins discovered in this study. We confirmed the overexpression of vitronectin and sortilin 1 in an independent set of urine samples. Altogether, this study provides molecular candidates for biomarker development in gastric cancer, and the findings also support the promise of urinary proteomics for noninvasive diagnostics and personalized/precision medicine in the oncology clinic.
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Affiliation(s)
- Neha Joshi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Firdous Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anikha Bellad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anu Jain
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Liu N, Wang J, Wang X, Zhang M. Analysis of urine differential proteins in patients with allergic rhinitis. Heliyon 2023; 9:e17323. [PMID: 37426793 PMCID: PMC10329111 DOI: 10.1016/j.heliyon.2023.e17323] [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: 06/07/2022] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Background Allergic rhinitis (AR) is one of the most common clinical allergic diseases. Early diagnosis and medical intervention will benefit patients with allergic rhinitis. In this study, we focused on changes in urine proteomics in AR patients to investigate their potential clinical utility in AR diagnosis and evaluation. Material and methods TMT-labeled mass spectrometry-based proteomics was carried out to identify differentially expressed proteins (DEPs) in urine between allergic rhinitis patients and normal control groups. The molecular biological role of DEPs was investigated by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) network analysis. Results Enrichment analysis showed that the differentially expressed proteins were mainly related to cell-cell adhesion, complement and coagulation cascades, peptidase activity regulation, MAP kinase activity, etc. Compared with the NC group, HLA-DRB1, WFDC12, and DEFA4, among the top ten up-regulated proteins in the urine of the AR group, were related to the biological process of the humoral immune response. Among the top 10 down-regulated proteins, GUSB, SQSTM1, and KIT are related to protein domain-specific binding in terms of molecular function. Conclusions We found differential protein changes between AR patients and normal subjects may be related to the pathophysiological changes of AR, which provides the possibility for further exploration of urinary proteomics biomarkers in the future.
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Affiliation(s)
- Na Liu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Peking University Ninth School of Clinical Medicine, Beijing, China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Jitu Wang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Peking University Ninth School of Clinical Medicine, Beijing, China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Xueyan Wang
- Department of Allergy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Peking University Ninth School of Clinical Medicine, Beijing, China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
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De Beer D, Mels CMC, Schutte AE, Delles C, Mary S, Mullen W, Latosinska A, Mischak H, Kruger R. Identifying a urinary peptidomics profile for hypertension in young adults: The African-PREDICT study: Urinary peptidomics and hypertension: Urinary peptidomics and hypertension. Proteomics 2023; 23:e2200444. [PMID: 36943111 DOI: 10.1002/pmic.202200444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Hypertension is one of the most important and complex risk factors for cardiovascular diseases (CVDs). By using urinary peptidomics analyses, we aimed to identify peptides associated with hypertension, building a framework for future research towards improved prediction and prevention of premature development of CVD. We included 78 hypertensive and 79 normotensive participants from the African-PREDICT study (aged 20-30 years), matched for sex (51% male) and ethnicity (49% black and 51% white). Urinary peptidomics data were acquired using capillary-electrophoresis-time-of-flight-mass-spectrometry. Hypertension-associated peptides were identified and combined into a support vector machine-based multidimensional classifier. When comparing the peptide data between the normotensive and hypertensive groups, 129 peptides were nominally differentially abundant (Wilcoxon p < 0.05). Nonetheless, only three peptides, all derived from collagen alpha-1(III), remained significantly different after rigorous adjustments for multiple comparisons. The 37 most significant peptides (all p ≤ 0.001) served as basis for the development of a classifier, with 20 peptides being combined into a unifying score, resulting in an AUC of 0.85 in the ROC analysis (p < 0.001), with 83% sensitivity at 80% specificity. Our study suggests potential value of urinary peptides in the classification of hypertension, which could enable earlier diagnosis and better understanding of the pathophysiology of hypertension and premature cardiovascular disease development.
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Affiliation(s)
- Dalene De Beer
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Catharina M C Mels
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Aletta E Schutte
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
- School of Population Health, The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sheon Mary
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ruan Kruger
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
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Rroji M, Figurek A, Spasovski G. Proteomic Approaches and Potential Applications in Autosomal Dominant Polycystic Kidney Disease and Fabry Disease. Diagnostics (Basel) 2023; 13:1152. [PMID: 36980460 PMCID: PMC10047122 DOI: 10.3390/diagnostics13061152] [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: 02/02/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Although rare, hereditary diseases, such as autosomal dominant polycystic kidney disease (ADPKD) and Fabry disease (FD) may significantly progress towards severe nephropathy. It is crucial to characterize it accurately, predict the course of the illness and estimate treatment effectiveness. A huge effort has been undertaken to find reliable biomarkers that might be useful for an early prevention of the disease progression and/or any invasive diagnostic procedures. The study of proteomics, or the small peptide composition of a sample, is a field of study under continuous development. Over the past years, several strategies have been created to study and define the proteome of samples from widely varying origins. However, urinary proteomics has become essential for discovering novel biomarkers in kidney disease. Here, the extracellular vesicles in human urine that contain cell-specific marker proteins from every segment of the nephron, offer a source of potentially valuable urinary biomarkers, and may play an essential role in kidney development and kidney disease. This review summarizes the relevant literature investigating the proteomic approaches and potential applications in the regular studies of ADPKD and FD.
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Affiliation(s)
- Merita Rroji
- Department of Nephrology, Faculty of Medicine, University of Medicine Tirana, 1001 Tirana, Albania
| | - Andreja Figurek
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Goce Spasovski
- University Clinic for Nephrology, Medical Faculty, University St. Cyril and Methodius, 1000 Skopje, North Macedonia
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Liu N, Wang J, Wang X, Qiu S, Zhang M. Bilirubin level is decreased in patients with allergic rhinitis. J Proteomics 2023; 272:104787. [PMID: 36470582 DOI: 10.1016/j.jprot.2022.104787] [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: 03/16/2022] [Revised: 06/07/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND There are limitations in detecting methods for early diagnosis and screening of allergic rhinitis. Considering the anti-inflammatory and anti-oxidative effects of bilirubin, this study aims to explore the relationship between bilirubin and allergic rhinitis and to identify bilirubin-related candidate urinary protein biomarkers associated with allergic rhinitis. METHODS 63 allergic rhinitis patients (AR group) and 86 healthy controls (NC group) were enrolled. Venous blood was obtained to measure serum total IgE levels and bilirubin parameters. Patients in the AR group were then classified into the AR1 group (IgE > 125 IU/mL) and the AR2 group (IgE ≤ 125 IU/mL). After randomly selecting ten urine samples from the AR1 group, ten samples were chosen from the AR2 and the NC groups, respectively, according to age and gender matching. We employed a Tandem Mass Tag-Based liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) proteomics approach and targeted parallel-reaction monitoring(PRM) to identify and validate urinary biomarkers for allergic rhinitis. RESULTS Compared with the NC group, the bilirubin levels of the AR group, AR1 group, and AR2 group were significantly lower. Although the bilirubin level of the AR1 group was lower than that of the AR2 group, the difference was not significant. Further urinary proteomics analysis found that the expression levels of proteins related to bilirubin metabolism and transportation in the AR1 and AR2 groups, including ABCC1, GSTA1, GSTO1, GSTM3, GSTM5, and BLVRB, were significantly higher than those in the NC group. By PRM-based quantification, GSTA1 and GSTO1 showed significant differences in different degrees of Allergic Rhinitis groups and healthy controls. The AUC of the combined diagnosis of GSTA1 and GSTO1 was 0.79 (95% CI 0.583-0.997, P = 0.007), and the sensitivity and specificity were 100% and 60.0%, respectively. CONCLUSIONS Bilirubin levels are associated with allergic rhinitis. Our study revealed that urine proteomics has a specific value for exploring the pathophysiological mechanism of bilirubin changes in AR patients and screening possible biomarkers.
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Affiliation(s)
- Na Liu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Jitu Wang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Xueyan Wang
- Department of Allergy, Beijing Shijitan Hospital,Capital Medical University, Beijing, China
| | - Sainan Qiu
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Peking University Ninth School of Clinical Medicine, Beijing, China; Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China.
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Cisneros E, Martínez-Padilla A, Cardenas C, Márquez J, Ortega de Mues A, Roza C. Identification of Potential Visceral Pain Biomarkers in Colon Exudates from Mice with Experimental Colitis: An Exploratory In Vitro Study. THE JOURNAL OF PAIN 2023; 24:874-887. [PMID: 36638875 DOI: 10.1016/j.jpain.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023]
Abstract
Chronic visceral pain (CVP) is extremely difficult to diagnose, and available analgesic treatment options are quite limited. Identifying the proteins secreted from the colonic nociceptors, or their neighbor cells within the tube walls, in the context of disorders that course with visceral pain, might be useful to decipher the mechanism involved in the establishment of CVP. Addressing this question in human with gastrointestinal disorders entails multiple difficulties, as there is not a clear classification of disease severity, and colonic secretion is not easy to manage. We propose using of a murine model of colitis to identify new algesic molecules and pathways that could be explored as pain biomarkers or analgesia targets. Descending colons from naïve and colitis mice with visceral hyperalgesia were excised and maintained ex vivo. The proteins secreted in the perfusion fluid before and during acute noxious distension were evaluated using high-resolution mass spectrometry (MS). Haptoglobin (Hp), PZD and LIM domain protein 3 (Pdlim3), NADP-dependent malic enzyme (Me1), and Apolipoprotein A-I (Apoa1) were increased during visceral insult, whilst Triosephosphate isomerase (Tpi1), Glucose-6-phosphate isomerase (Gpi1), Alpha-enolase (Eno1), and Isoform 2 of Tropomyosin alpha-1 chain (Tpm1) were decreased. Most identified proteins have been described in the context of different chronic pain conditions and, according to gene ontology analysis, they are also involved in diverse biological processes of relevance. Thus, animal models that mimic human conditions in combination with unbiased omics approaches will ultimately help to identify new pathophysiological mechanisms underlying pain that might be useful in diagnosing and treating pain. PERSPECTIVE: Our study utilizes an unbiased proteomic approach to determine, first, the clinical relevance of a murine model of colitis and, second, to identify novel molecules/pathways involved in nociception that would be potential biomarkers or targets for chronic visceral pain.
