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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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Thielemans R, Speeckaert R, Delrue C, De Bruyne S, Oyaert M, Speeckaert MM. Unveiling the Hidden Power of Uromodulin: A Promising Potential Biomarker for Kidney Diseases. Diagnostics (Basel) 2023; 13:3077. [PMID: 37835820 PMCID: PMC10572911 DOI: 10.3390/diagnostics13193077] [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: 07/31/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Uromodulin, also known as Tamm-Horsfall protein, represents the predominant urinary protein in healthy individuals. Over the years, studies have revealed compelling associations between urinary and serum concentrations of uromodulin and various parameters, encompassing kidney function, graft survival, cardiovascular disease, glucose metabolism, and overall mortality. Consequently, there has been a growing interest in uromodulin as a novel and effective biomarker with potential applications in diverse clinical settings. Reduced urinary uromodulin levels have been linked to an elevated risk of acute kidney injury (AKI) following cardiac surgery. In the context of chronic kidney disease (CKD) of different etiologies, urinary uromodulin levels tend to decrease significantly and are strongly correlated with variations in estimated glomerular filtration rate. The presence of uromodulin in the serum, attributable to basolateral epithelial cell leakage in the thick ascending limb, has been observed. This serum uromodulin level is closely associated with kidney function and histological severity, suggesting its potential as a biomarker capable of reflecting disease severity across a spectrum of kidney disorders. The UMOD gene has emerged as a prominent locus linked to kidney function parameters and CKD risk within the general population. Extensive research in multiple disciplines has underscored the biological significance of the top UMOD gene variants, which have also been associated with hypertension and kidney stones, thus highlighting the diverse and significant impact of uromodulin on kidney-related conditions. UMOD gene mutations are implicated in uromodulin-associated kidney disease, while polymorphisms in the UMOD gene show a significant association with CKD. In conclusion, uromodulin holds great promise as an informative biomarker, providing valuable insights into kidney function and disease progression in various clinical scenarios. The identification of UMOD gene variants further strengthens its relevance as a potential target for better understanding kidney-related pathologies and devising novel therapeutic strategies. Future investigations into the roles of uromodulin and regulatory mechanisms are likely to yield even more profound implications for kidney disease diagnosis, risk assessment, and management.
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Affiliation(s)
- Raïsa Thielemans
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium; (R.T.); (C.D.)
| | | | - Charlotte Delrue
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium; (R.T.); (C.D.)
| | - Sander De Bruyne
- Department of Laboratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (S.D.B.); (M.O.)
| | - Matthijs Oyaert
- Department of Laboratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (S.D.B.); (M.O.)
| | - Marijn M. Speeckaert
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium; (R.T.); (C.D.)
- Research Foundation Flanders, 1000 Brussels, Belgium
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Schiel R, Block M, Steveling A, Stein G, Lücking S, Scherberich J. Serum Uromodulin in Children and Adolescents with Type 1 Diabetes Mellitus and Controls: Its Potential Role in Kidney Health. Exp Clin Endocrinol Diabetes 2023; 131:142-152. [PMID: 36104158 DOI: 10.1055/a-1944-2686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Uromodulin is a kidney-specific tubular protein, and its assessment in serum (sUMOD) reveals the potential as a novel marker for function and the integrity of renal parenchymal cells and does not directly depend on the glomerular filtration rate. Early diabetic nephropathy parallels glomerular hyperfiltration, often leading to diagnostic misinterpretation. Moreover, traditional kidney function markers are not able to diagnose structural lesions. Recent data show that sUMOD is linked to glucose intolerance in adults. Thus, we launched to assess the hypothesis that sUMOD is also associated with kidney function, biometric data, and quality of metabolic control in children/adolescents with type 1 diabetes. PATIENTS AND METHODS Patients with type 1 diabetes (n=135) and healthy controls (n=69) were recruited to participate in the trial. Clinical, biometrical data, sUMOD, and other laboratory parameters were assessed. RESULTS The mean concentrations of sUMOD in diabetic patients and controls were comparable (201.19±103.22 vs. 198.32±84.27 ng/mL, p=0.832). However, in contrast to healthy controls, sUMOD levels in patients with diabetes were associated with serum-creatinine (r=-0.368, p<0.0001), age (r=-0.350, p<0.0001), height (r=-0.379, p<0.0001), body weight (r=-0.394, p<0.0001), Body mass index (r=-0.292, p=0.001), daily insulin dosage (r=-0.300, p<0.0001), HbA1c (%) (r=-0.190, p=0.027), standardized HbA1c/IFCC (mmol/mol) (r=-0.189, p=0.028), and systolic (r=-0.299, p<0.0001) and diastolic (r=-0.235, p=0.006) arterial blood pressure. CONCLUSIONS Our study shows that children/adolescents with type 1 diabetes disclose similar sUMOD concentrations as healthy controls. Serum UMOD appears to indicate higher risks for kidney tissue remodeling and possibly subsequent cardiovascular alterations. However, further studies are mandatory to settle these findings.
