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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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Jordaens S, Zwaenepoel K, Tjalma W, Deben C, Beyers K, Vankerckhoven V, Pauwels P, Vorsters A. Urine biomarkers in cancer detection: A systematic review of preanalytical parameters and applied methods. Int J Cancer 2023; 152:2186-2205. [PMID: 36647333 DOI: 10.1002/ijc.34434] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/25/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023]
Abstract
The aim of this review was to explore the status of urine sampling as a liquid biopsy for noninvasive cancer research by reviewing used preanalytical parameters and protocols. We searched two main health sciences databases, PubMed and Web of Science. From all eligible publications (2010-2022), information was extracted regarding: (a) study population characteristics, (b) cancer type, (c) urine preanalytics, (d) analyte class, (e) isolation method, (f) detection method, (g) comparator used, (h) biomarker type, (i) conclusion and (j) sensitivity and specificity. The search query identified 7835 records, of which 924 unique publications remained after screening the title, abstract and full text. Our analysis demonstrated that many publications did not report information about the preanalytical parameters of their urine samples, even though several other studies have shown the importance of standardization of sample handling. Interestingly, it was noted that urine is used for many cancer types and not just cancers originating from the urogenital tract. Many different types of relevant analytes have been shown to be found in urine. Additionally, future considerations and recommendations are discussed: (a) the heterogeneous nature of urine, (b) the need for standardized practice protocols and (c) the road toward the clinic. Urine is an emerging liquid biopsy with broad applicability in different analytes and several cancer types. However, standard practice protocols for sample handling and processing would help to elaborate the clinical utility of urine in cancer research, detection and disease monitoring.
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Affiliation(s)
- Stephanie Jordaens
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Novosanis NV, Wijnegem, Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Wiebren Tjalma
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Multidisciplinary Breast Clinic, Gynecological Oncology Unit, Department of Obstetrics and Gynecology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Christophe Deben
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | | | - Vanessa Vankerckhoven
- Novosanis NV, Wijnegem, Belgium.,Center for Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Alex Vorsters
- Center for Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
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Peng L, Cao Z, Wang Q, Fang L, Yan S, Xia D, Wang J, Bi L. Screening of possible biomarkers and therapeutic targets in kidney renal clear cell carcinoma: Evidence from bioinformatic analysis. Front Oncol 2022; 12:963483. [PMID: 36313709 PMCID: PMC9606658 DOI: 10.3389/fonc.2022.963483] [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: 06/11/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Renal cell carcinoma (RCC), as one of the most common urological malignancies, has many histologic and molecular subtypes, among which clear cell renal cell carcinoma (ccRCC) is one of the most common causes of tumor-related deaths. However, the molecular mechanism of ccRCC remains unclear. In order to identify the candidate genes that may exist in the occurrence and development of ccRCC, microarray datasets GSE6344, GSE16441, GSE36895, GSE53757 and GSE76351 had been downloaded from Gene Expression Omnibus (GEO) database. Apart from that, the differentially expressed genes (DEGs) were screened through Bioinformatics & Evolutionary Genomics. In addition, the protein-protein interaction network (PPI) was constructed, and the module analysis was performed using STRING and Cytoscape. By virtue of DAVID online database, GO/KEGG enrichment analysis of DEGs was performed. Consequently, a total of 118 DEGs were screened, including 24 up-regulated genes and 94 down-regulated genes. The plug-in MCODE of Cytoscape was adopted to analyze the most significant modules of DEGs. What’s more, the genes with degree greater than 10 in DEGs were selected as the hub genes. The overall survival (OS) and disease progression free survival (DFS) of 9 hub genes were analyzed through GEPIA2 online platform. As shown by the survival analysis, SLC34A1, SLC12A3, SLC12A1, PLG, and ENO2 were closely related to the OS of ccRCC, whereas SLC34A1 and LOX were closely related to DFS. Among 11 SLC members, 6 SLC members were highly expressed in non-cancerous tissues (SLC5A2, SLC12A1, SLC12A3, SLC34A1, SLC34A2, SLC34A3). Besides, SLC12A5 and SLC12A7 were highly expressed in ccRCC. Furthermore, SLC12A1-A7, SLC34A1 and SLC34A3 were closely related to OS, whereas SLC12A2/A4/A6/A7 and SLC34A1/A3 were closely related to DFS. In addition, 5 algorithms were used to analyze hub genes, the overlapping genes were AQP2 and KCNJ1. To sum up, hub gene can help us understand the molecular mechanism of the occurrence and development of ccRCC, thereby providing a theoretical basis for the diagnosis and targeted therapy of ccRCC.
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Revealing the Hidden Diagnostic Clues of Male Infertility from Human Seminal Plasma by Dispersive Solid Phase Extraction and MALDI-TOF MS. Int J Mol Sci 2022; 23:ijms231810786. [PMID: 36142695 PMCID: PMC9506103 DOI: 10.3390/ijms231810786] [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: 07/27/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Seminal plasma (SP) mirrors the local pathophysiology of the male reproductive system and represents a non-invasive fluid for the study of infertility. Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) provides a high-throughput platform to rapidly extrapolate the diagnostic profiles of information-rich patterns. In this study, dispersive solid phase extraction (d-SPE) combined with MALDI-TOF-MS was applied for the first time to the human SP, with the aim of revealing a diagnostic signature for male infertility. Commercially available octadecyl (C18)-, octyl (C8)-bonded silica sorbents and hexagonal mesoporous silica (HMS) were tested and the robustness of MALDI-TOF peptide profiling was evaluated. Best performances were obtained for C18-bonded silica with the highest detection of peaks and the lowest variation of spectral features. To assess the diagnostic potential of the method, C18-bonded silica d-SPE and MALDI-TOF-MS were used to generate enriched endogenous peptide profiles of SP from 15 fertile and 15 non-fertile donors. Principal component analysis (PCA) successfully separated fertile from non-fertile men into two different clusters. An array of seven semenogelin-derived peptides was found to distinguish the two groups, with high statistical significance. These findings, while providing a rapid and convenient route to selectively enrich native components of SP peptidome, strongly reinforce the prominent role of semenogelins in male infertility.