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Affiliation(s)
- Elsa Cisneros
- Facultad de Ciencias de la Salud, Universidad Internacional de la Rioja (UNIR), Logroño, La Rioja, Spain
| | - Anabel Martínez-Padilla
- Canceromics Lab, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto de Investigación Biomédica de Málaga (IBIMA-Plataforma BIONAND), Universidad de Málaga, Málaga, Spain
| | - Casimiro Cardenas
- Canceromics Lab, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto de Investigación Biomédica de Málaga (IBIMA-Plataforma BIONAND), Universidad de Málaga, Málaga, Spain; Proteomics Unit, Central Facility of Research Infrastructures (SCAI), Universidad de Málaga, Málaga, Spain
| | - Javier Márquez
- Canceromics Lab, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias e Instituto de Investigación Biomédica de Málaga (IBIMA-Plataforma BIONAND), Universidad de Málaga, Málaga, Spain
| | | | - Carolina Roza
- Departamento de Biología de Sistemas, Facultad de Medicina, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain.
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Murugesan S, Saha A, Deepthi B, Kaur M, Basak T, Sengupta S, Batra V, Upadhyay AD. Urinary Apolipoprotein A1 and Neutrophil Gelatinase-associated Lipocalin in Children with Idiopathic Nephrotic Syndrome. SAUDI JOURNAL OF KIDNEY DISEASES AND TRANSPLANTATION 2023; 34:13-20. [PMID: 38092712 DOI: 10.4103/1319-2442.390998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Urinary biomarkers are a promising diagnostic modality whose role was explored in nephrotic syndrome (NS). We estimated urinary apolipoprotein A1 (Apo A1) and neutrophil gelatinase-associated lipocalin (NGAL) in children with first-episode NS (FENS) and controls with a longitudinal follow-up to see the serial changes during remission. The study groups comprised 35 children with FENS and an equal number of age- and sex-matched controls. Patients were followed up at regular intervals, and 32 patients were classified as having steroid-sensitive NS (SSNS) and 3 as having steroid-resistant NS (SRNS). The mean follow-up period was 8.7 ± 4.2 months. Three patients in the SSNS group were labeled as having frequent relapses or steroid-dependent disease during follow-up. Of the three children with SRNS, two had minimal changes in the disease and one had idiopathic membranous nephropathy. The levels of Apo A1:creatinine, NGAL:creatinine, and spot urinary protein:urinary creatinine ratios were significantly higher in children with FENS compared with controls. The levels of the urine biomarkers decreased significantly at subsequent follow-up with remission. The Apo A1 and NGAL levels in SSNS patients were significantly high compared with both the controls and FENS patients. Urinary Apo A1 levels in SRNS patients were lower at initial presentation. This longitudinal study revealed changes in the urinary Apo A1 and NGAL in NS over the course of the disease.
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Affiliation(s)
- Suresh Murugesan
- Department of Pediatrics, Division of Pediatric Nephrology, Postgraduate Institute of Medical Education and Research and Associated Dr. Ram Manohar Lohia Hospital, Baba Kharak Singh Marg, New Delhi, India
| | - Abhijeet Saha
- Department of Pediatrics, Division of Pediatric Nephrology, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Bobbity Deepthi
- Department of Pediatrics, Division of Pediatric Nephrology, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Manpreet Kaur
- Department of Pediatrics, Division of Pediatric Nephrology, Postgraduate Institute of Medical Education and Research and Associated Dr. Ram Manohar Lohia Hospital, Baba Kharak Singh Marg, New Delhi, India
| | - Trayambak Basak
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Department of Biological Sciences (CSIR-IGIB), Academy of Scientific and Innovative Research, Delhi, India
| | - Shantanu Sengupta
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Department of Biological Sciences (CSIR-IGIB), Academy of Scientific and Innovative Research, Delhi, India
| | - Vineeta Batra
- Department of Pathology, GB Pant Hospital, New Delhi, India
| | - Ashish Dutt Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
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Johnson AC, Silva JAF, Kim SC, Larsen CP. Progress in kidney transplantation: The role for systems immunology. Front Med (Lausanne) 2022; 9:1070385. [PMID: 36590970 PMCID: PMC9800623 DOI: 10.3389/fmed.2022.1070385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
The development of systems biology represents an immense breakthrough in our ability to perform translational research and deliver personalized and precision medicine. A multidisciplinary approach in combination with use of novel techniques allows for the extraction and analysis of vast quantities of data even from the volume and source limited samples that can be obtained from human subjects. Continued advances in microfluidics, scalability and affordability of sequencing technologies, and development of data analysis tools have made the application of a multi-omics, or systems, approach more accessible for use outside of specialized centers. The study of alloimmune and protective immune responses after solid organ transplant offers innumerable opportunities for a multi-omics approach, however, transplant immunology labs are only just beginning to adopt the systems methodology. In this review, we focus on advances in biological techniques and how they are improving our understanding of the immune system and its interactions, highlighting potential applications in transplant immunology. First, we describe the techniques that are available, with emphasis on major advances that allow for increased scalability. Then, we review initial applications in the field of transplantation with a focus on topics that are nearing clinical integration. Finally, we examine major barriers to adapting these methods and discuss potential future developments.
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Urine and Saliva: Relevant Specimens for Malaria Diagnosis? Diagnostics (Basel) 2022; 12:diagnostics12122989. [PMID: 36552996 PMCID: PMC9777261 DOI: 10.3390/diagnostics12122989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Blood remains the specimen of preference for malaria diagnosis, whether it is for microscopic, nucleic acid-based or biomarker detection of Plasmodium present in a patient. However, concerning the disadvantages of blood drawing, specimens that can be non-invasively collected under non-hygienic settings would come in handy for malaria diagnosis in endemic areas with limited resources. Although the current approaches using saliva or urine might not be as sensitive and specific as using blood, the potential of these two specimens should not be underestimated and efforts in developing diagnostic methods for Plasmodium detection specifically in these two specimens should continue without giving up. This review not only compiles and summarizes the sensitivity and specificity achieved by various detection approaches when using these samples for malaria diagnosis, it also intends to enhance the possibility of using saliva and urine for diagnostic purposes by describing how Plasmodium nucleic acid and antigens may likely be present in these samples. This review may hopefully encourage and motivate researchers in developing saliva- and urine-based diagnostic methods for Plasmodium detection to facilitate the control and eradication of malaria. In summary, the presence of Plasmodium DNA and antigens in urine and saliva makes these two specimens relevant and useful for malaria diagnosis.
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Moreira-Pais A, Nogueira-Ferreira R, Reis S, Aveiro S, Barros A, Melo T, Matos B, Duarte JA, Seixas F, Domingues P, Amado F, Fardilha M, Oliveira PA, Ferreira R, Vitorino R. Tracking Prostate Carcinogenesis over Time through Urine Proteome Profiling in an Animal Model: An Exploratory Approach. Int J Mol Sci 2022; 23:ijms23147560. [PMID: 35886909 PMCID: PMC9315930 DOI: 10.3390/ijms23147560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Prostate cancer (PCa) is one of the most lethal diseases in men, which justifies the search for new diagnostic tools. The aim of the present study was to gain new insights into the progression of prostate carcinogenesis by analyzing the urine proteome. To this end, urine from healthy animals and animals with prostate adenocarcinoma was analyzed at two time points: 27 and 54 weeks. After 54 weeks, the incidence of pre-neoplastic and neoplastic lesions in the PCa animals was 100%. GeLC-MS/MS and subsequent bioinformatics analyses revealed several proteins involved in prostate carcinogenesis. Increased levels of retinol-binding protein 4 and decreased levels of cadherin-2 appear to be characteristic of early stages of the disease, whereas increased levels of enolase-1 and T-kininogen 2 and decreased levels of isocitrate dehydrogenase 2 describe more advanced stages. With increasing age, urinary levels of clusterin and corticosteroid-binding globulin increased and neprilysin levels decreased, all of which appear to play a role in prostate hyperplasia or carcinogenesis. The present exploratory analysis can be considered as a starting point for studies targeting specific human urine proteins for early detection of age-related maladaptive changes in the prostate that may lead to cancer.
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Affiliation(s)
- Alexandra Moreira-Pais
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.-P.); (S.R.); (T.M.); (P.D.); (F.A.); (R.F.)
- Laboratory for Integrative and Translational Research in Population Health (ITR), Research Center in Physical Activity, Health and Leisure (CIAFEL), Faculty of Sports, University of Porto (FADEUP), 4200-450 Porto, Portugal;
- Centre for Research and Technology of Agro Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-Os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal;
| | - Rita Nogueira-Ferreira
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; (R.N.-F.); (A.B.)
| | - Stephanie Reis
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.-P.); (S.R.); (T.M.); (P.D.); (F.A.); (R.F.)
| | - Susana Aveiro
- GreenCoLab-Green Ocean Association, University of Algarve, 8005-139 Faro, Portugal;
| | - António Barros
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; (R.N.-F.); (A.B.)
| | - Tânia Melo
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.-P.); (S.R.); (T.M.); (P.D.); (F.A.); (R.F.)
- CESAM-Centre for Environmental and Marine Studies, Department of Chemistry, Santiago University Campus, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bárbara Matos
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (B.M.); (M.F.)
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - José Alberto Duarte
- Laboratory for Integrative and Translational Research in Population Health (ITR), Research Center in Physical Activity, Health and Leisure (CIAFEL), Faculty of Sports, University of Porto (FADEUP), 4200-450 Porto, Portugal;
- TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Avenida Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Fernanda Seixas
- Animal and Veterinary Research Center (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
| | - Pedro Domingues
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.-P.); (S.R.); (T.M.); (P.D.); (F.A.); (R.F.)
| | - Francisco Amado
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.-P.); (S.R.); (T.M.); (P.D.); (F.A.); (R.F.)
| | - Margarida Fardilha
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (B.M.); (M.F.)
| | - Paula A. Oliveira
- Centre for Research and Technology of Agro Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-Os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal;
| | - Rita Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.-P.); (S.R.); (T.M.); (P.D.); (F.A.); (R.F.)
| | - Rui Vitorino
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; (R.N.-F.); (A.B.)