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Affiliation(s)
- Ralf Schiel
- MEDIGREIF-Inselklinik Heringsdorf GmbH, Department of Diabetes and Metabolic Diseases, Ostseebad Heringsdorf, Germany
| | - Mathias Block
- Euroimmun Medizinische Labordiagnostika AG, Lübeck, Germany
| | - Antje Steveling
- University of Greifswald, School of Medicine, Internal Medicine A, Greifswald, Germany
| | - Günter Stein
- Friedrich-Schiller-University, School of Medicine, Internal Medicine, Nephrology, Jena, Germany
| | - Sarah Lücking
- MEDIGREIF-Inselklinik Heringsdorf GmbH, Department of Diabetes and Metabolic Diseases, Ostseebad Heringsdorf, Germany
| | - Jürgen Scherberich
- Klinikum München-Harlaching, München-Klinik, Teaching Hospital of The Ludwig-Maximilians University, München
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Li B, Chen X, Ma W, Li N, Chen Q, Liao J, Luo S, Lu X, Zhang Y, Li S, Wang X, Xu F. An endogenous amniotic fluid-derived 10-amino acid peptide improves lung development and hyperoxia injury. Transl Pediatr 2023; 12:46-55. [PMID: 36798938 PMCID: PMC9926127 DOI: 10.21037/tp-22-681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) is a chronic lung disease that occurs in preterm infants and lacks effective treatment. We aim to reveal the relationship between amniotic fluid (AF) peptides and lung development by analyzing the differences in the composition of AF peptides at different gestational periods, thus providing a new means of prevention and treatment for BPD. METHODS Based on the stages of lung development, we collected AF by amniocentesis in two different gestational periods, using the 25th week of pregnancy as the cut-off. We conducted a peptide omics analysis of these AF samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Additionally, we verified the regulatory effects of hyperoxia and the peptide COL5A2 on BPD-related cells [(mouse lung epithelial (MLE-12) cells] by 5-Ethynyl-2'-deoxyuridine (EdU) staining, JC-1 staining, flow cytometry, and reactive oxygen species (ROS) assay. RESULTS There were 131 differentially expressed peptides, including 85 up-regulated and 46 down-regulated [fold change (FC) ≥1.2 or ≤1/1.2, P<0.05], in the ≥25 weeks' gestation group compared to the <25 weeks' gestation group. Further bioinformatics analysis revealed that the precursor proteins of the differentially expressed peptides between these two groups were involved in the regulation of the developmental process, anatomical structure development, and other biological processes, suggesting that these differential peptides may play a key role in lung development. We found peptide COL5A2 with the sequence GPPGEPGPPG and verified the regulatory effects of COL5A2 on the proliferation, apoptosis, cell viability, and ROS levels of MLE-12 cells by cell assays. CONCLUSIONS In this study, peptidomic studies using AF from different gestational periods revealed that peptides in AF may be involved in lung development. They could be used in the future to assist in the postnatal development of preterm infants and provide new therapeutic prospects for BPD.
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Affiliation(s)
- Baihe Li
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China.,Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neonatology, International Peace Maternity and Child Health Hospital of China Welfare Institution, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Chen
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neonatology, Nanjing Children's Hospital (Children's Hospital Affiliated to Nanjing Medical University), Nanjing, China
| | - Weihui Ma
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Li
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Qin Chen
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Jinfeng Liao
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Sanfeng Luo
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Xiaomei Lu
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Yaozhong Zhang
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Siping Li
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
| | - Xingyun Wang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fengdan Xu
- Department of Neonatology, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, China
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Caira S, Picariello G, Renzone G, Arena S, Troise AD, De Pascale S, Ciaravolo V, Pinto G, Addeo F, Scaloni A. Recent developments in peptidomics for the quali-quantitative analysis of food-derived peptides in human body fluids and tissues. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Saudenova M, Promnitz J, Ohrenschall G, Himmerkus N, Böttner M, Kunke M, Bleich M, Theilig F. Behind every smile there's teeth: Cathepsin B's function in health and disease with a kidney view. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119190. [PMID: 34968578 DOI: 10.1016/j.bbamcr.2021.119190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Cathepsin B (CatB) is a very abundant lysosomal protease with endo- and carboxydipeptidase activities and even ligase features. In this review, we will provide a general characterization of CatB and describe structure, structure-derived properties and location-dependent proteolytic actions. We depict CatB action within lysosome and its important roles in lysosomal biogenesis, lysosomal homeostasis and autophagy rendering this protease a key player in orchestrating lysosomal functions. Lysosomal leakage and subsequent escape of CatB into the cytosol lead to harmful actions, e.g. the role in activating the NLPR3 inflammasome, affecting immune responses and cell death. The second focus of this review addresses CatB functions in the kidney, i.e. the glomerulus, the proximal tubule and collecting duct with strong emphasis of its role in pathology of the respective segment. Finally, observations regarding CatB functions that need to be considered in cell culture will be discussed. In conclusion, CatB a physiologically important molecule may, upon aberrant expression in different cellular context, become a harmful player effectively showing its teeth behind its smile.