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Johnson M, Nowlan S, Sahin G, Barnett DA, Joy AP, Touaibia M, Cuperlovic-Culf M, Zofija Avizonis D, Turcotte S. Decrease of Intracellular Glutamine by STF-62247 Results in the Accumulation of Lipid Droplets in von Hippel-Lindau Deficient Cells. Front Oncol 2022; 12:841054. [PMID: 35223522 PMCID: PMC8865074 DOI: 10.3389/fonc.2022.841054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
Kidney cancer is one of the top ten cancer diagnosed worldwide and its incidence has increased the last 20 years. Clear Cell Renal Cell Carcinoma (ccRCC) are characterized by mutations that inactivate the von Hippel-Lindau (VHL) tumor suppressor gene and evidence indicated alterations in metabolic pathways, particularly in glutamine metabolism. We previously identified a small molecule, STF-62247, which target VHL-deficient renal tumors by affecting late-stages of autophagy and lysosomal signaling. In this study, we investigated ccRCC metabolism in VHL-deficient and proficient cells exposed to the small molecule. Metabolomics profiling using 1H NMR demonstrated that STF-62247 increases levels of glucose, pyruvate, glycerol 3-phosphate while glutamate, asparagine, and glutathione significantly decreased. Diminution of glutamate and glutamine was further investigated using mass spectrometry, western blot analyses, enzymatic activities, and viability assays. We found that expression of SLC1A5 increases in VHL-deficient cells treated with STF-62247, possibly to stimulate glutamine uptake intracellularly to counteract the diminution of this amino acid. However, exogenous addition of glutamine was not able to rescue cell viability induced by the small molecule. Instead, our results showed that VHL-deficient cells utilize glutamine to produce fatty acid in response to STF-62247. Surprisingly, this occurs through oxidative phosphorylation in STF-treated cells while control cells use reductive carboxylation to sustain lipogenesis. We also demonstrated that STF-62247 stimulated expression of stearoyl-CoA desaturase (SCD1) and peripilin2 (PLIN2) to generate accumulation of lipid droplets in VHL-deficient cells. Moreover, the carnitine palmitoyltransferase 1A (CPT1A), which control the entry of fatty acid into mitochondria for β-oxidation, also increased in response to STF-62247. CPT1A overexpression in ccRCC is known to limit tumor growth. Together, our results demonstrated that STF-62247 modulates cellular metabolism of glutamine, an amino acid involved in the autophagy-lysosome process, to support lipogenesis, which could be implicated in the signaling driving to cell death.
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Affiliation(s)
- Mathieu Johnson
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Sarah Nowlan
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Gülsüm Sahin
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
| | | | - Andrew P Joy
- Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Mohamed Touaibia
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | | | | | - Sandra Turcotte
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada.,Atlantic Cancer Research Institute, Moncton, NB, Canada
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6
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Flitcroft JG, Verheyen J, Vemulkar T, Welbourne EN, Rossi SH, Welsh SJ, Cowburn RP, Stewart GD. Early detection of kidney cancer using urinary proteins: a truly non-invasive strategy. BJU Int 2021; 129:290-303. [PMID: 34570419 DOI: 10.1111/bju.15601] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES To review urinary protein biomarkers as potential non-invasive, easily obtainable, early diagnostic tools in renal cell carcinoma (RCC). METHODS A PubMed database search was performed up to the year 2020 to identify primary studies reporting potential urinary protein biomarkers for RCC. Separate searches were conducted to identify studies describing appropriate methods of developing cancer screening programmes and detection of cancer biomarkers. RESULTS Several urinary protein biomarkers are under validation for RCC diagnostics, e.g. aquaporin-1, perilipin-2, carbonic anhydrase-9, Raf-kinase inhibitory protein, nuclear matrix protein-22, 14-3-3 Protein β/α and neutrophil gelatinase-associated lipocalin. However, none has yet been validated or approved for clinical use due to low sensitivity or specificity, inconsistencies in appropriate study design, or lack of external validation. CONCLUSIONS Evaluation of biomarkers' feasibility, sample preparation and storage, biomarker validation, and the application of novel technologies may provide a solution that maximises the potential for a truly non-invasive biomarker in early RCC diagnostics.
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Affiliation(s)
- Jordan G Flitcroft
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Jeroen Verheyen
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Tarun Vemulkar
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Emma N Welbourne
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Sabrina H Rossi
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Sarah J Welsh
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Russell P Cowburn
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Grant D Stewart
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
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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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Clark DJ, Zhang H. Proteomic approaches for characterizing renal cell carcinoma. Clin Proteomics 2020; 17:28. [PMID: 32742246 PMCID: PMC7391522 DOI: 10.1186/s12014-020-09291-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 12/24/2022] Open
Abstract
Renal cell carcinoma is among the top 15 most commonly diagnosed cancers worldwide, comprising multiple sub-histologies with distinct genomic, proteomic, and clinicopathological features. Proteomic methodologies enable the detection and quantitation of protein profiles associated with the disease state and have been explored to delineate the dysregulated cellular processes associated with renal cell carcinoma. In this review we highlight the reports that employed proteomic technologies to characterize tissue, blood, and urine samples obtained from renal cell carcinoma patients. We describe the proteomic approaches utilized and relate the results of studies in the larger context of renal cell carcinoma biology. Moreover, we discuss some unmet clinical needs and how emerging proteomic approaches can seek to address them. There has been significant progress to characterize the molecular features of renal cell carcinoma; however, despite the large-scale studies that have characterized the genomic and transcriptomic profiles, curative treatments are still elusive. Proteomics facilitates a direct evaluation of the functional modules that drive pathobiology, and the resulting protein profiles would have applications in diagnostics, patient stratification, and identification of novel therapeutic interventions.