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (B.M.); (M.F.)
- Correspondence:
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Garzarelli V, Ferrara F, Primiceri E, Chiriacò MS. Biofluids manipulation methods for liquid biopsy in minimally-invasive assays. MethodsX 2022; 9:101759. [PMID: 35774416 PMCID: PMC9237943 DOI: 10.1016/j.mex.2022.101759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/10/2022] [Indexed: 12/05/2022] Open
Abstract
The Liquid Biopsy (LB) is an opportunity for non-invasive diagnosis and prognosis of various diseases. To date, it isn't possible to consider that tissue biopsy can represent a pathology entirety. Then, body fluids are rich in a large number and variety of biomarkers and they can provide information about several diseases.Recently, other biological fluids, easy to be collected are rising for their significant content of biomarkers and for the possibility to collect and manipulate them without the intervention of medical staff. The management of biological fluids requires suitable storage methods. Temperature, storage time and physical stresses due to sample handling can lead to chemical and physical changes that may induce sample degradation and incorrect analysis. The reliability of a diagnostic or screening test depends on its sensitivity and specificity. As the liquid biopsy is a 'snapshot' of a pathophysiological condition, it is crucial that its components do not degrade due to the improper handling of the body fluid. In this review, some handling methods of Saliva, Urine, Stool, Seminal Fluid, Tears and Sweat samples will be described, as well as protocols to facilitate the analysis of metabolites, nucleic acids, proteins and Extracellular Vesicles (EVs) from those unusual body fluids.
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Affiliation(s)
- Valeria Garzarelli
- University of Salento, Dept. of Mathematics & Physics E. de Giorgi, Via Arnesano, 73100, Lecce, Italy.,CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
| | - Francesco Ferrara
- CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy.,STMicroelectronics s.r.l., via per Monteroni, 73100, Lecce, Italy
| | - Elisabetta Primiceri
- CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
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Garbett NC, Schneider G. Sample Processing Considerations for Protein Stability Studies of Low
Concentration Biofluid Samples using Differential Scanning Calorimetry. Protein Pept Lett 2022; 29:485-495. [DOI: 10.2174/0929866529666220416164305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 11/22/2022]
Abstract
Background:
The analysis of biofluid samples with low protein content (e.g., urine or
saliva) can be challenging for downstream analysis methods with limited sensitivity. To circumvent
this problem, sample processing methods are employed to increase the protein concentration in
analyzed samples. However, for some techniques, like differential scanning calorimetry (DSC) that
characterizes thermally-induced unfolding of biomolecules, sample processing must not affect
native protein structure and stability.
Methods:
We evaluated centrifugal concentration and stirred cell ultrafiltration, two common
methods of sample concentration characterized by a low risk of protein denaturation, with the goal
of establishing a protocol for DSC analysis of low concentration biospecimens.
Results:
Our studies indicate that both methods can affect protein stability assessed by DSC and,
even after optimization of several parameters, the obtained DSC profile (thermogram) suggested
that sample processing affects the structure or intermolecular interactions of component proteins
contributing to altered thermal stability detectable by DSC. We also found a relationship between
changes in thermograms and low protein concentration, indicating that diluting biospecimens to
concentrations below 0.1 mg/mL can perturb the intermolecular environment and affect the
structure of proteins present in the solution.
Conclusions:
Dilution of samples below 0.1 mg/mL, as well as concentration of samples with low
protein content, resulted in affected thermogram shapes suggesting changes in protein stability. This
should be taken into account when concentrating dilute samples or employing techniques that lower
the protein concentration (e.g., fractionation), when downstream applications include techniques,
such as DSC, that require the preservation of native protein forms.
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Affiliation(s)
- Nichola C. Garbett
- UofL Health – Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine,
University of Louisville, Louisville, KY 40202, USA
| | - Gabriela Schneider
- UofL Health – Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine,
University of Louisville, Louisville, KY 40202, USA
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Torres-Sangiao E, Giddey AD, Leal Rodriguez C, Tang Z, Liu X, Soares NC. Proteomic Approaches to Unravel Mechanisms of Antibiotic Resistance and Immune Evasion of Bacterial Pathogens. Front Med (Lausanne) 2022; 9:850374. [PMID: 35586072 PMCID: PMC9108449 DOI: 10.3389/fmed.2022.850374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
The profound effects of and distress caused by the global COVID-19 pandemic highlighted what has been known in the health sciences a long time ago: that bacteria, fungi, viruses, and parasites continue to present a major threat to human health. Infectious diseases remain the leading cause of death worldwide, with antibiotic resistance increasing exponentially due to a lack of new treatments. In addition to this, many pathogens share the common trait of having the ability to modulate, and escape from, the host immune response. The challenge in medical microbiology is to develop and apply new experimental approaches that allow for the identification of both the microbe and its drug susceptibility profile in a time-sensitive manner, as well as to elucidate their molecular mechanisms of survival and immunomodulation. Over the last three decades, proteomics has contributed to a better understanding of the underlying molecular mechanisms responsible for microbial drug resistance and pathogenicity. Proteomics has gained new momentum as a result of recent advances in mass spectrometry. Indeed, mass spectrometry-based biomedical research has been made possible thanks to technological advances in instrumentation capability and the continuous improvement of sample processing and workflows. For example, high-throughput applications such as SWATH or Trapped ion mobility enable the identification of thousands of proteins in a matter of minutes. This type of rapid, in-depth analysis, combined with other advanced, supportive applications such as data processing and artificial intelligence, presents a unique opportunity to translate knowledge-based findings into measurable impacts like new antimicrobial biomarkers and drug targets. In relation to the Research Topic “Proteomic Approaches to Unravel Mechanisms of Resistance and Immune Evasion of Bacterial Pathogens,” this review specifically seeks to highlight the synergies between the powerful fields of modern proteomics and microbiology, as well as bridging translational opportunities from biomedical research to clinical practice.
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Affiliation(s)
- Eva Torres-Sangiao
- Clinical Microbiology Lab, University Hospital Marqués de Valdecilla, Santander, Spain
- Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), Santander, Spain
- *Correspondence: Eva Torres-Sangiao,
| | - Alexander Dyason Giddey
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cristina Leal Rodriguez
- Copenhagen Prospectives Studies on Asthma in Childhood, COPSAC, Copenhagen University Hospital, Herlev-Gentofte, Denmark
| | - Zhiheng Tang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Nelson C. Soares
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Nelson C. Soares,
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20
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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21
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Mbhele T, Tanyanyiwa DM, Moepya RJ, Bhana S, Makatini MM. Relationship between amino acid ratios and decline in estimated glomerular filtration rate in diabetic and non-diabetic patients in South Africa. Afr J Lab Med 2021; 10:1398. [PMID: 34956850 PMCID: PMC8678941 DOI: 10.4102/ajlm.v10i1.1398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 07/16/2021] [Indexed: 11/29/2022] Open
Abstract
Background Diabetic kidney disease is a major complication resulting from type 1 and type 2 diabetes. Currently, the microalbuminuria test is used to monitor renal function; however, it does not detect albumin until progressive loss of renal function has occurred. Objective This study analysed the relationship between changes in amino acid ratios and estimated glomerular filtration rate (eGFR) decline in diabetic and non-diabetic patients. Methods Urine samples were collected from participants between February 2019 to April 2019 and analysed from November 2020 to January 2021. Diabetic (glycated haemoglobin > 6.4%) and non-diabetic patients (glycated haemoglobin ≤ 6.4%) from Chris Hani Baragwanath Hospital, South Africa, were further categorised based on the degree of renal function predicted by the eGFRs. Amino acids were quantified using tandem mass spectrometry to determine the concentrations and ratios of tyrosine/phenylalanine, ornithine/arginine, arginine/citrulline and citrulline/ornithine at different stages of the chronic kidney disease. Results Among diabetic patients, the tyrosine/phenylalanine ratio showed a statistically significant increase (p = 0.04) as the eGFR declined from stage 1 to stage 4; the ornithine/arginine ratio showed a strong negative correlation with eGFR. The citrulline/ornithine ratio differed between the diabetic and non-diabetic patients in stage 1 of chronic kidney disease. Conclusion Amino acid ratios (ornithine/arginine and tyrosine/phenylalanine) are affected by the progression of diabetes and can be correlated to renal function. The citrulline/ornithine ratios differ between the studied groups in stage 1 of the disease and may be utilised to predict the onset of chronic kidney disease.
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Affiliation(s)
- Thapelo Mbhele
- Molecular Sciences Institute, School of Chemistry, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Donald M. Tanyanyiwa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Chemical Pathology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Refilwe J. Moepya
- Molecular Sciences Institute, School of Chemistry, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Sindeep Bhana
- School of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maya M. Makatini
- Molecular Sciences Institute, School of Chemistry, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
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22
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Urinary Protein and Peptide Markers in Chronic Kidney Disease. Int J Mol Sci 2021; 22:ijms222212123. [PMID: 34830001 PMCID: PMC8625140 DOI: 10.3390/ijms222212123] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic kidney disease (CKD) is a non-specific type of kidney disease that causes a gradual decline in kidney function (from months to years). CKD is a significant risk factor for death, cardiovascular disease, and end-stage renal disease. CKDs of different origins may have the same clinical and laboratory manifestations but different progression rates, which requires early diagnosis to determine. This review focuses on protein/peptide biomarkers of the leading causes of CKD: diabetic nephropathy, IgA nephropathy, lupus nephritis, focal segmental glomerulosclerosis, and membranous nephropathy. Mass spectrometry (MS) approaches provided the most information about urinary peptide and protein contents in different nephropathies. New analytical approaches allow urinary proteomic-peptide profiles to be used as early non-invasive diagnostic tools for specific morphological forms of kidney disease and may become a safe alternative to renal biopsy. MS studies of the key pathogenetic mechanisms of renal disease progression may also contribute to developing new approaches for targeted therapy.