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Affiliation(s)
- Makhabbat Saudenova
- Institute of Anatomy, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Jessica Promnitz
- Institute of Anatomy, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Gerrit Ohrenschall
- Institute of Anatomy, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Nina Himmerkus
- Institute of Physiology, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Martina Böttner
- Institute of Anatomy, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Madlen Kunke
- Institute of Anatomy, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Markus Bleich
- Institute of Physiology, Department of Medicine, Christian-Albrechts-University Kiel, Germany
| | - Franziska Theilig
- Institute of Anatomy, Department of Medicine, Christian-Albrechts-University Kiel, Germany.
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An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease. Nat Commun 2022; 13:888. [PMID: 35173144 PMCID: PMC8850430 DOI: 10.1038/s41467-022-28353-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 01/20/2022] [Indexed: 12/11/2022] Open
Abstract
Celiac disease (CeD) is an autoimmune disorder induced by consuming gluten proteins from wheat, barley, and rye. Glutens resist gastrointestinal proteolysis, resulting in peptides that elicit inflammation in patients with CeD. Despite well-established connections between glutens and CeD, chemically defined, bioavailable peptides produced from dietary proteins have never been identified from humans in an unbiased manner. This is largely attributable to technical challenges, impeding our knowledge of potentially diverse peptide species that encounter the immune system. Here, we develop a liquid chromatographic-mass spectrometric workflow for untargeted sequence analysis of the urinary peptidome. We detect over 600 distinct dietary peptides, of which ~35% have a CeD-relevant T cell epitope and ~5% are known to stimulate innate immune responses. Remarkably, gluten peptides from patients with CeD qualitatively and quantitatively differ from controls. Our results provide a new foundation for understanding gluten immunogenicity, improving CeD management, and characterizing the dietary and urinary peptidomes. Gluten peptides from wheat enter the bloodstream and are excreted in urine but are yet to be chemically characterised. Here, the authors show by mass spectrometry that quantitative and qualitative differences in urinary peptides can be detected between healthy people and patients with celiac disease.
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8
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Reproducibility Evaluation of Urinary Peptide Detection Using CE-MS. Molecules 2021; 26:molecules26237260. [PMID: 34885840 PMCID: PMC8658976 DOI: 10.3390/molecules26237260] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/19/2021] [Accepted: 11/28/2021] [Indexed: 11/29/2022] Open
Abstract
In recent years, capillary electrophoresis coupled to mass spectrometry (CE-MS) has been increasingly applied in clinical research especially in the context of chronic and age-associated diseases, such as chronic kidney disease, heart failure and cancer. Biomarkers identified using this technique are already used for diagnosis, prognosis and monitoring of these complex diseases, as well as patient stratification in clinical trials. CE-MS allows for a comprehensive assessment of small molecular weight proteins and peptides (<20 kDa) through the combination of the high resolution and reproducibility of CE and the distinct sensitivity of MS, in a high-throughput system. In this study we assessed CE-MS analytical performance with regards to its inter- and intra-day reproducibility, variability and efficiency in peptide detection, along with a characterization of the urinary peptidome content. To this end, CE-MS performance was evaluated based on 72 measurements of a standard urine sample (60 for inter- and 12 for intra-day assessment) analyzed during the second quarter of 2021. Analysis was performed per run, per peptide, as well as at the level of biomarker panels. The obtained datasets showed high correlation between the different runs, low variation of the ten highest average individual log2 signal intensities (coefficient of variation, CV < 10%) and very low variation of biomarker panels applied (CV close to 1%). The findings of the study support the analytical performance of CE-MS, underlining its value for clinical application.