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Affiliation(s)
- David J. Clark
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA
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Abstract
A crucial step for tumor cell extravasation and metastasis is the migration through the extracellular matrix, which requires proteolytic activity. Hence, proteases, particularly matrix metalloproteases (MMPs), have been discussed as therapeutic targets and their inhibition should diminish tumor growth and metastasis. The metalloproteases meprin α and meprin β are highly abundant on intestinal enterocytes and their expression was associated with different stages of colorectal cancer. Due to their ability to cleave extracellular matrix (ECM) components, they were suggested as pro-tumorigenic enzymes. Additionally, both meprins were shown to have pro-inflammatory activity by cleaving cytokines and their receptors, which correlates with chronic intestinal inflammation and associated conditions. On the other hand, meprin β was identified as an essential enzyme for the detachment and renewal of the intestinal mucus, important to prevent bacterial overgrowth and infection. Considering this, it is hard to estimate whether high activity of meprins is generally detrimental or if these enzymes have also protective functions in certain cancer types. For instance, for colorectal cancer, patients with high meprin β expression in tumor tissue exhibit a better survival prognosis, which is completely different to prostate cancer. This demonstrates that the very same enzyme may have contrary effects on tumor initiation and growth, depending on its tissue and subcellular localization. Hence, precise knowledge about proteolytic enzymes is required to design the most efficient therapeutic options for cancer treatment. In this review, we summarize the current findings on meprins' functions, expression, and cancer-associated variants with possible implications for tumor progression and metastasis.
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10
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Identification of Prognostic Biomarkers in the Urinary Peptidome of the Small Renal Mass. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:2366-2376. [DOI: 10.1016/j.ajpath.2019.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 01/10/2023]
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11
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Kandil NS, Ghazala RA, El Sharkawy RM, Youssif TA, Noha Abouseda N. Evaluation of Protein Profiling in a Cohort of Egyptian Population with Renal Cell Carcinoma and Benign Kidney Neoplasms. Asian Pac J Cancer Prev 2019; 20:2145-2152. [PMID: 31350978 PMCID: PMC6745217 DOI: 10.31557/apjcp.2019.20.7.2145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/13/2019] [Indexed: 12/27/2022] Open
Abstract
Abdominal imaging leads to the detection of a large number of renal tumors without the ability to distinguish the type of tumor detected. It is necessary to find a precise way to know the type of tumor to determine the appropriate treatment. The use of urine samples for detecting new biomarkers especially proteins has a great potential. In this work we assessed the proteomic profiling difference in a cohort of Egyptian population with renal neoplasms. Methods: This cohort study was conducted on 85 subjects. They were classified as 40 RCC, 15 benign kidney patients, and 30 healthy controls. Morning urine samples were used for peptidome separation using magnetic beads. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was applied Using FlexControlTM software. Results: Benign tumors were differentiated from controls by 5 integrated peaks, 12 significant and 2 integrated significant peaks, 17:3,418.8 and 25:4,173.41. While RCC were differentiated from benign by 5 integrated, 28 significant and one integrated significant peak. The RCC group was discriminated from the controls by 5 peaks which were integrated from which 1 was integrated and significant (with mass to charge ratio of 12:3,408.97). The three groups showed protein profiles ranging from 1 to 10 kDa. The external validation was performed for the RCC group versus the control reveled sensitivity of 88.7% and specificity of 73.2% by genetic algorithm. Conclusion: Proteomic approach can be used as a sensitive urinary marker differentiating renal masses in an early diagnostic approach.
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Affiliation(s)
- Noha Said Kandil
- Department of Chemical Pathology, Medical Research Institute, Faculty of Medicine, Alexandria University, Egypt.
| | | | - Rania Mohamed El Sharkawy
- Department of Chemical Pathology, Medical Research Institute, Faculty of Medicine, Alexandria University, Egypt.
| | - Tamer Abou Youssif
- Department of Urology, Faculty of Medicine, Alexandria University, Egypt
| | - Noha Noha Abouseda
- Department of Microbiology, Faculty of Medicine, Alexandria University, Egypt
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12
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Frantzi M, Latosinska A, Belczacka I, Mischak H. Urinary proteomic biomarkers in oncology: ready for implementation? Expert Rev Proteomics 2018; 16:49-63. [PMID: 30412678 DOI: 10.1080/14789450.2018.1547193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Biomarkers are expected to improve the management of cancer patients by enabling early detection and prediction of therapeutic response. Proteins reflect a molecular phenotype, have high potential as biomarkers, and also are key targets for intervention. Given the ease of collection and proximity to certain tumors, the urinary proteome is a rich source of biomarkers and several proteins have been already implemented. Areas covered: We examined the literature on urine proteins and proteome analysis in oncology from reports published during the last 5 years to generate an overview on the status of urine protein and peptide biomarkers, with emphasis on their actual clinical value. Expert commentary: A few studies report on biomarkers that are ready to be implemented in patient management, among others in bladder cancer and cholangiocarcinoma. These reports are based on multi-marker approaches. A high number of biomarkers, though, has been described in studies with low statistical power. In fact, several of them have been consistently reported across different studies. The latter should be the focus of attention and be tested in properly designed confirmatory and ultimately, prospective investigations. It is expected that multi-marker classifiers for a specific context-of-use, will be the preferred path toward clinical implementation.