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23
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Helena H, Ivona V, Roman Ř, František F. Current applications of capillary electrophoresis-mass spectrometry for the analysis of biologically important analytes in urine (2017 to mid-2021): A review. J Sep Sci 2021; 45:305-324. [PMID: 34538010 PMCID: PMC9292318 DOI: 10.1002/jssc.202100621] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/17/2022]
Abstract
Capillary electrophoresis coupled online with mass detection is a modern tool for analyzing wide ranges of compounds in complex samples, including urine. Capillary electrophoresis with mass spectrometry allows the separation and identification of various analytes spanning from small ions to high molecular weight protein complexes. Similarly to the much more common liquid chromatography‐mass spectrometry techniques, the capillary electrophoresis separation reduces the complexity of the mixture of analytes entering the mass spectrometer resulting in reduced ion suppression and a more straightforward interpretation of the mass spectrometry data. This review summarizes capillary electrophoresis with mass spectrometry studies published between the years 2017 and 2021, aiming at the determination of various compounds excreted in urine. The properties of the urine, including its diagnostical and analytical features and chemical composition, are also discussed including general protocols for the urine sample preparation. The mechanism of the electrophoretic separation and the instrumentation for capillary electrophoresis with mass spectrometry coupling is also included. This review shows the potential of the capillary electrophoresis with mass spectrometry technique for the analyses of different kinds of analytes in a complex biological matrix. The discussed applications are divided into two main groups (capillary electrophoresis with mass spectrometry for the determination of drugs and drugs of abuse in urine and capillary electrophoresis with mass spectrometry for the studies of urinary metabolome).
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Affiliation(s)
- Hrušková Helena
- Institute of Analytical Chemistry, Czech Academy of Sciences, Brno, Czech Republic.,Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Voráčová Ivona
- Institute of Analytical Chemistry, Czech Academy of Sciences, Brno, Czech Republic
| | - Řemínek Roman
- Institute of Analytical Chemistry, Czech Academy of Sciences, Brno, Czech Republic
| | - Foret František
- Institute of Analytical Chemistry, Czech Academy of Sciences, Brno, Czech Republic
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24
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Shnayder NA, Sharavii VB, Petrova MM, Moskaleva PV, Pozhilenkova EA, Kaskaeva DS, Tutynina OV, Popova TE, Garganeeva NP, Nasyrova RF. Candidate Genes and Proteomic Biomarkers of Serum and Urine in Medication-Overuse Headache. Int J Mol Sci 2021; 22:9024. [PMID: 34445731 PMCID: PMC8396559 DOI: 10.3390/ijms22169024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 01/03/2023] Open
Abstract
Chronic headache is a topical problem of neurology, psychiatry and general practice. The medication-overuse headache (MOH) is one of the leading pathologies in the structure of chronic headache. However, early diagnosis of the MOH is challenging. We analyzed potential proteomic biomarkers of serum and urine in patients with MOH. METHODS We searched PubMed, Springer, Scopus, Web of Science, ClinicalKey, and Google Scholar databases for English publications over the past 10 years using keywords and their combinations. RESULTS We found and analyzed seven studies that met the search criteria for the purpose of the review, including 24 serum proteomic biomarkers and 25 urine proteomic biomarkers of MOH. Moreover, the candidate genes and locus of the studied serum (vitamin D-binding protein, lipocalin-type prostaglandin D2 synthase, apolipoprotein E, etc.) and urine proteomic biomarkers (uromodulin, alpha-1-microglobulin, zinc-alpha-2-glycoprotein, etc.) of MOH are presented in this review. CONCLUSIONS The serum and urine proteomic biomarkers of MOH can potentially help with the identification of patients with MOH development. Due to the relevance of the problem, the authors believe that further investigation of the MOH proteomic biomarkers in different ethnic and racial groups of patients with primary headache is necessary. In addition, it is important to investigate whether medications of different drug classes influence the levels of serum and urine proteomic biomarkers.
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Affiliation(s)
- Natalia A. Shnayder
- The Center of Personalized Psychiatry and Neurology, V. M. Bekhterev National Medical Research Center for Neurology and Psychiatry, 192019 Saint-Petersburg, Russia;
- The Center of Collective Usage “Molecular and Cell Technologies”, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (P.V.M.); (E.A.P.); (D.S.K.); (O.V.T.)
| | - Victoria B. Sharavii
- The International School Medicine of the Future, I. M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Marina M. Petrova
- The Center of Collective Usage “Molecular and Cell Technologies”, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (P.V.M.); (E.A.P.); (D.S.K.); (O.V.T.)
| | - Polina V. Moskaleva
- The Center of Collective Usage “Molecular and Cell Technologies”, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (P.V.M.); (E.A.P.); (D.S.K.); (O.V.T.)
| | - Elena A. Pozhilenkova
- The Center of Collective Usage “Molecular and Cell Technologies”, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (P.V.M.); (E.A.P.); (D.S.K.); (O.V.T.)
| | - Darya S. Kaskaeva
- The Center of Collective Usage “Molecular and Cell Technologies”, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (P.V.M.); (E.A.P.); (D.S.K.); (O.V.T.)
| | - Olga. V. Tutynina
- The Center of Collective Usage “Molecular and Cell Technologies”, V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (M.M.P.); (P.V.M.); (E.A.P.); (D.S.K.); (O.V.T.)
| | - Tatiana E. Popova
- The Yakutsk Scientific Center for Complex Medicine Problems, The Department of Epidemiology of Non-Infectious Diseases, 677018 Yakutsk, Russia;
| | - Natalia P. Garganeeva
- The Department of General Medical Practice and Polyclinic Therapy, The Siberian State Medical University, 634050 Tomsk, Russia;
| | - Regina F. Nasyrova
- The Center of Personalized Psychiatry and Neurology, V. M. Bekhterev National Medical Research Center for Neurology and Psychiatry, 192019 Saint-Petersburg, Russia;
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25
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Prasanna JS, Sumadhura C. Estimation of neopterin as a biomarker in biofluids of pre and post-menopausal women after initial periodontal therapy: A biochemical assay. J Indian Soc Periodontol 2021; 25:300-306. [PMID: 34393400 PMCID: PMC8336780 DOI: 10.4103/jisp.jisp_516_19] [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: 10/06/2019] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 11/17/2022] Open
Abstract
Context: Periodontitis (PDD) is a chronic inflammatory condition by nature which destroys the surrounding tooth structures. Menopause (pre and post) worsens the inflammatory state. Biofluids could serve as sources of biomarkers that could diagnose or indicate the intensity and extent of both conditions. Aims: This study aimed to guestimate the various biofluids of neopterin (NP) levels in premenopause (pre-m) and postmenopausal (post-m) women with PDD after initial periodontal therapy (IPT). Settings and Design: This was an interventional cross-sectional study. Materials and Methods: Based on menstrual history, within the age range of 40–60 years, 30 female patients having PDD participated, who were grouped into pre-m and post-m, each group comprised 15 subjects. A biochemical test of NP levels was done at the initial and three months following IPT. Statistics used: Group comparisons and percentage decrement using independent sample t-test and paired t-test for intragroup comparison were done with the version 21, IBM SPSS software. Results: Intragroup NP analysis at different time points showed significant improvement. Intergroup comparison, however, has shown significant improvement in the premenopausal group (Group I) only. Conclusions: Reduced levels of NP were found in pre-m and post-m groups 3 months after IPT, inferring that IPT is a paragon in periodontal therapy and NP might be a good diagnostic marker to detect PDD.
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Affiliation(s)
- Jammula Surya Prasanna
- Department of Periodontics, Panineeya Institute of Dental Sciences and Research Centre, Hyderabad, Telangana, India
| | - Chinta Sumadhura
- Department of Periodontics, Panineeya Institute of Dental Sciences and Research Centre, Hyderabad, Telangana, India
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26
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Kumar R, Ali SA, Singh SK, Bhushan V, Kaushik JK, Mohanty AK, Kumar S. Peptide profiling in cow urine reveals molecular signature of physiology-driven pathways and in-silico predicted bioactive properties. Sci Rep 2021; 11:12427. [PMID: 34127704 PMCID: PMC8203733 DOI: 10.1038/s41598-021-91684-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/04/2021] [Indexed: 12/05/2022] Open
Abstract
Peptidomics allows the identification of peptides that are derived from proteins. Urinary peptidomics has revolutionized the field of diagnostics as the samples represent complete systemic changes happening in the body. Moreover, it can be collected in a non-invasive manner. We profiled the peptides in urine collected from different physiological states (heifer, pregnancy, and lactation) of Sahiwal cows. Endogenous peptides were extracted from 30 individual cows belonging to three groups, each group comprising of ten animals (biological replicates n = 10). Nano Liquid chromatography Mass spectrometry (nLC-MS/MS) experiments revealed 5239, 4774, and 5466 peptides in the heifer, pregnant and lactating animals respectively. Urinary peptides of <10 kDa size were considered for the study. Peptides were extracted by 10 kDa MWCO filter. Sequences were identified by scanning the MS spectra ranging from 200 to 2200 m/z. The peptides exhibited diversity in sequences across different physiological states and in-silico experiments were conducted to classify the bioactive peptides into anti-microbial, anti-inflammatory, anti-hypertensive, and anti-cancerous groups. We have validated the antimicrobial effect of urinary peptides on Staphylococcus aureus and Escherichia coli under an in-vitro experimental set up. The origin of these peptides was traced back to certain proteases viz. MMPs, KLKs, CASPs, ADAMs etc. which were found responsible for the physiology-specific peptide signature of urine. Proteins involved in extracellular matrix structural constituent (GO:0005201) were found significant during pregnancy and lactation in which tissue remodeling is extensive. Collagen trimers were prominent molecules under cellular component category during lactation. Homophilic cell adhesion was found to be an important biological process involved in embryo attachment during pregnancy. The in-silico study also highlighted the enrichment of progenitor proteins on specific chromosomes and their relative expression in context to specific physiology. The urinary peptides, precursor proteins, and proteases identified in the study offers a base line information in healthy cows which can be utilized in biomarker discovery research for several pathophysiological studies.