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Bhat M, Clotet-Freixas S, Baciu C, Pasini E, Hammad A, Ivanics T, Reid S, Azhie A, Angeli M, Ghanekar A, Fischer S, Sapisochin G, Konvalinka A. Combined proteomic/transcriptomic signature of recurrence post-liver transplantation for hepatocellular carcinoma beyond Milan. Clin Proteomics 2021; 18:27. [PMID: 34794390 PMCID: PMC8600773 DOI: 10.1186/s12014-021-09333-x] [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: 06/08/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023] Open
Abstract
Background and aims Liver transplantation (LT) can be offered to patients with Hepatocellular carcinoma (HCC) beyond Milan criteria. However, there are currently limited molecular markers on HCC explant histology to predict recurrence, which arises in up to 20% of LT recipients. The goal of our study was to derive a combined proteomic/transcriptomic signature on HCC explant predictive of recurrence post-transplant using unbiased, high-throughput approaches. Methods Patients who received a LT for HCC beyond Milan criteria in the context of hepatitis B cirrhosis were identified. Tumor explants from patients with post-transplant HCC recurrence (N = 7) versus those without recurrence (N = 4) were analyzed by mass spectrometry and gene expression array. Univariate analysis was used to generate a combined proteomic/transcriptomic signature linked to recurrence. Significantly predictive genes and proteins were verified and internally validated by immunoblotting and immunohistochemistry. Results Seventy-nine proteins and 636 genes were significantly differentially expressed in HCC tumors with subsequent recurrence (p < 0.05). Univariate survival analysis identified Aldehyde Dehydrogenase 1 Family Member A1 (ALDH1A1) gene (HR = 0.084, 95%CI 0.01–0.68, p = 0.0152), ALDH1A1 protein (HR = 0.039, 95%CI 0.16–0.91, p = 0.03), Galectin 3 Binding Protein (LGALS3BP) gene (HR = 7.14, 95%CI 1.20–432.96, p = 0.03), LGALS3BP protein (HR = 2.6, 95%CI 1.1–6.1, p = 0.036), Galectin 3 (LGALS3) gene (HR = 2.89, 95%CI 1.01–8.3, p = 0.049) and LGALS3 protein (HR = 2.6, 95%CI 1.2–5.5, p = 0.015) as key dysregulated analytes in recurrent HCC. In concordance with our proteome findings, HCC recurrence was linked to decreased ALDH1A1 and increased LGALS3 protein expression by Western Blot. LGALS3BP protein expression was validated in 29 independent HCC samples. Conclusions Significantly increased LGALS3 and LGALS3BP gene and protein expression on explant were associated with post-transplant recurrence, whereas increased ALDH1A1 was associated with absence of recurrence in patients transplanted for HCC beyond Milan criteria. This combined proteomic/transcriptomic signature could help in predicting HCC recurrence risk and guide post-transplant surveillance. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09333-x.
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Affiliation(s)
- Mamatha Bhat
- Ajmera Transplant Program, University Health Network, Toronto, Canada. .,Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Canada. .,Toronto General Hospital Research Institute, Toronto, Canada. .,Institute of Medical Science, University of Toronto, Toronto, Canada.
| | - Sergi Clotet-Freixas
- Ajmera Transplant Program, University Health Network, Toronto, Canada.,Toronto General Hospital Research Institute, Toronto, Canada
| | - Cristina Baciu
- Ajmera Transplant Program, University Health Network, Toronto, Canada
| | - Elisa Pasini
- Ajmera Transplant Program, University Health Network, Toronto, Canada
| | - Ahmed Hammad
- Ajmera Transplant Program, University Health Network, Toronto, Canada.,Department of General Surgery, Mansoura University, Mansoura, Egypt
| | - Tommy Ivanics
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Canada
| | - Shelby Reid
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Amirhossein Azhie
- Ajmera Transplant Program, University Health Network, Toronto, Canada
| | - Marc Angeli
- Ajmera Transplant Program, University Health Network, Toronto, Canada
| | - Anand Ghanekar
- Ajmera Transplant Program, University Health Network, Toronto, Canada.,Toronto General Hospital Research Institute, Toronto, Canada.,Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Canada
| | - Sandra Fischer
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Canada
| | - Gonzalo Sapisochin
- Ajmera Transplant Program, University Health Network, Toronto, Canada.,Division of Multi-Organ Transplant and HPB Surgical Oncology, Department of General Surgery, University Health Network, Toronto, Canada
| | - Ana Konvalinka
- Ajmera Transplant Program, University Health Network, Toronto, Canada. .,Toronto General Hospital Research Institute, Toronto, Canada. .,Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Canada. .,Institute of Medical Science, University of Toronto, Toronto, Canada. .,Division of Nephrology, Department of Medicine, University Health Network, Toronto, Canada. .,University Health Network, 585 University Avenue, Room 11-PMB-189, Toronto, ON, M5G 2N2, Canada.