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Affiliation(s)
- Maria Frantzi
- a Research and Development , Mosaiques Diagnostics GmbH , Hannover , Germany
| | | | - Iwona Belczacka
- a Research and Development , Mosaiques Diagnostics GmbH , Hannover , Germany
| | - Harald Mischak
- a Research and Development , Mosaiques Diagnostics GmbH , Hannover , Germany
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Lichner Z, Saleeb R, Butz H, Ding Q, Nofech-Mozes R, Riad S, Farag M, Varkouhi AK, Dos Santos CC, Kapus A, Yousef GM. Sunitinib induces early histomolecular changes in a subset of renal cancer cells that contribute to resistance. FASEB J 2018; 33:1347-1359. [PMID: 30148679 DOI: 10.1096/fj.201800596r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sunitinib is the standard-of-care, first-line treatment for advanced renal cell carcinoma (RCC). Characteristics of treatment-resistant RCC have been described; however, complex tumor adaptation mechanisms obstruct the identification of significant operators in resistance. We hypothesized that resistance is a late manifestation of early, treatment-induced histomolecular alterations; therefore, studying early drug response may identify drivers of resistance. We describe an epithelioid RCC growth pattern in RCC xenografts, which emerges in sunitinib-sensitive tumors and is augmented during resistance. This growth modality is molecularly and morphologically related to the RCC spheroids that advance during in vitro treatment. Based on time-lapse microscopy, mRNA and microRNA screening, and tumor behavior-related characteristics, we propose that the spheroid and adherent RCC growth patterns differentially respond to sunitinib. Gene expression analysis indicated that sunitinib promoted spheroid formation, which provided a selective survival advantage under treatment. Functional studies confirm that E-cadherin is a key contributor to the survival of RCC cells under sunitinib treatment. In summary, we suggest that sunitinib-resistant RCC cells exist in treatment-sensitive tumors and are histologically identifiable.-Lichner, Z., Saleeb, R., Butz, H., Ding, Q., Nofech-Mozes, R., Riad, S., Farag, M., Varkouhi, A. K., dos Santos, C. C., Kapus, A., Yousef, G. M. Sunitinib induces early histomolecular changes in a subset of renal cancer cells that contribute to resistance.
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Affiliation(s)
- Zsuzsanna Lichner
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rola Saleeb
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Henriett Butz
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University (HAS-SE), Budapest, Hungary
| | - Qiang Ding
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Roy Nofech-Mozes
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Sara Riad
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Mina Farag
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Amir K Varkouhi
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Viral Vector and Cell Therapy Core (VICTOR), St. Michael's Hospital, Toronto, Ontario, Canada
| | - Claudia C Dos Santos
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Viral Vector and Cell Therapy Core (VICTOR), St. Michael's Hospital, Toronto, Ontario, Canada.,Interdepartmental Division of Critical Care University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - András Kapus
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Surgery, University of Toronto, Toronto, Ontario, Canada; and.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - George M Yousef
- The Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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14
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Papale M, Vocino G, Lucarelli G, Rutigliano M, Gigante M, Rocchetti MT, Pesce F, Sanguedolce F, Bufo P, Battaglia M, Stallone G, Grandaliano G, Carrieri G, Gesualdo L, Ranieri E. Urinary RKIP/p-RKIP is a potential diagnostic and prognostic marker of clear cell renal cell carcinoma. Oncotarget 2018; 8:40412-40424. [PMID: 28418894 PMCID: PMC5522321 DOI: 10.18632/oncotarget.16341] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/21/2017] [Indexed: 11/25/2022] Open
Abstract
Clear cell Renal Cell Carcinoma (ccRCC) causes over 13,000 deaths each year, and about 20,000 new cases/year in Europe. In most cases, the causes are unknown and, most importantly, there are no reliable biomarkers for the diagnosis and prognosis of this disease. The search for sensitive biomarkers for early diagnosis and prognosis of clear cell Renal Cell Carcinoma (ccRCC) is currently a fast growing field. We carried out proteomics analysis of 93 urinary samples of healthy subjects (HS) and patients affected by ccRCC, prostate cancer (PCa) and chronic kidney disease (CKD), that was able to successfully distinguish each group. The most significant candidate biomarker was identified by mass spectrometry as Raf Kinase Inhibitor Protein (RKIP), a key regulator of cell signaling, already described in several cancer types as a metastasis suppressor. By combining ELISA, immunoblotting and tissue microarray, we demonstrated that, in ccRCC, urinary excretion of RKIP and its phosphorylated form (p-RKIP) reflected the tissue expression of these putative biomarkers. Baseline urinary RKIP, evaluated in an independent cohort of 56 ccRCC patients and 28 HS, successfully distinguished both groups and, most importantly, a cut-off value of 10 ng/mg/g Pr/uCr enabled a highly accurate prediction of Cancer-specific survival and Progression-free survival. Furthermore, p-RKIP was totally undetectable in both tissue and urine samples of ccRCC, showing a great potential for diagnostics purposes. Our data indicate that urinary RKIP encompasses both the unphosphorylated and the phosphorylated form and that their combined evaluation can help in the diagnosis and prognosis of ccRCC.