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Affiliation(s)
- Rohit Kumar
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India
| | - Syed Azmal Ali
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India
| | - Sumit Kumar Singh
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India
| | - Vanya Bhushan
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India
| | - Jai Kumar Kaushik
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India
| | - Ashok Kumar Mohanty
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India
| | - Sudarshan Kumar
- ICAR-National Dairy Research Institute, Cell Biology and Proteomics Lab, Animal Biotechnology Center (ABTC), Karnal, Haryana, 132001, India.
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27
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Label-Free Protein Detection by Micro-Acoustic Biosensor Coupled with Electrical Field Sorting. Theoretical Study in Urine Models. SENSORS 2021; 21:s21072555. [PMID: 33917374 PMCID: PMC8038679 DOI: 10.3390/s21072555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/20/2022]
Abstract
Diagnostic devices for point-of-care (POC) urine analysis (urinalysis) based on microfluidic technology have been actively developing for several decades as an alternative to laboratory based biochemical assays. Urine proteins (albumin, immunoglobulins, uromodulin, haemoglobin etc.) are important biomarkers of various pathological conditions and should be selectively detected by urinalysis sensors. The challenge is a determination of different oligomeric forms of the same protein, e.g., uromodulin, which have similar bio-chemical affinity but different physical properties. For the selective detection of different types of proteins, we propose to use a shear bulk acoustic resonator sensor with an additional electrode on the upper part of the bioliquid-filled channel for protein electric field manipulation. It causes modulation of the protein concentration over time in the near-surface region of the acoustic sensor, that allows to distinguish proteins based on their differences in diffusion coefficients (or sizes) and zeta-potentials. Moreover, in order to improve the sensitivity to density, we propose to use structured sensor interface. A numerical study of this approach for the detection of proteins was carried out using the example of albumin, immunoglobulin, and oligomeric forms of uromodulin in model urine solutions. In this contribution we prove the proposed concept with numerical studies for the detection of albumin, immunoglobulin, and oligomeric forms of uromodulin in urine models.
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28
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Iwan K, Clayton R, Mills P, Csanyi B, Gissen P, Mole SE, Palmer DN, Mills K, Heywood WE. Urine proteomics analysis of patients with neuronal ceroid lipofuscinoses. iScience 2021; 24:102020. [PMID: 33532713 PMCID: PMC7822952 DOI: 10.1016/j.isci.2020.102020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/11/2020] [Accepted: 12/29/2020] [Indexed: 01/18/2023] Open
Abstract
The neuronal ceroid lipofuscinoses (NCL) are a group of 13 rare neurodegenerative disorders characterized by accumulation of cellular storage bodies. There are few therapeutic options, and existing tests do not monitor disease progression and treatment response. However, urine biomarkers could address this need. Proteomic analysis of CLN2 patient urine revealed activation of immune response pathways and pathways associated with the unfolded protein response. Analysis of CLN5 and CLN6 sheep model urine showed subtle changes. To confirm and investigate the relevance of candidate biomarkers a targeted LC-MS/MS proteomic assay was created. We applied this assay to additional CLN2 samples as well as other patients with NCL (CLN1, CLN3, CLN5, CLN6, and CLN7) and demonstrated that hexosaminidase-A, aspartate aminotransferase-1, and LAMP1 are increased in NCL samples and betaine-homocysteine S-methyltransferase-1 was specifically increased in patients with CLN2. These proteins could be used to monitor the effectiveness of future therapies aimed at treating systemic NCL disease. The urine proteome is altered in humans and animals with NCL Hexosaminidase A and LAMP1 are increased in patients with NCL Betaine-homocysteine S-methyltransferase 1 is elevated in CLN2 patients Proteins altered in CLN5 and CLN6 sheep models are not affected in humans
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Affiliation(s)
- Katharina Iwan
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Robert Clayton
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Philippa Mills
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | | | - Paul Gissen
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.,Great Ormond Street Hospital for Children, London, UK
| | - Sara E Mole
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.,MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - David N Palmer
- Department of Molecular Biosciences, Agriculture and Life Sciences Faculty, University Lincoln 7647, Canterbury, New Zealand
| | - Kevin Mills
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Wendy E Heywood
- Inborn Errors of Metabolism Section, Genetics & Genomic Medicine Unit, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
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29
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Aitekenov S, Gaipov A, Bukasov R. Review: Detection and quantification of proteins in human urine. Talanta 2021; 223:121718. [PMID: 33303164 PMCID: PMC7554478 DOI: 10.1016/j.talanta.2020.121718] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/31/2022]
Abstract
Extensive medical research showed that patients, with high protein concentration in urine, have various kinds of kidney diseases, referred to as proteinuria. Urinary protein biomarkers are useful for diagnosis of many health conditions - kidney and cardio vascular diseases, cancers, diabetes, infections. This review focuses on the instrumental quantification (electrophoresis, chromatography, immunoassays, mass spectrometry, fluorescence spectroscopy, the infrared spectroscopy, and Raman spectroscopy) of proteins (the most of all albumin) in human urine matrix. Different techniques provide unique information on what constituents of the urine are. Due to complex nature of urine, a separation step by electrophoresis or chromatography are often used for proteomics study of urine. Mass spectrometry is a powerful tool for the discovery and the analysis of biomarkers in urine, however, costs of the analysis are high, especially for quantitative analysis. Immunoassays, which often come with fluorescence detection, are major qualitative and quantitative tools in clinical analysis. While Infrared and Raman spectroscopies do not give extensive information about urine, they could become important tools for the routine clinical diagnostics of kidney problems, due to rapidness and low-cost. Thus, it is important to review all the applicable techniques and methods related to urine analysis. In this review, a brief overview of each technique's principle is introduced. Where applicable, research papers about protein determination in urine are summarized with the main figures of merits, such as the limit of detection, the detectable range, recovery and accuracy, when available.
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Affiliation(s)
- Sultan Aitekenov
- School of Sciences and Humanities, Department of Chemistry, Nazarbaev University, Nur-Sultan, Kazakhstan
| | - Abduzhappar Gaipov
- School of Medicine, Department of Clinical Sciences, Nazarbaev University, Nur-Sultan, Kazakhstan
| | - Rostislav Bukasov
- School of Sciences and Humanities, Department of Chemistry, Nazarbaev University, Nur-Sultan, Kazakhstan.
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30
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Zhang T, Duran V, Vanarsa K, Mohan C. Targeted urine proteomics in lupus nephritis - a meta-analysis. Expert Rev Proteomics 2021; 17:767-776. [PMID: 33423575 DOI: 10.1080/14789450.2020.1874356] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Proteomic approaches are central in biomarker discovery. While mass-spectrometry-based techniques are widely used, novel targeted proteomic platforms have enabled the high-throughput detection of low-abundance proteins in an affinity-based manner. Urine has gained growing attention as an ideal biofluid for monitoring renal disease including lupus nephritis (LN). METHODS Pubmed was screened for targeted proteomic studies of LN urine interrogating ≥1000 proteins. Data from the primary studies were combined and a meta-analysis was performed. Shared proteins elevated in active LN across studies were identified, and relevant pathways were elucidated using ingenuity pathway and gene ontology analysis. Urine proteomic data was cross-referenced against renal single-cell RNAseq data from LN kidneys. RESULTS Two high-throughput targeted proteomic platforms with capacity to interrogate ≥1000 proteins have been used to investigate LN urine. Twenty-three urine proteins were significantly elevated in both studies, including 10 chemokines, and proteins implicated in angiogenesis, and extracellular matrix turnover. Of these, Cathepsin S, CXCL10, FasL, ferritin, macrophage migration inhibitory factor (MIF), and resistin were also significantly elevated within LN kidneys. CONCLUSION Targeted urinary proteomics have uncovered multiple novel biomarkers for LN. Further validation in prospective cohorts and mechanistic studies are warranted to establish their clinical utility.
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Affiliation(s)
- Ting Zhang
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
| | - Valeria Duran
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
| | - Kamala Vanarsa
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
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31
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Chantada-Vázquez MDP, García Vence M, Serna A, Núñez C, Bravo SB. SWATH-MS Protocols in Human Diseases. Methods Mol Biol 2021; 2259:105-141. [PMID: 33687711 DOI: 10.1007/978-1-0716-1178-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of molecular biomarkers for human diseases is one of the most important disciplines in translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and depth needed to succeed in this task. In this chapter, we show different sample processing methods (major protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several proteins in different types of samples (serum/plasma, saliva, urine, tears).
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Affiliation(s)
| | - María García Vence
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | | | - Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain.
| | - Susana B Bravo
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain.