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Hartman E, Mahdavi S, Kjellström S, Schmidtchen A. Peptimetric: Quantifying and Visualizing Differences in Peptidomic Data. FRONTIERS IN BIOINFORMATICS 2021; 1:722466. [PMID: 36303760 PMCID: PMC9581017 DOI: 10.3389/fbinf.2021.722466] [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: 06/08/2021] [Accepted: 08/11/2021] [Indexed: 12/01/2022] Open
Abstract
Finding new sustainable means of diagnosing and treating diseases is one of the most pressing issues of our time. In recent years, several endogenous peptides have been found to be both excellent biomarkers for many diseases and to possess important physiological roles which may be utilized in treatments. The detection of peptides has been facilitated by the rapid development of biological mass spectrometry and now the combination of fast and sensitive high resolution MS instruments and stable nano HP-LC equipment sequences thousands of peptides in one single experiment. In most research conducted with these advanced systems, proteolytically cleaved proteins are analyzed and the specific peptides are identified by software dedicated for protein quantification using different proteomics workflows. Analysis of endogenous peptides with peptidomics workflows also benefit from the novel sensitive and advanced instrumentation, however, the generated peptidomic data is vast and subsequently laborious to visualize and examine, creating a bottleneck in the analysis. Therefore, we have created Peptimetric, an application designed to allow researchers to investigate and discover differences between peptidomic samples. Peptimetric allows the user to dynamically and interactively investigate the proteins, peptides, and some general characteristics of multiple samples, and is available as a web application at https://peptimetric.herokuapp.com. To illustrate the utility of Peptimetric, we’ve applied it to a peptidomic dataset of 15 urine samples from diabetic patients and corresponding data from healthy subjects.
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Affiliation(s)
- Erik Hartman
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden
- *Correspondence: Erik Hartman,
| | - Simon Mahdavi
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Sven Kjellström
- Division of Mass Spectrometry, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Dermatology Skåne University Hospital, Lund, Sweden
- Copenhagen Wound Healing Center, Bispebjerg Hospital, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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Boder P, Mary S, Mark PB, Leiper J, Dominiczak AF, Padmanabhan S, Rampoldi L, Delles C. Mechanistic interactions of uromodulin with the thick ascending limb: perspectives in physiology and hypertension. J Hypertens 2021; 39:1490-1504. [PMID: 34187999 PMCID: PMC7611110 DOI: 10.1097/hjh.0000000000002861] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hypertension is a significant risk factor for cardiovascular disease and mortality worldwide. The kidney is a major regulator of blood pressure and electrolyte homeostasis, with monogenic disorders indicating a link between abnormal ion transport and salt-sensitive hypertension. However, the association between salt and hypertension remains controversial. Thus, there is continued interest in deciphering the molecular mechanisms behind these processes. Uromodulin (UMOD) is the most abundant protein in the normal urine and is primarily synthesized by the thick ascending limb epithelial cells of the kidney. Genome-wide association studies have linked common UMOD variants with kidney function, susceptibility to chronic kidney disease and hypertension independent of renal excretory function. This review will discuss and provide predictions on the role of the UMOD protein in renal ion transport and hypertension based on current observational, biochemical, genetic, pharmacological and clinical evidence.
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Affiliation(s)
- Philipp Boder
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sheon Mary
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick B. Mark
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - James Leiper
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christian Delles
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
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12
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Wu Q, Fenton RA. Urinary proteomics for kidney dysfunction: insights and trends. Expert Rev Proteomics 2021; 18:437-452. [PMID: 34187288 DOI: 10.1080/14789450.2021.1950535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introduction: Kidney dysfunction poses a high burden on patients and health care systems. Early detection and accurate prediction of kidney disease progression remains a major challenge. Compared to existing clinical parameters, urinary proteomics has the potential to reveal molecular alterations within the kidney that may alter its function before the onset of clinical symptoms. Thus, urinary proteomics has greater prognostic potential for assessment of kidney dysfunction progression.Areas covered: Advances in urinary proteomics for major causes of kidney dysfunction are discussed. The application of urinary extracellular vesicles for studying kidney dysfunction are discussed. Technological advances in urinary proteomics are discussed. The literature was identified using a database search for titles containing 'proteom*' and 'urin*' and published within the past 5 years. Retrieved literature was manually filtered to retain kidney dysfunctions-related studies.Expert opinion: Despite major advances, diagnosis by urinary proteomics has not been fully applied in any clinical settings. This could be attributed to the complex nature of kidney diseases, in addition to the constraints on study power and feasibility of incorporating mass spectrometry techniques in daily routine analysis. Nevertheless, we are confident that advances in urinary proteomics will soon provide superior insights into kidney disease beyond existing clinical parameters.