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Affiliation(s)
- Massimo Papale
- Molecular Medicine Center, Section of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy.,Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Grazia Vocino
- Molecular Medicine Center, Section of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Giuseppe Lucarelli
- Division of Urology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Monica Rutigliano
- Division of Urology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Margherita Gigante
- Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Maria Teresa Rocchetti
- Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Francesco Pesce
- Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | | | - Pantaleo Bufo
- Department of Pathology, University of Foggia, Foggia, Italy
| | - Michele Battaglia
- Division of Urology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Giovanni Stallone
- Division of Nephrology, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Giuseppe Grandaliano
- Division of Nephrology, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Giuseppe Carrieri
- Division of Urology, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Loreto Gesualdo
- Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Elena Ranieri
- Molecular Medicine Center, Section of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
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15
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MALDI-TOF-MS analysis in discovery and identification of serum proteomic patterns of ovarian cancer. BMC Cancer 2017; 17:472. [PMID: 28683725 PMCID: PMC5501370 DOI: 10.1186/s12885-017-3467-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/30/2017] [Indexed: 12/11/2022] Open
Abstract
Background Due to high mortality and lack of efficient screening, new tools for ovarian cancer (OC) diagnosis are urgently needed. To broaden the knowledge on the pathological processes that occur during ovarian cancer tumorigenesis, protein-peptide profiling was proposed. Methods Serum proteomic patterns in samples from OC patients were obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Eighty nine serum samples (44 ovarian cancer and 45 healthy controls) were pretreated using solid-phase extraction method. Next, a classification model with the most discriminative factors was identified using chemometric algorithms. Finally, the results were verified by external validation on an independent test set of samples. Results Main outcome of this study was an identification of potential OC biomarkers by applying liquid chromatography coupled with tandem mass spectrometry. Application of this novel strategy enabled the identification of four potential OC serum biomarkers (complement C3, kininogen-1, inter-alpha-trypsin inhibitor heavy chain H4, and transthyretin). The role of these proteins was discussed in relation to OC pathomechanism. Conclusions The study results may contribute to the development of clinically useful multi-component diagnostic tools in OC. In addition, identifying a novel panel of discriminative proteins could provide a new insight into complex signaling and functional networks associated with this multifactorial disease. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3467-2) contains supplementary material, which is available to authorized users.
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16
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Di Meo A, Bartlett J, Cheng Y, Pasic MD, Yousef GM. Liquid biopsy: a step forward towards precision medicine in urologic malignancies. Mol Cancer 2017; 16:80. [PMID: 28410618 PMCID: PMC5391592 DOI: 10.1186/s12943-017-0644-5] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/28/2017] [Indexed: 12/12/2022] Open
Abstract
There is a growing trend towards exploring the use of a minimally invasive "liquid biopsy" to identify biomarkers in a number of cancers, including urologic malignancies. Multiple aspects can be assessed in circulating cell-free DNA, including cell-free DNA levels, integrity, methylation and mutations. Other prospective liquid biopsy markers include circulating tumor cells, circulating RNAs (miRNA, lncRNAs and mRNAs), cell-free proteins, peptides and exosomes have also emerged as non-invasive cancer biomarkers. These circulating molecules can be detected in various biological fluids, including blood, urine, saliva and seminal plasma. Liquid biopsies hold great promise for personalized medicine due to their ability to provide multiple non-invasive global snapshots of the primary and metastatic tumors. Molecular profiling of circulating molecules has been a stepping-stone to the successful introduction of several non-invasive multi-marker tests into the clinic. In this review, we provide an overview of the current state of cell-free DNA-based kidney, prostate and bladder cancer biomarker research and discuss the potential utility other circulating molecules. We will also discuss the challenges and limitations facing non-invasive cancer biomarker discovery and the benefits of this growing area of translational research.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Jenni Bartlett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Maria D Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, ON, Canada
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.
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17
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Chinello C, L'imperio V, Stella M, Smith AJ, Bovo G, Grasso A, Grasso M, Raimondo F, Pitto M, Pagni F, Magni F. The proteomic landscape of renal tumors. Expert Rev Proteomics 2016; 13:1103-1120. [PMID: 27748142 DOI: 10.1080/14789450.2016.1248415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids. Expert commentary: Currently, no reliable biomarkers or targets for RCC have been translated into the clinical setting. Moreover, despite the efforts of proteomics and other -omics disciplines, only a small number of them have been observed as shared targets between the different analytical platforms and biological specimens. The difficulty to define a specific molecular pattern for RCC and its subtypes highlights a peculiar profile and a heterogeneity that must be taken into account in future studies.