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32
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Debernardi S, O’Brien H, Algahmdi AS, Malats N, Stewart GD, Plješa-Ercegovac M, Costello E, Greenhalf W, Saad A, Roberts R, Ney A, Pereira SP, Kocher HM, Duffy S, Blyuss O, Crnogorac-Jurcevic T. A combination of urinary biomarker panel and PancRISK score for earlier detection of pancreatic cancer: A case-control study. PLoS Med 2020; 17:e1003489. [PMID: 33301466 PMCID: PMC7758047 DOI: 10.1371/journal.pmed.1003489] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/23/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, with around 9% of patients surviving >5 years. Asymptomatic in its initial stages, PDAC is mostly diagnosed late, when already a locally advanced or metastatic disease, as there are no useful biomarkers for detection in its early stages, when surgery can be curative. We have previously described a promising biomarker panel (LYVE1, REG1A, and TFF1) for earlier detection of PDAC in urine. Here, we aimed to establish the accuracy of an improved panel, including REG1B instead of REG1A, and an algorithm for data interpretation, the PancRISK score, in additional retrospectively collected urine specimens. We also assessed the complementarity of this panel with CA19-9 and explored the daily variation and stability of the biomarkers and their performance in common urinary tract cancers. METHODS AND FINDINGS Clinical specimens were obtained from multiple centres: Barts Pancreas Tissue Bank, University College London, University of Liverpool, Spanish National Cancer Research Center, Cambridge University Hospital, and University of Belgrade. The biomarker panel was assayed on 590 urine specimens: 183 control samples, 208 benign hepatobiliary disease samples (of which 119 were chronic pancreatitis), and 199 PDAC samples (102 stage I-II and 97 stage III-IV); 50.7% were from female individuals. PDAC samples were collected from patients before treatment. The samples were assayed using commercially available ELISAs. Statistical analyses were performed using non-parametric Kruskal-Wallis tests adjusted for multiple comparisons, and multiple logistic regression. Training and validation datasets for controls and PDAC samples were obtained after random division of the whole available dataset in a 1:1 ratio. The substitution of REG1A with REG1B enhanced the performance of the panel to detect resectable PDAC. In a comparison of controls and PDAC stage I-II samples, the areas under the receiver operating characteristic curve (AUCs) increased from 0.900 (95% CI 0.843-0.957) and 0.926 (95% CI 0.843-1.000) in the training (50% of the dataset) and validation sets, respectively, to 0.936 in both the training (95% CI 0.903-0.969) and the validation (95% CI 0.888-0.984) datasets for the new panel including REG1B. This improved panel showed both sensitivity (SN) and specificity (SP) to be >85%. Plasma CA19-9 enhanced the performance of this panel in discriminating PDAC I-II patients from controls, with AUC = 0.992 (95% CI 0.983-1.000), SN = 0.963 (95% CI 0.913-1.000), and SP = 0.967 (95% CI 0.924-1.000). We demonstrate that the biomarkers do not show significant daily variation, and that they are stable for up to 5 days at room temperature. The main limitation of our study is the low number of stage I-IIA PDAC samples (n = 27) and lack of samples from individuals with hereditary predisposition to PDAC, for which specimens collected from control individuals were used as a proxy. CONCLUSIONS We have successfully validated our urinary biomarker panel, which was improved by substituting REG1A with REG1B. At a pre-selected cutoff of >80% SN and SP for the affiliated PancRISK score, we demonstrate a clinically applicable risk stratification tool with a binary output for risk of developing PDAC ('elevated' or 'normal'). PancRISK provides a step towards precision surveillance for PDAC patients, which we will test in a prospective clinical study, UroPanc.
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Affiliation(s)
- Silvana Debernardi
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Harrison O’Brien
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Asma S. Algahmdi
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nuria Malats
- Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid Spain
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Marija Plješa-Ercegovac
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Eithne Costello
- Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - William Greenhalf
- Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Amina Saad
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Rhiannon Roberts
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Alexander Ney
- Institute for Liver and Digestive Health, University College London, London, United Kingdom
| | - Stephen P. Pereira
- Institute for Liver and Digestive Health, University College London, London, United Kingdom
| | - Hemant M. Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Stephen Duffy
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
| | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, United Kingdom
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child Health, Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Tatjana Crnogorac-Jurcevic
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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Rada MP, Ciortea R, Măluţan AM, Doumouchtsis SK, Bucuri CE, Clim A, Roman A, Mihu D. The profile of urinary biomarkers in overactive bladder. Neurourol Urodyn 2020; 39:2305-2313. [PMID: 32813897 DOI: 10.1002/nau.24487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
AIMS In overactive bladder (OAB) research, different biomarkers have been proposed as diagnostic tools and may be used to create individual patient profiles. Assessing the diagnostic performance of biomarkers would better outline their utility. Therefore, our aim was to investigate the diagnostic value of four urinary biomarkers: human brain derived neurotrophic factor (hBDNF), malondialdehyde (MDA), h nerve growth factor (hNGF) and h 8-hydroxydeoxyguanosine in women with OAB. These are neurotrophins/oxidative stress markers that have been linked to lower urinary tract symptoms. METHODS A total of 105 women were included in the study and distributed in two groups: a group with OAB (n = 53) and a control group (n = 50). The levels of the biomarkers were determined using enzyme-linked immunosorbent assay technique and they were compared between the groups. If the Mann-Whitney test demonstrated a statistically significant difference, receiver operating curves (ROC) analysis was undertaken. RESULTS When normalized to urinary creatinine, hBDNF, MDA, and hNGF showed significantly increased values in women with OAB as compared to controls, whereas 8-OHdG showed no significant difference. The diagnostic performance of these biomarkers was analyzed based on the area under the ROC curve (AUC). MDA had the highest AUC (0.75), followed by hNGF (0.69) and hBDNF (0.67). CONCLUSIONS Our findings suggest that MDA, a relatively novel biomarker in OAB research, has a fair performance as a diagnostic tool for OAB. Moreover, urinary neurotrophins (NGF and BDNF) as biomarkers may have a role in the diagnostic pathways of women with OAB symptoms.
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Affiliation(s)
- Maria Patricia Rada
- 2nd Department of Obstetrics-Gynaecology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Răzvan Ciortea
- 2nd Department of Obstetrics-Gynaecology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andrei Mihai Măluţan
- 2nd Department of Obstetrics-Gynaecology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Stergios K Doumouchtsis
- Department of Obstetrics and Gynaecology, Epsom & St Helier University Hospitals NHS Trust, UK
- Institute of Medical and Biomedical Education, St George's University of London, London, UK
- Laboratory of Experimental Surgery and Surgical Research N S Christeas, Athens University Medical School, Athens, Greece
- American University of the Caribbean School of Medicine, Florida
| | - Carmen Elena Bucuri
- 2nd Department of Obstetrics-Gynaecology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adelina Clim
- 2nd Department of Obstetrics-Gynaecology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andrei Roman
- Department of Radiology, "Prof. Dr. Ion Chiricuţă" Oncology Institute Cluj-Napoca, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Dan Mihu
- 2nd Department of Obstetrics-Gynaecology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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García-Bonillo C, Texidó R, Reyes-Carmenaty G, Gilabert-Porres J, Borrós S. Study of the Human Albumin Role in the Formation of a Bacterial Biofilm on Urinary Devices Using QCM-D. ACS APPLIED BIO MATERIALS 2020; 3:3354-3364. [PMID: 35025378 DOI: 10.1021/acsabm.0c00286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catheter-associated urinary tract infections (CAUTIs) are the most common health care-associated infections due to rapid bacterial colonization+ and biofilm formation in urinary catheters. This behavior has been extensively documented in medical devices. However, there is a few literature works on CAUTI providing a model that allows the exhaustive study of biofilm formation in a urinary environment. The development of an effective model would be helpful to identify the factors that promote the biofilm formation and identify strategies to avoid it. In this work, we have developed a model to test biofilm formation on urinary medical device surfaces by simulating environmental and physical conditions using a quartz crystal microbalance with dissipation (QCM-D) module with an uropathogenic strain. Moreover, we used the developed model to study the role of human albumin present in artificial urine at high concentrations because of renal failure or heart-diseases in patients. Despite model limitations using artificial urine, these tests show that human albumin can be considered as a promoter of biofilm formation on hydrophobic surfaces, being a possible risk factor to developing a CAUTI.
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Affiliation(s)
| | - Robert Texidó
- Tractivus SL, Via Augusta, 394, 08017 Barcelona, Spain
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Prasanna JS, Sumadhura C. Biochemical Analysis of Three Biological Fluids and its Response to Non-Surgical Periodontal Therapy in Pre and Postmenopausal Women with Periodontitis. J Menopausal Med 2020; 25:149-157. [PMID: 32307940 PMCID: PMC6952703 DOI: 10.6118/jmm.18179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/02/2019] [Accepted: 11/03/2019] [Indexed: 12/23/2022] Open
Abstract
Objectives Periodontitis is a common chronic inflammatory disease characterized by the destruction of the supporting structures of the teeth. The stages of menopause also worsen inflammatory condition. Biomarkers from biological fluids can be used as a diagnostic indicator to correlate these two conditions of present and future disease activity. The aim of the present study was to evaluate the neopterin levels in three biological fluids obtained from pre- and postmenopausal women with periodontitis following non-surgical periodontal therapy (NSPT, that is, scaling). Methods This was a cross-sectional interventional study. Thirty women, aged 40–60 years, with periodontitis were selected according to their menstrual history. They were divided into the pre- and postmenopausal groups, with each group including 15 participants. The neopterin levels were measured in both groups at baseline and 3 months after NSPT. Intergroup comparison and percentage decrement analysis were performed using the independent sample t test, and intragroup comparison was performed using the paired t test. Results There were statistically significant reductions in the mean values of saliva, urine, and plasma from baseline to 3 months after NSPT in the groups. Intergroup comparison showed no significant values in the postmenopausal group, and a significant reduction was seen in the mean values was seen in the mean values. Conclusions Neopterin levels decreased at 3 months after NSPT in both the groups, suggesting that NSPT can be a gold standard therapy and that the neopterin level could be a indicator to identify periodontal destruction.
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Affiliation(s)
- Jammula Surya Prasanna
- Department of Periodontics, Panineeya Institute of Dental Sciences and Research Centre, Hyderabad, India.
| | - Chinta Sumadhura
- Department of Periodontics, Panineeya Institute of Dental Sciences and Research Centre, Hyderabad, India
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Paul P, Antonydhason V, Gopal J, Haga SW, Hasan N, Oh JW. Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. Int J Mol Sci 2020; 21:E961. [PMID: 32024005 PMCID: PMC7038205 DOI: 10.3390/ijms21030961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023] Open
Abstract
The clinical sampling of urine is noninvasive and unrestricted, whereby huge volumes can be easily obtained. This makes urine a valuable resource for the diagnoses of diseases. Urinary and renal proteomics have resulted in considerable progress in kidney-based disease diagnosis through biomarker discovery and treatment. This review summarizes the bioinformatics tools available for this area of proteomics and the milestones reached using these tools in clinical research. The scant research publications and the even more limited bioinformatic tool options available for urinary and renal proteomics are highlighted in this review. The need for more attention and input from bioinformaticians is highlighted, so that progressive achievements and releases can be made. With just a handful of existing tools for renal and urinary proteomic research available, this review identifies a gap worth targeting by protein chemists and bioinformaticians. The probable causes for the lack of enthusiasm in this area are also speculated upon in this review. This is the first review that consolidates the bioinformatics applications specifically for renal and urinary proteomics.