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Affiliation(s)
- Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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13
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Trindade F, Barros AS, Silva J, Vlahou A, Falcão-Pires I, Guedes S, Vitorino C, Ferreira R, Leite-Moreira A, Amado F, Vitorino R. Mining the Biomarker Potential of the Urine Peptidome: From Amino Acids Properties to Proteases. Int J Mol Sci 2021; 22:5940. [PMID: 34073067 PMCID: PMC8197949 DOI: 10.3390/ijms22115940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
Native biofluid peptides offer important information about diseases, holding promise as biomarkers. Particularly, the non-invasive nature of urine sampling, and its high peptide concentration, make urine peptidomics a useful strategy to study the pathogenesis of renal conditions. Moreover, the high number of detectable peptides as well as their specificity set the ground for the expansion of urine peptidomics to the identification of surrogate biomarkers for extra-renal diseases. Peptidomics further allows the prediction of proteases (degradomics), frequently dysregulated in disease, providing a complimentary source of information on disease pathogenesis and biomarkers. Then, what does urine peptidomics tell us so far? In this paper, we appraise the value of urine peptidomics in biomarker research through a comprehensive analysis of all datasets available to date. We have mined > 50 papers, addressing > 30 different conditions, comprising > 4700 unique peptides. Bioinformatic tools were used to reanalyze peptide profiles aiming at identifying disease fingerprints, to uncover hidden disease-specific peptides physicochemical properties and to predict the most active proteases associated with their generation. The molecular patterns found in this study may be further validated in the future as disease biomarker not only for kidney diseases but also for extra-renal conditions, as a step forward towards the implementation of a paradigm of predictive, preventive and personalized (3P) medicine.
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Affiliation(s)
- Fábio Trindade
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - António S. Barros
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - Jéssica Silva
- iBiMED—Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece;
| | - Inês Falcão-Pires
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - Sofia Guedes
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
| | - Carla Vitorino
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Center for Neurosciences and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Rita Ferreira
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
| | - Adelino Leite-Moreira
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
| | - Francisco Amado
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
| | - Rui Vitorino
- UnIC—Cardiovascular Research and Development Centre, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (A.S.B.); (I.F.-P.); (A.L.-M.)
- iBiMED—Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal;
- LAQV-REQUIMTE, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (S.G.); (R.F.); (F.A.)
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14
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Nanamatsu A, Mori T, Ando F, Furusho T, Mandai S, Susa K, Sohara E, Rai T, Uchida S. Vasopressin Induces Urinary Uromodulin Secretion By Activating PKA (Protein Kinase A). Hypertension 2021; 77:1953-1963. [PMID: 33896194 DOI: 10.1161/hypertensionaha.121.17127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Azuma Nanamatsu
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Taisuke Furusho
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Tatemitsu Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, (TMDU) Bunkyo, Japan
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15
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Abstract
INTRODUCTION The continuous technical improvement in sensitivity and specificity placed mass spectrometry as an alternative method for analyzing clinical samples. In parallel to the rapid development of discovery proteomics, targeted acquisition has been implemented as a complementary option for measuring a small set of proteins with high sensitivity and robustness in a large sample cohort. The combination of trapped ion mobility with a rapid time-of-flight (TOF) mass spectrometer improves the sensitivity even further and triggers the development of prm-PASEF. AREAS COVERED This article discusses the development of prm-PASEF and its advantages over the existing targeted and discovery methods for analyzing clinical samples. We are also highlighting the different requirements for the use of prm-PASEF on clinical samples. EXPERT OPINION prm-PASEF takes advantage of a dual ion-mobility trap enabling highly multiplexed targeted acquisition. It allows the implementation of a short chromatographic separation setup without sacrificing the number of targeted peptides. Analyzing clinical samples by prm-PASEF holds the promise to significantly improve throughput while maintaining sensitivity to detect the selected target proteins.