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Affiliation(s)
- Clizia Chinello
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Vincenzo L'imperio
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Martina Stella
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Andrew James Smith
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Giorgio Bovo
- b Pathology unit , San Gerardo Hospital , Monza , Italy
| | - Angelica Grasso
- c Department of Specialistic Surgical Sciences, Urology unit , Ospedale Maggiore Policlinico Foundation , Milano , Italy
| | - Marco Grasso
- d Department of Urology , San Gerardo Hospital , Monza , Italy
| | - Francesca Raimondo
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Marina Pitto
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Fabio Pagni
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Fulvio Magni
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
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18
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Meo AD, Pasic MD, Yousef GM. Proteomics and peptidomics: moving toward precision medicine in urological malignancies. Oncotarget 2016; 7:52460-52474. [PMID: 27119500 PMCID: PMC5239567 DOI: 10.18632/oncotarget.8931] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
Urological malignancies are a major cause of morbidity and mortality worldwide. Advances in early detection, diagnosis, prognosis and prediction of treatment response can significantly improve patient care. Proteomic and peptidomic profiling studies are at the center of kidney, prostate and bladder cancer biomarker discovery and have shown great promise for improved clinical assessment. Mass spectrometry (MS) is the most widely employed method for proteomic and peptidomic analyses. A number of MS platforms have been developed to facilitate accurate identification of clinically relevant markers in various complex biological samples including tissue, urine and blood. Furthermore, protein profiling studies have been instrumental in the successful introduction of several diagnostic multimarker tests into the clinic. In this review, we will provide a brief overview of high-throughput technologies for protein and peptide based biomarker discovery. We will also examine the current state of kidney, prostate and bladder cancer biomarker research as well as review the journey toward successful clinical implementation.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Maria D. Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, Ontario, Canada
| | - George M. Yousef
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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19
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Challenges in biomarker discovery with MALDI-TOF MS. Clin Chim Acta 2016; 458:84-98. [PMID: 27134187 DOI: 10.1016/j.cca.2016.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Abstract
MALDI-TOF MS technique is commonly used in system biology and clinical studies to search for new potential markers associated with pathological conditions. Despite numerous concerns regarding a sample preparation or processing of complex data, this strategy is still recognized as a popular tool and its awareness has risen in the proteomic community over the last decade. In this review, we present comprehensive application of MALDI mass spectrometry with special focus on profiling research. We also discuss major advantages and disadvantages of universal sample preparation methods such as micro-SPE columns, immunodepletion or magnetic beads, and we show the potential of nanostructured materials in capturing low molecular weight subproteomes. Furthermore, as the general protocol considerably affects spectra quality and interpretation, an alternative solution for improved ion detection, including hydrophobic constituents, data processing and statistical analysis is being considered in up-to-date profiling pattern. In conclusion, many reports involving MALDI-TOF MS indicated highly abundant proteins as valuable indicators, and at the same time showed the inaccuracy of available methods in the detection of low abundant proteome that is the most interesting from the clinical perspective. Therefore, the analytical aspects of sample preparation methods should be standardized to provide a reproducible, low sample handling and credible procedure.
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20
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Arena S, Salzano AM, Scaloni A. Identification of protein markers for the occurrence of defrosted material in milk through a MALDI-TOF-MS profiling approach. J Proteomics 2016; 147:56-65. [PMID: 26910555 DOI: 10.1016/j.jprot.2016.02.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/10/2016] [Accepted: 02/16/2016] [Indexed: 12/30/2022]
Abstract
UNLABELLED Mozzarella di Bufala Campana is a soft, stretched curd Italian cheese made from fresh buffalo milk that obtained the Protected Designation of Origin (PDO) registration in EU legislation. Seasonality of buffalo milk production, rapid cheese decay and transport of its preserving liquid have relevant practical/economic consequences for mozzarella production; consequently, a progressive diffusion of cheese products realized with frozen curd or frozen milk has recently been observed. In order to meet the demand of the dairy producers and consumers for a reduction of starting material adulterations and for the certification of the raw milk used for cheese manufacturing, we have developed a rapid/robust MALDI-TOF-MS polypeptide profiling procedure that assays material quality through the identification of specific markers of its freshness. Massive analysis of fresh and frozen buffalo milks (stored for different times) was realized to this purpose; a tough statistical evaluation of the resulting data ultimately permitted the typing of milk samples. We identified 28 polypeptide markers of the milk freezing storage, among which 13 and 15 showed down- and over-representation, respectively. Quantitative data were confirmed by an independent analytical approach on selected markers. GLYCAM1-derived phosphopeptides (1-53), β-casein-derived phosphopeptides (1-68), β-casein-derived γ2-, γ3- and γ4-fragments, α-lactalbumin and β-lactoglobulin were components showing the highest significance. The occurrence of the first compounds in buffalo milk is here described for the first time; their formation in the frozen material was ascribed to the activity of plasmin or of unknown bacterial proteases/peptidases stable at low temperatures. In conclusion, data reported here suggest the application of this MALDI-TOF-MS polypeptide profiling platform to other high-quality dairy productions, in which milk freshness has important consequences on final product organoleptic properties. BIOLOGICAL SIGNIFICANCE In the last decades, several studies have provided the molecular basis underlying the relation between food quality and human wellness/health. In this context, Foodomics emerged as a novel scientific discipline studying food and nutrition domains through the application of advanced omics technologies, including genomics, transcriptomics, proteomics and/or metabolomics. Above-mentioned technologies have been used in an integrated, holistic way to study foods for: i) compound profiling, authenticity, and/or biomarker-detection related to product quality or safety; ii) contaminants and their whole toxicity; iii) bioactivity and general effects on human health; iv) their digestion and assumption in human body; v) development of new transgenic products; and vi) evaluation of their modifications within the digestive tract. In the first context, a highly reproducible MALDI-TOF-MS polypeptide profiling procedure is here presented, which provides information on buffalo milk quality through the identification of specific markers of its freshness. Among identified markers, some were indicative of the action of various proteolytic enzymes and the resulting occurrence of specific defense components in buffalo milk having the physiological role to limit bacterial/virus content in this biological fluid. Data suggest the possible application of similar MALDI-TOF-based platforms to other high-quality food productions, where storage conditions of the starting materials may have important consequences on final product characteristics.
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Affiliation(s)
- Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Anna Maria Salzano
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy.
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy.