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Affiliation(s)
- Piby Paul
- St. Jude Childrens Cancer Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA;
| | - Vimala Antonydhason
- Department of Microbiology and Immunology, Institute for Biomedicine, Gothenburg University, 413 90 Gothenburg, Sweden;
| | - Judy Gopal
- Department of Environmental Health Sciences, Konkuk University, Seoul 143-701, Korea;
| | - Steve W. Haga
- Department of Computer Science and Engineering, National Sun Yat Sen University, Kaohsiung 804, Taiwan;
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
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Zhang Y, Zhao W, Zhao Y, Mao Y, Su T, Zhong Y, Wang S, Zhai R, Cheng J, Fang X, Zhu J, Yang H. Comparative Glycoproteomic Profiling of Human Body Fluid between Healthy Controls and Patients with Papillary Thyroid Carcinoma. J Proteome Res 2019; 19:2539-2552. [PMID: 31800250 DOI: 10.1021/acs.jproteome.9b00672] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Zhao
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 102206, China
| | - Yonghong Mao
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Thoracic Surgery Research Labouratory, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Su
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yi Zhong
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shisheng Wang
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rui Zhai
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 102206, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiang Fang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 102206, China
| | - Jingqiang Zhu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
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A Proteomics-Based Approach Reveals Differential Regulation of Urine Proteins between Metabolically Healthy and Unhealthy Obese Patients. Int J Mol Sci 2019; 20:ijms20194905. [PMID: 31623319 PMCID: PMC6801506 DOI: 10.3390/ijms20194905] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
Metabolic dysfunction associated with obesity threatens to inundate health care resources by increasing the incidences of obesity-related diseases. The aim of the present study was to investigate the changes in the urinary proteome of 18 individuals classified into metabolically healthy obese (MHO) and metabolically unhealthy obese (MUHO) patients. Proteome analysis was performed using the two-dimensional difference in gel electrophoresis (2D-DIGE) coupled with mass spectrometry (MS). Upon analysis, a total of 54 proteins were found to be affected with ≥1.5-fold change (ANOVA, p ≤ 0.05), of which 44 proteins were upregulated and 10 proteins were downregulated. These differentially abundant proteins were related to nuclear factor κB (NF-κB) and p38 mitogen-activated protein (MAP) kinase pathways and were involved in cellular compromise, inflammatory response, and cancer. Proteins involved in inflammation (fibrinogen alpha (FIBA), serotransferrin (TRFE, and kininogen-1 (KNG1)) and insulin resistance (ADP-ribosylation factor (ARF)-like protein 15 (ARL15) and retinol-binding protein 4 (RET4)) were found to be significantly increased in the urine samples of MUHO compared to MHO patients. Investigating the effects of obesity on urinary proteins can help in developing efficient diagnostic procedures for early detection and prevention of obesity-related complications.
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Zhang Y, Jing H, Meng B, Qian X, Ying W. L-cysteine functionalized straticulate C 3N 4 for the selective enrichment of glycopeptides. J Chromatogr A 2019; 1610:460545. [PMID: 31551124 DOI: 10.1016/j.chroma.2019.460545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 02/05/2023]
Abstract
The facile enrichment of glycopeptides or glycoproteins poses great challenges for glycoproteomic research. In this study, a novel hydrophilic material, named zwitterionic hydrophilic L-cysteine derivatized straticulate-C3N4 composites (LCAC), were synthesized and evaluated for the enrichment of N-glycopeptides. LCAC exhibited good biocompatibility, excellent hydrophilicity and selectivity, by virtue of the large surface of C3N4 and the zwitterionic property offered by cysteine. LCAC demonstrated excellent performance for N-glycopeptide enrichment with the sensitivity of 0.033 fmol/µL, selectivity of 1:100, and high recovery rate (∼85%). The performance of LCAC was demonstrated by the identification of 35 N-glycopeptides from IgG, as well as capturing 1809 human urine N-glycopeptides corresponding to 876 N-glycoproteins. Comparing the LCAC with our developed phenylboronic acid functionalized material showed a certain complementary due to the different binding mechanism. The simple production and enhanced hydrophilic properties make the material a promising choice for glycoproteomics researches.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongyu Jing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Siwy J, Mischak H, Zürbig P. Proteomics and personalized medicine: a focus on kidney disease. Expert Rev Proteomics 2019; 16:773-782. [DOI: 10.1080/14789450.2019.1659138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Justyna Siwy
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Harald Mischak
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Petra Zürbig
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
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Metabolomic Analysis of Membranous Glomerulonephritis: Identification of a Diagnostic Panel and Pathogenic Pathways. Arch Med Res 2019; 50:159-169. [DOI: 10.1016/j.arcmed.2019.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/08/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022]
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Husi H, Fernandes M, Skipworth RJ, Miller J, Cronshaw AD, Fearon KCH, Ross JA. Identification of diagnostic upper gastrointestinal cancer tissue type-specific urinary biomarkers. Biomed Rep 2019; 10:165-174. [PMID: 30906545 PMCID: PMC6423495 DOI: 10.3892/br.2019.1190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023] Open
Abstract
Several potential urinary biomarkers exhibiting an association with upper gastrointestinal tumour growth have been previously identified, of which S100A6, S100A9, rabenosyn-5 and programmed cell death 6-interacting protein (PDCD6IP) were further validated and found to be upregulated in malignant tumours. The cancer cohort from our previous study was subclassified to assess whether distinct molecular markers can be identified for each individual cancer type using a similar approach. Urine samples from patients with cancers of the stomach, oesophagus, oesophagogastric junction or pancreas were analysed by surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry using both CM10 and IMAC30 (Cu2+-complexed) chip types and LC-MS/MS-based mass spectrometry after chromatographic enrichment. This was followed by protein identification, pattern matching and validation by western blotting. We found 8 m/z peaks with statistical significance for the four cancer types investigated, of which m/z 2447 and 2577 were identified by pattern matching as fragments of cathepsin-B (CTSB) and cystatin-B (CSTB); both molecules are indicative of pancreatic cancer. Additionally, we observed a potential association of upregulated α-1-antichymotrypsin with pancreatic and gastric cancers, of PDCD6IP, vitelline membrane outer layer protein 1 homolog (VMO1) and triosephosphate isomerase (TPI1) with oesophagogastric junctional cancers, and of complement C4-A, prostatic acid phosphatase, azurocidin and histone-H1 with oesophageal cancer. Furthermore, the potential pancreatic cancer biomarkers CSTB and CTSB were validated independently by western blotting. Therefore, the present study identified two new potential urinary biomarkers that appear to be associated with pancreatic cancer. This may provide a simple, non-invasive screening test for use in the clinical setting.
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Affiliation(s)
- Holger Husi
- Department of Diabetes and Cardiovascular Science, University of the Highlands and Islands, Inverness IV2 3JH, UK.,BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK.,School of Clinical Sciences and Community Health, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Marco Fernandes
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Richard J Skipworth
- School of Clinical Sciences and Community Health, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Janice Miller
- School of Clinical Sciences and Community Health, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Andrew D Cronshaw
- School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Kenneth C H Fearon
- School of Clinical Sciences and Community Health, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - James A Ross
- School of Clinical Sciences and Community Health, University of Edinburgh, Edinburgh EH16 4SB, UK
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Bellei E, Monari E, Bergamini S, Pini LA, Aldo T, Ozben T. Urinary Proteomics in Biomarker Discovery of Kidney-Related Disorders: Diabetic Nephropathy and Drug-Induced Nephrotoxicity in Chronic Headache. EJIFCC 2018; 29:290-297. [PMID: 30574040 PMCID: PMC6295592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
OBJECTIVE Urinary proteomics is primarily applied to the study of renal and urogenital tract disorders. Here are reported two distinct successful examples of this approach for the discovery of early urinary biomarkers of kidney-related dysfunctions: diabetic nephropathy (DN), a well-known complication of diabetes frequently leading to dialysis, and drug-induced nephrotoxicity, a possible condition caused by medication-overuse headache (MOH). Early detection of kidney disorders based on selective biomarkers could permit to diagnose patients at the initial stage of the disease, where the therapy may be suspended or prevent disease advancement. METHODS Urine samples were first concentrated and desalted. Subsequently, they were subjected to two-dimensional gel electrophoresis (2-DE) coupled to mass spectrometry (MS) for protein identification. Furthermore, some proteins were verified by Western blot and ELISA test. RESULTS In diabetes-related study, 11 differentially expressed proteins were detected (8 up-regulated and 3 down-regulated) in type 2 diabetic (T2D) and T2DN patients compared to the healthy control subjects. In the MOH study, a total of 21 over-excreted proteins were revealed in urine of non-steroidal anti-inflammatory drugs (NSAIDs) and mixtures abusers vs controls. Particularly, 4 proteins were positively validated by immunob-lotting and EUSA. CONCLUSION Urinary proteomics allows non-invasive assessment of renal diseases at an early stage by the identification of characteristic protein pattern.
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Affiliation(s)
- Elisa Bellei
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Emanuela Monari
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefania Bergamini
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Luigi Alberto Pini
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, Modena, Italy, Headache and Drug Abuse Study Center, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Tomasi Aldo
- Department of Diagnostic Medicine, Clinic and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Tomris Ozben
- Department of Clinical Biochemistry, Medical Faculty, Akdeniz University, Antalya, Turkey,Corresponding author: Tomris Ozben Department of Clinical Biochemistry Akdeniz University Dumlupinar Boulevard 07058 Konyaalti, Antalya Turkey E-mail:
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44
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Vinaiphat A, Charngkaew K, Thongboonkerd V. More complete polarization of renal tubular epithelial cells by artificial urine. Cell Death Discov 2018; 4:47. [PMID: 30323952 PMCID: PMC6180081 DOI: 10.1038/s41420-018-0112-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
Cell polarization using Transwell is a common method employed to study renal tubular epithelial cells. However, this conventional protocol does not precisely recapitulate renal tubular epithelial cell phenotypes. In this study, we simulated renal physiological microenvironment by replacing serum-containing culture medium in upper chamber of the Transwell with physiologic artificial urine (AU) (to mimic renal tubular fluid), whereas the lower chamber still contained serum-containing medium (to mimic plasma-enriched renal interstitium). Comparing to the conventional protocol (control), the AU-assisted protocol offered more complete polarization of MDCK renal tubular cells as indicated by higher transepithelial electrical resistance (TER) and greater levels of tight junction (TJ) proteins (ZO-1 and occludin). Transmission electron microscopy (TEM) showed greater densities of TJ and desmosome, narrower intercellular spaces, greater cell height, and longer microvilli in the AU-treated cells. Secretome analysis revealed that the AU-treated cells secreted greater proportion of the proteins matched to normal human urinary proteome via both classical and non-classical secretory pathways. Finally, modifying/omitting each component of AU (one at a time) followed by validation revealed that urea was responsible for such property of AU to improve cell polarization. These data indicate that replacing AU on the upper chamber of Transwell can improve or optimize renal cell polarization for more precise investigations of renal physiology and cell biology in vitro.