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Affiliation(s)
- Antoine Lesur
- Head of the Proteomics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Gunnar Dittmar
- Co-Head of the Quantitative Biology Unit, Proteomics of Cellular Signaling Research Group Luxembourg Institute of Health, Strassen, Luxembourg
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16
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Mavrogeorgis E, Mischak H, Beige J, Latosinska A, Siwy J. Understanding glomerular diseases through proteomics. Expert Rev Proteomics 2021; 18:137-157. [PMID: 33779448 DOI: 10.1080/14789450.2021.1908893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Chronic kidney disease is avery common and complex chronic disease. Uncovering the pathological patterns of CKD on the molecular level of bio-fluids and tissue appears to be both vital and promising for a more favorable outcome. We reviewed recently discovered proteomics biomarkers for CKD to provide new insight into disease pathology. AREAS COVERED We review the application of proteome analysis in the context of CKD with various etiologies within the last 5 years. Proteins and peptides associated with CKD as derived from multiple sources (urine, blood and tissue) are reported along with their various biological pathways. EXPERT OPINION A systematic and theoretical comprehension of the CKD pathology is essential for its successful management. The underlying complexity of the disease further requires specific conditions for reliable and interpretable results. In this context, clinical proteomics has resulted in first encouraging findings in CKD. A more complete understanding of the biological pathways related to the disease, based on the scope of a holistic proteomic approach, could improve substantially the management of CKD, especially when in conjunction with the current trend of personalized medicine.
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Affiliation(s)
| | - H Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - J Beige
- Division of Nephrology and KfH Renal Unit, Hospital St. Georg, Leipzig, Germany.,Department of Internal Medicine 2 (Nephrology, Rheumatology, Endocrinology), Martin-Luther-University Halle, Wittenberg, Germany
| | | | - J Siwy
- Mosaiques Diagnostics GmbH, Hannover, Germany
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17
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Abstract
Uromodulin, a protein exclusively produced by the kidney, is the most abundant urinary protein in physiological conditions. Already described several decades ago, uromodulin has gained the spotlight in recent years, since the discovery that mutations in its encoding gene UMOD cause a renal Mendelian disease (autosomal dominant tubulointerstitial kidney disease) and that common polymorphisms are associated with multifactorial disorders, such as chronic kidney disease, hypertension, and cardiovascular diseases. Moreover, variations in uromodulin levels in urine and/or blood reflect kidney functioning mass and are of prognostic value for renal function, cardiovascular events, and overall mortality. The clinical relevance of uromodulin reflects its multifunctional nature, playing a role in renal ion transport and immunomodulation, in protection against urinary tract infections and renal stones, and possibly as a systemic antioxidant. Here, we discuss the multifaceted roles of this protein in kidney physiology and its translational relevance.
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Affiliation(s)
- Céline Schaeffer
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy;
| | - Olivier Devuyst
- Mechanisms of Inherited Kidney Disorders Group, University of Zurich, CH-8057 Zurich, Switzerland
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy;
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18
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Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.
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Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
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19
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In vitro and in silico analysis of dual-function peptides derived from casein hydrolysate. FOOD SCIENCE AND HUMAN WELLNESS 2021. [DOI: 10.1016/j.fshw.2020.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Inhibition of BRD4 Reduces Neutrophil Activation and Adhesion to the Vascular Endothelium Following Ischemia Reperfusion Injury. Int J Mol Sci 2020; 21:ijms21249620. [PMID: 33348732 PMCID: PMC7767067 DOI: 10.3390/ijms21249620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
Renal ischemia reperfusion injury (IRI) is associated with inflammation, including neutrophil infiltration that exacerbates the initial ischemic insult. The molecular pathways involved are poorly characterized and there is currently no treatment. We performed an in silico analysis demonstrating changes in NFκB-mediated gene expression in early renal IRI. We then evaluated NFκB-blockade with a BRD4 inhibitor on neutrophil adhesion to endothelial cells in vitro, and tested BRD4 inhibition in an in vivo IRI model. BRD4 inhibition attenuated neutrophil adhesion to activated endothelial cells. In vivo, IRI led to increased expression of cytokines and adhesion molecules at 6 h post-IRI with sustained up-regulated expression to 48 h post-IRI. These effects were attenuated, in part, with BRD4 inhibition. Absolute neutrophil counts increased significantly in the bone marrow, blood, and kidney 24 h post-IRI. Activated neutrophils increased in the blood and kidney at 6 h post-IRI and remained elevated in the kidney until 48 h post-IRI. BRD4 inhibition reduced both total and activated neutrophil counts in the kidney. IRI-induced tubular injury correlated with neutrophil accumulation and was reduced by BRD4 inhibition. In summary, BRD4 inhibition has important systemic and renal effects on neutrophils, and these effects are associated with reduced renal injury.