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21
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Raimondo F, Cerra D, Magni F, Pitto M. Urinary proteomics for the study of genetic kidney diseases. Expert Rev Proteomics 2016; 13:309-24. [DOI: 10.1586/14789450.2016.1136218] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Chinello C, Cazzaniga M, De Sio G, Smith AJ, Grasso A, Rocco B, Signorini S, Grasso M, Bosari S, Zoppis I, Mauri G, Magni F. Tumor size, stage and grade alterations of urinary peptidome in RCC. J Transl Med 2015; 13:332. [PMID: 26482227 PMCID: PMC4617827 DOI: 10.1186/s12967-015-0693-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/10/2015] [Indexed: 01/23/2023] Open
Abstract
Background Several promising biomarkers have been found for RCC, but none of them has been used in clinical practice for predicting tumour progression. The most widely used features for predicting tumour aggressiveness still remain the cancer stage, size and grade. Therefore, the aim of our study is to investigate the urinary peptidome to search and identify peptides whose concentrations in urine are linked to tumour growth measure and clinical data. Methods A proteomic approach applied to ccRCC urinary peptidome (n = 117) based on prefractionation with activated magnetic beads followed by MALDI-TOF profiling was used. A systematic correlation study was performed on urinary peptide profiles obtained from MS analysis. Peptide identity was obtained by LC–ESI–MS/MS. Results Fifteen, twenty-six and five peptides showed a statistically significant alteration of their urinary concentration according to tumour size, pT and grade, respectively. Furthermore, 15 and 9 signals were observed to have urinary levels statistically modified in patients at different pT or grade values, even at very early stages. Among them, C1RL, A1AGx, ZAG2G, PGBM, MMP23, GP162, ADA19, G3P, RSPH3, DREB, NOTC2 SAFB2 and CC168 were identified. Conclusions We identified several peptides whose urinary abundance varied according to tumour size, stage and grade. Among them, several play a possible role in tumorigenesis, progression and aggressiveness. These results could be a useful starting point for future studies aimed at verifying their possible use in the managements of RCC patients. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0693-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clizia Chinello
- Department of Health Science, School of Medicine, University of Milano-Bicocca (UNIMIB), Via Cadore, 48, 20900, Monza, Italy.
| | - Marta Cazzaniga
- Department of Health Science, School of Medicine, University of Milano-Bicocca (UNIMIB), Via Cadore, 48, 20900, Monza, Italy.
| | - Gabriele De Sio
- Department of Health Science, School of Medicine, University of Milano-Bicocca (UNIMIB), Via Cadore, 48, 20900, Monza, Italy.
| | - Andrew James Smith
- Department of Health Science, School of Medicine, University of Milano-Bicocca (UNIMIB), Via Cadore, 48, 20900, Monza, Italy.
| | - Angelica Grasso
- Urology Unit, Department of Specialistic Surgical Sciences, Ospedale Maggiore Policlinico Foundation, Milan, Italy.
| | - Bernardo Rocco
- Urology Unit, Department of Specialistic Surgical Sciences, Ospedale Maggiore Policlinico Foundation, Milan, Italy.
| | | | - Marco Grasso
- Department of Surgical Pathology, Cytology, Medical Genetics and Nephropathology, Azienda Ospedaliera San Gerardo, Monza, Italy.
| | - Silvano Bosari
- Department of Medicine, Surgery and Dental Sciences, Pathology Unit, IRCCS-Policlinico Foundation, Mangiagalli and Regina Elena, University of Milan, Milan, Italy.
| | - Italo Zoppis
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
| | - Giancarlo Mauri
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.
| | - Fulvio Magni
- Department of Health Science, School of Medicine, University of Milano-Bicocca (UNIMIB), Via Cadore, 48, 20900, Monza, Italy.
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23
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Sandim V, Pereira DDA, Kalume DE, Oliveira-Carvalho AL, Ornellas AA, Soares MR, Alves G, Zingali RB. Proteomic analysis reveals differentially secreted proteins in the urine from patients with clear cell renal cell carcinoma. Urol Oncol 2015; 34:5.e11-25. [PMID: 26420021 DOI: 10.1016/j.urolonc.2015.07.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/04/2015] [Accepted: 07/26/2015] [Indexed: 12/01/2022]
Abstract
OBJECTIVE The aim of this study was to evaluate the differentially secreted protein profile in the urine from patients with clear cell renal cell carcinoma (ccRCC) using mass spectrometry-based methods. Urine composition can reflect kidney physiology and can be used to detect markers for renal diseases. Moreover, characterization of the secretome is likely to assist in the investigation of new drugs for biological targets and diagnose the ccRCC at an early stage. METHODS AND MATERIALS Urine samples from patients were divided according to Fuhrman degree (FI-IV), which was associated with the cellular differentiation as good prognosis (GP) and poor prognosis (PP). Healthy individuals were used as the control group (CG). We used both qualitative and quantitative mass spectrometry-based analyses that involved the following approaches: 1-dimensional gel electrophoresis combined with liquid chromatography mass spectrometry in tandem (1DE LC-MS/MS), in-solution digestion combined with label-free 1-dimensional LC-MS(E) (1D LC-MS(E)), and bidimensional gel electrophoresis combined with matrix-assisted laser desorption/ionization time of flight in tandem (2DE MALDI-TOF/TOF) or combined with LC-MS/MS. RESULTS All the strategies allowed the identification of 354 proteins from the CG, GP, and PP groups. Qualitative experiments using 1DE LC-MS/MS analysis detected different protein profiles, and 224 proteins were identified in all groups. The label-free MS(E) quantitative analysis identified 113 proteins and generated novel information on secreted protein profiles, including 49 up-secreted proteins in the urine from patients with ccRCC and 40 down-secreted proteins related to the CG. Proteins such as kininogen-1, uromodulin, apolipoprotein D, polyubiquitin, and CD59 glycoprotein were down secreted according to the groups CG>GP>PP. In contrast, apolipoprotein A, fibrinogen, and haptoglobin were up secreted in patient groups. The same expression profile observed for kininogen-1, apolipoprotein D, fibrinogen, and haptoglobin was corroborated by 2DE LC-MS/MS or 2DE MALDI-TOF/TOF analyses. These 2 strategies also showed 13 differentially secreted proteins among the 3 groups. CONCLUSIONS The proteins kininogen-1, apolipoprotein D, fibrinogen, and haptoglobin presented similar quantitative protein profiles according to MS(E) and 2DE approaches. The latter proteins were up secreted and the former ones were down-regulated. The strategies used proved to be valuable in identifying proteins that were differentially secreted in urine from patients with RCC.