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Affiliation(s)
- Arada Vinaiphat
- 1Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,2Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komgrid Charngkaew
- 3Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- 1Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,4Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand
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45
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Lim JH, Lee CH, Kim KY, Jung HY, Choi JY, Cho JH, Park SH, Kim YL, Baek MC, Park JB, Kim YH, Chung BH, Lee SH, Kim CD. Novel urinary exosomal biomarkers of acute T cell-mediated rejection in kidney transplant recipients: A cross-sectional study. PLoS One 2018; 13:e0204204. [PMID: 30226858 PMCID: PMC6143249 DOI: 10.1371/journal.pone.0204204] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/05/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Acute rejection is hazardous to graft survival in kidney transplant recipients (KTRs). We aimed to identify novel biomarkers for early diagnosis of acute T cell-mediated rejection (TCMR) in urinary exosomes of KTRs. METHODS Among 458 graft biopsies enrolled in a cross-sectional multicenter study, 22 patients with stable graft function (STA) who had not shown pathologic abnormality and 25 patients who diagnosed biopsy-proven TCMR were analyzed. We performed proteomic analysis using nano-ultra performance liquid chromatography-tandem mass spectrometry (nano-UPLC-MS/MS) to identify candidate biomarkers for early TCMR diagnosis on urinary exosomes. We confirmed the protein levels of each candidate biomarker by western blot analysis. RESULTS A total of 169 urinary exosome proteins were identified by nano-UPLC-MS/MS. Forty-six proteins showed increased expression in STA patients, while 17 proteins were increased in TCMR patients. Among them, we selected five proteins as candidate biomarkers for early diagnosis of TCMR according to significance, degree of quantity variance, and information from the ExoCarta database. We confirmed the proteomic expression levels of five candidate biomarkers by western blot analysis in each patient. Of all candidate biomarkers, tetraspanin-1 and hemopexin were significantly higher in TCMR patients (STA:TCMR ratio = 1:1.8, P = 0.009, and 1:3.5, P = 0.046, respectively). CONCLUSIONS Tetraspanin-1 and hemopexin were detected in KTR urine and could act as potential diagnostic proteins for TCMR.
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Affiliation(s)
- Jeong-Hoon Lim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Chan-Hyeong Lee
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Kyu Yeun Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Hee-Yeon Jung
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Ji-Young Choi
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Jang-Hee Cho
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Sun-Hee Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Yong-Lim Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Moon-Chang Baek
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Berm Park
- Department of Surgery, Samsung Medical Center, Seoul, South Korea
| | - Young-Hoon Kim
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Inje University, Pusan, South Korea
| | - Byung Ha Chung
- Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sang-Ho Lee
- Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Chan-Duck Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
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46
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Phenylboronic acid functionalized C 3N 4 facultative hydrophilic materials for enhanced enrichment of glycopeptides. Talanta 2018; 191:509-518. [PMID: 30262092 DOI: 10.1016/j.talanta.2018.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/02/2023]
Abstract
It is challenging to capture N-glycopeptides with high recovery and high specificity from complicated biosystems. Herein, we present a facile and economical procedure to generate a novel self-assembling 4-Mercaptobenzene boronic acid functionalized and Au-doped Straticulate C3N4 (MASC), with enhanced affinity capability towards glycopeptides. The materials possess low pH value adaptation, high hydrophilicity and stability, good repeatability and recyclability, and provided high selectivity (1:100), low limit of detection (0.33 fmol/μL), high enrichment efficiency (~ 80%) and high recovery rate (~ 90%) towards glycopeptides. The materials can capture glycopeptides unbiasedly, as demonstrated by the identification of 37 glycopeptides from IgG and 21 glycopeptides from horseradish peroxidase (HRP). The performance of MASC on human urine and serum glycoproteome analysis was also tested. An average of 1465 glycopeptides from 839 glycoproteins and 1553 glycopeptides from 884 glycoproteins were identified from female and male urine samples in a single mass spectrometry analysis. O-glycopeptides from human urine were also significantly enriched. Additionally, 463 glycopeptides assigned to 209 glycoproteins were identified from 5 μL of human serum. All of these results indicate that MASC presents a good performance and applicability in the field of glycoproteomic research.
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47
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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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48
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Husi H, MacDonald A, Skipworth RJE, Miller J, Cronshaw A, Greig C, Fearon KCH, Ross JA. Urinary diagnostic proteomic markers for dynapenia in cancer patients. Biomed Rep 2018; 8:547-556. [PMID: 29904611 DOI: 10.3892/br.2018.1092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/19/2018] [Indexed: 12/24/2022] Open
Abstract
Dynapenia is defined as the age-related loss of muscle strength, and plays a significant role in the loss of physical function and increased risk of disability among older individuals. The need for an early diagnosis supports the search for a biomarker that reflects muscle 'weakening'. This has previously proven difficult due to patient heterogeneity at presentation and lack of understanding of the underlying molecular mechanisms. The aim of the present study was to identify potential urinary biomarkers of dynapenia in patients undergoing potentially curative surgery for upper gastrointestinal cancer. Maximum isometric knee extensor strength (strain gauge) and maximum leg extensor power (Nottingham power rig) measurements were taken. Cut-off values for dynapenia were based on the Allied Dunbar national fitness survey. Values below the 5th percentile for the population matched for age and sex on the Allied Dunbar national fitness survey were used to stratify the cohort into dynapenic or normal. Urine samples taken at induction of anaesthesia were analysed by SELDI-TOF mass spectrometry using CM10 and IMAC30 chip-types to establish statistically significant m/z peak fingerprint patterns, followed by in-gel LC-MS/MS to identify molecular constituents. Statistical analysis of decision-tree calculations using Biomarker Pattern software resulted in models with sensitivities of 86 and 96%, specificities of 81 and 89%, and overall correctness of 84 and 93%, when applied to the entire cohort for power and strength measurement-based stratifications using the IMAC30 chip-type and the CM10 chip-type, respectively. The molecular identities of 10 peaks of interest were further investigated. After subtraction of potentially unrelated proteins, they were identified as fragments of Annexin A1, collagen α-1 (XV), perlecan and myotrophin. These results demonstrate that urinary screening can be used to define cancer-associated muscle weakness, and the identification of potential biomarkers could be invaluable in establishing a rapid test to measure and assess dynapenia in the clinical setting.
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Affiliation(s)
- Holger Husi
- Department of Diabetes and Cardiovascular Science, University of the Highlands and Islands, Centre for Health Science, IV2 3JH Inverness, UK
| | - Alisdair MacDonald
- School of Clinical Sciences, University of Edinburgh, EH16 4SB Edinburgh, UK
| | | | - Janice Miller
- School of Clinical Sciences, University of Edinburgh, EH16 4SB Edinburgh, UK
| | - Andrew Cronshaw
- School of Biological Sciences, University of Edinburgh, EH16 4SB Edinburgh, UK
| | - Carolyn Greig
- School of Clinical Sciences, University of Edinburgh, EH16 4SB Edinburgh, UK
| | - Kenneth C H Fearon
- School of Clinical Sciences, University of Edinburgh, EH16 4SB Edinburgh, UK
| | - James A Ross
- School of Clinical Sciences, University of Edinburgh, EH16 4SB Edinburgh, UK
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49
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Magalhães P, Pontillo C, Pejchinovski M, Siwy J, Krochmal M, Makridakis M, Carrick E, Klein J, Mullen W, Jankowski J, Vlahou A, Mischak H, Schanstra JP, Zürbig P, Pape L. Comparison of Urine and Plasma Peptidome Indicates Selectivity in Renal Peptide Handling. Proteomics Clin Appl 2018; 12:e1700163. [DOI: 10.1002/prca.201700163] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Pedro Magalhães
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
| | - Claudia Pontillo
- Department of Toxicology and Pharmacology; Hannover Medical School; 30625 Hannover Germany
| | | | - Justyna Siwy
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | | | - Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Emma Carrick
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Julie Klein
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joachim Jankowski
- RWTH Aachen University Hospital; 52074 Aachen Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht; University of Maastricht; 6211 Maastricht The Netherlands
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joost P. Schanstra
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - Petra Zürbig
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | - Lars Pape
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
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50
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Candidate Urine Peptide Biomarkers for IgA Nephropathy: Where Are We Now? DISEASE MARKERS 2018; 2018:5205831. [PMID: 29606986 PMCID: PMC5827886 DOI: 10.1155/2018/5205831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/29/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022]
Abstract
Early detection, prognosis, and management of IgA nephropathy (IgAN) remain a challenge. Histological examination of renal tissue still comprises the only way to confirm an IgAN diagnosis. It is of great importance to establish noninvasive diagnostic, prognostic, and predictive biomarkers that would improve the clinical care and outcome of patients suffering from IgAN. This review summarises the findings from previous mass spectrometry- (MS-) based studies dedicated to the discovery of urinary peptide profiles specific to IgAN. There is a substantial number of urinary peptides that have been discovered to date, which show promise as biomarkers of IgAN; however, all of them require further, rigorous validation in well-planned studies, involving a large number of subjects who represent diverse and numerous populations.
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