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21
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Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nat Rev Nephrol 2020; 17:205-219. [PMID: 33028957 DOI: 10.1038/s41581-020-00348-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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22
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Latosinska A, Siwy J, Faguer S, Beige J, Mischak H, Schanstra JP. Value of Urine Peptides in Assessing Kidney and Cardiovascular Disease. Proteomics Clin Appl 2020; 15:e2000027. [PMID: 32710812 DOI: 10.1002/prca.202000027] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/18/2020] [Indexed: 12/14/2022]
Abstract
Urinary peptides gained significant attention as potential biomarkers especially in the context of kidney and cardiovascular disease. In this manuscript the recent literature since 2015 on urinary peptide investigation in human kidney and cardiovascular disease is reviewed. The technology most commonly used in this context is capillary electrophoresis coupled mass spectrometry, in part owed to the large database available and the well-defined dataspace. Several studies based on over 1000 subjects are reported in the recent past, especially examining CKD273, a classifier for assessment of chronic kidney disease based on 273 urine peptides. Interestingly, the most abundant urinary peptides are generally collagen fragments, which may have gone undetected for some time as they are typically modified via proline hydroxylation. The data available suggest that urinary peptides specifically depict inflammation and fibrosis, and may serve as a non-invasive tool to assess fibrosis, which appears to be a key driver in kidney and cardiovascular disease. The recent successful completion of the first urinary peptide guided intervention trial, PRIORITY, is expected to further spur clinical application of urinary peptidomics, aiming especially at early detection of chronic diseases, prediction of progression, and prognosis of drug response.
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Affiliation(s)
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Stanislas Faguer
- Département de Néphrologie et Transplantation d'organes, Centre de référence des maladies rénales rares, Centre Hospitalier Universitaire de Toulouse, 1, Avenue Jean Poulhes, Toulouse, 31059, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France.,Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
| | - Joachim Beige
- Department of Nephrology and Kuratorium for Dialysis and Transplantation Renal Unit, Hospital St Georg, Delitzscher Str. 141, 04129, Leipzig, Germany.,Department of Nephrology, Martin-Luther-University Halle/Wittenberg, Universitätsplatz 10, 06108, Halle (Saale), Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France.,Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
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23
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Van JAD, Clotet-Freixas S, Hauschild AC, Batruch I, Jurisica I, Elia Y, Mahmud FH, Sochett E, Diamandis EP, Scholey JW, Konvalinka A. Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes. PLoS One 2020; 15:e0233639. [PMID: 32453760 PMCID: PMC7250451 DOI: 10.1371/journal.pone.0233639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/09/2020] [Indexed: 01/09/2023] Open
Abstract
Diabetes is the leading cause of end-stage renal disease worldwide. Our understanding of the early kidney response to chronic hyperglycemia remains incomplete. To address this, we first investigated the urinary proteomes of otherwise healthy youths with and without type 1 diabetes and subsequently examined the enriched pathways that might be dysregulated in early disease using systems biology approaches. This cross-sectional study included two separate cohorts for the discovery (N = 30) and internal validation (N = 30) of differentially excreted proteins. Discovery proteomics was performed on a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer. We then searched the pathDIP, KEGG, and Reactome databases to identify enriched pathways in early diabetes; the Integrated Interactions Database to retrieve protein-protein interaction data; and the PubMed database to compare fold changes of our signature proteins with those published in similarly designed studies. Proteins were selected for internal validation based on pathway enrichment and availability of commercial enzyme-linked immunosorbent assay kits. Of the 2451 proteins identified, 576 were quantified in all samples from the discovery cohort; 34 comprised the urinary signature for early diabetes after Benjamini-Hochberg adjustment (Q < 0.05). The top pathways associated with this signature included lysosome, glycosaminoglycan degradation, and innate immune system (Q < 0.01). Notably, all enzymes involved in keratan sulfate degradation were significantly elevated in urines from youths with diabetes (|fold change| > 1.6). Increased urinary excretion of monocyte differentiation antigen CD14, hexosaminidase A, and lumican was also observed in the validation cohort (P < 0.05). Twenty-one proteins from our signature have been reported elsewhere as potential mediators of early diabetes. In this study, we identified a urinary proteomic signature for early type 1 diabetes, of which lysosomal enzymes were major constituents. Our findings highlight novel pathways such as keratan sulfate degradation in the early kidney response to hyperglycemia.
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Affiliation(s)
- Julie A. D. Van
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- * E-mail:
| | - Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Anne-Christin Hauschild
- Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Mathematics & Computer Science, University of Marburg, Marburg, Germany
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Yesmino Elia
- Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, University of Toronto, Toronto, Canada
| | - James W. Scholey
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
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