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Affiliation(s)
- Vanessa Sandim
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Instituto Nacional de Biologia Estrutural e Bioimagem (INBEB), Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Laboratório de Genética Aplicada, Serviço de Hematologia, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil; Laboratório de Marcadores Circulantes, Departamento de Patologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil
| | - Denise de Abreu Pereira
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Instituto Nacional de Biologia Estrutural e Bioimagem (INBEB), Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Laboratório de Genética Aplicada, Serviço de Hematologia, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil; Coordenação Geral de Ensino e Pesquisa, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil
| | - Dário Eluan Kalume
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz - IOC, Fundação Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Lucia Oliveira-Carvalho
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Instituto Nacional de Biologia Estrutural e Bioimagem (INBEB), Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Antonio Augusto Ornellas
- Serviço de Urologia, Instituto Nacional de Câncer - INCA, Rio de Janeiro, Brazil; Serviço de Urologia, Hospital Mário Kroeff, Rio de Janeiro, Brazil
| | - Marcia Regina Soares
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Gilda Alves
- Laboratório de Genética Aplicada, Serviço de Hematologia, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil; Laboratório de Marcadores Circulantes, Departamento de Patologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro - UERJ, Rio de Janeiro, Brazil; Coordenação Geral de Ensino e Pesquisa, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil.
| | - Russolina Benedeta Zingali
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Instituto Nacional de Biologia Estrutural e Bioimagem (INBEB), Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil.
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24
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Majer W, Kluzek K, Bluyssen H, Wesoły J. Potential Approaches and Recent Advances in Biomarker Discovery in Clear-Cell Renal Cell Carcinoma. J Cancer 2015; 6:1105-13. [PMID: 26516358 PMCID: PMC4615346 DOI: 10.7150/jca.12145] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/12/2015] [Indexed: 02/06/2023] Open
Abstract
The early diagnosis and monitoring of clear-cell Renal Cell Carcinoma (ccRCC), which is the most common renal malignancy, remains challenging. The late diagnosis and lack of tools that can be used to assess the progression of the disease and metastasis significantly influence the chance of survival of ccRCC patients. Molecular biomarkers have been shown to aid the diagnosis and disease monitoring for other cancers, but such markers are not currently available for ccRCC. Recently, plasma and serum circulating nucleic acids, nucleic acids present in urine, and plasma and urine proteins gained interest in the field of cancer biomarker discovery. Here, we describe the applicability of plasma and urine nucleic acids as cancer biomarkers with a particular focus on DNA, small RNA, and protein markers for ccRCC.
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Affiliation(s)
- Weronika Majer
- 1. Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 61-614 Poznan, Poland, Tel. +4861 829 5832, Fax. +4861 829 5949
| | - Katarzyna Kluzek
- 2. Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 64-614 Poznan, Tel. +4861 829 5832
| | - Hans Bluyssen
- 2. Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 64-614 Poznan, Tel. +4861 829 5832
| | - Joanna Wesoły
- 1. Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 61-614 Poznan, Poland, Tel. +4861 829 5832, Fax. +4861 829 5949
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25
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Raimondo F, Corbetta S, Savoia A, Chinello C, Cazzaniga M, Rocco F, Bosari S, Grasso M, Bovo G, Magni F, Pitto M. Comparative membrane proteomics: a technical advancement in the search of renal cell carcinoma biomarkers. MOLECULAR BIOSYSTEMS 2015; 11:1708-16. [DOI: 10.1039/c5mb00020c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Set-up of a specific protocol for membrane protein analysis, applied to label free, comparative proteomics of renal cell carcinoma microdomains.
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Affiliation(s)
| | | | - Andrea Savoia
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Clizia Chinello
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Marta Cazzaniga
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Francesco Rocco
- Department of Specialistic Surgical Sciences
- Urology unit
- Ospedale Maggiore Policlinico Foundation
- IRCCS
- Milano
| | - Silvano Bosari
- Department of Medicine
- Surgery and Dental Sciences
- Pathology Unit
- Ospedale Maggiore Policlinico Foundation Milano
- IRCCS
| | - Marco Grasso
- Department of Surgical Pathology
- Cytology
- Medical Genetics and Nephropathology
- Azienda Ospedaliera San Gerardo
- Monza
| | - Giorgio Bovo
- Department of Surgical Pathology
- Cytology
- Medical Genetics and Nephropathology
- Azienda Ospedaliera San Gerardo
- Monza
| | - Fulvio Magni
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Marina Pitto
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
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26
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Bladergroen MR, van der Burgt YEM. Solid-phase extraction strategies to surmount body fluid sample complexity in high-throughput mass spectrometry-based proteomics. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:250131. [PMID: 25692071 PMCID: PMC4322654 DOI: 10.1155/2015/250131] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 05/08/2023]
Abstract
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential. Here we present high-throughput sample preparation solutions for balancing the speed of current MS-acquisitions and the time needed for analytical workup of body fluids. The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches. Various sample preparation methods that involve solid-phase extraction (SPE) including affinity enrichment strategies have been automated. Obtained peptide and protein fractions can be mass analyzed by direct infusion into an electrospray ionization (ESI) source or by means of matrix-assisted laser desorption ionization (MALDI) without further need of time-consuming liquid chromatography (LC) separations.
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Affiliation(s)
- Marco R. Bladergroen
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
- *Yuri E. M. van der Burgt:
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