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Carvalho LB, Martínez JLC, Lodeiro C, Bento R, Dhir R, Morrissey JJ, Pinheiro LC, Medeiros M, Santos HM. Biochemical network analysis of protein-protein interactions to follow-up T1 bladder cancer patients. J Proteomics 2023; 278:104865. [PMID: 36870676 DOI: 10.1016/j.jprot.2023.104865] [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: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Bladder cancer (BCa) is a prevalent disease with a high risk of aggressive recurrence in T1-stage patients. Despite the efforts to anticipate recurrence, a reliable method has yet to be developed. In this work, we employed high-resolution mass spectrometry to compare the urinary proteome of T1-stage BCa patients with recurring versus non-recurring disease to uncover actionable clinical information predicting recurrence. All patients were diagnosed with T1-stage bladder cancer between the ages of 51 and 91, and urine samples were collected before medical intervention. Our results suggest that the urinary myeloperoxidase to cubilin ratio could be used as a new tool for predicting recurrence and that dysregulation of the inflammatory and immune systems may be a key driver of disease worsening. Furthermore, we identified neutrophil degranulation and neutrophil extracellular traps (NETs) as key pathways in the progression of T1-stage BCa. We propose that proteomics follow-up of the inflammatory and immune systems may be useful for monitoring the effectiveness of therapy. SIGNIFICANCE: This article describes how proteomics can be used to characterize tumor aggressiveness in patients with the same diagnosis of bladder cancer (BCa). LC-MS/MS in combination with label free quantification (LFQ) were used to explore potential protein and pathway level changes related to the aggressiveness of the disease in 13 and 17 recurring and non-recurring T1 stage BCa patients. We have shown that the MPO/CUBN protein ratio is a candidate for a urine prognosis tool in BCa. Furthermore, we identify dysregulation of inflammation process as a driver for BCa recurrence and progression. Moreover, we propose using proteomics to track the effectiveness of therapy in the inflammatory and immune systems.
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Affiliation(s)
- Luís B Carvalho
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - José Luis Capelo Martínez
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - Rafael Bento
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jeremiah J Morrissey
- Department of Anesthesiology, Division of Clinical and Translational Research, School of Medicine and Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Luis Campos Pinheiro
- Urology Department, Central Lisbon Hospital Center, Lisbon, Portugal.; NOVA Medical School, NOVA University of Lisbon, Lisbon, Portugal
| | - Mariana Medeiros
- Urology Department, Central Lisbon Hospital Center, Lisbon, Portugal.; NOVA Medical School, NOVA University of Lisbon, Lisbon, Portugal
| | - Hugo M Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, NOVA University of Lisbon, Caparica 2829-516, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, Caparica 2825-182, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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Pathway-guided monitoring of the disease course in bladder cancer with longitudinal urine proteomics. COMMUNICATIONS MEDICINE 2023; 3:8. [PMID: 36646893 PMCID: PMC9842762 DOI: 10.1038/s43856-023-00238-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Monitoring bladder cancer over time requires invasive and costly procedures. Less invasive approaches are required using readily available biological samples such as urine. In this study, we demonstrate a method for longitudinal analysis of the urine proteome to monitor the disease course in patients with bladder cancer. METHODS We compared the urine proteomes of patients who experienced recurrence and/or progression (n = 13) with those who did not (n = 17). We identified differentially expressed proteins within various pathways related to the hallmarks of cancer. The variation of such pathways during the disease course was determined using our differential personal pathway index (dPPi) calculation, which could indicate disease progression and the need for medical intervention. RESULTS Seven hallmark pathways are used to develop the dPPi. We demonstrate that we can successfully longitudinally monitor the disease course in bladder cancer patients through a combination of urine proteomic analysis and the dPPi calculation, over a period of 62 months. CONCLUSIONS Using the information contained in the patient's urinary proteome, the dPPi reflects the individual's course of bladder cancer, and helps to optimise the use of more invasive procedures such as cystoscopy.
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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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Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics. Anal Chem 2020; 92:9164-9171. [PMID: 32484334 DOI: 10.1021/acs.analchem.0c01470] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We propose a new high-throughput ultrafast method for large-scale proteomics approaches by speeding up the classic filter aided sample preparation protocol, FASP, from overnight to 2.5 h. Thirty-six samples can be treated in 2.5 h, and the method is scalable to 96-well plate-based pipelines. After a modification of the FASP-tube, the steps of protein reduction, protein alkylation, and protein digestion of complex proteomes are done in just 5.25 min, each one under the effects of an ultrasonic field (7 cycles: 30 s on and 15 s off). The new method was compared to the standard overnight digestion FASP protocol, and no statistical differences were found for more than 92.4%, 92%, and 93.3% of the proteins identified by studying the proteome of E. coli, mouse brain, and mouse liver tissue samples, respectively. Furthermore, the successful relative label-free quantification of four spiked proteins in E. coli samples, BSA, β-lactoglobulin, α-casein, and α-lactalbumin, was achieved, using either the ultrasonic-based FASP protocol or the classic overnight one. The new US-FASP method matches the analytical minimalism rules as time, cost, sample requirement, reagent consumption, energy requirements, and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all of the advantages of the filter aided sample preparation protocol are maintained.
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Wang X, Gu Y, Zhang S, Li G, Liu T, Wang T, Qin H, Jiang B, Zhu L, Li Y, Lei H, Li M, Zhang Q, Yang R, Fang F, Guo H. Unbiased enrichment of urine exfoliated cells on nanostructured substrates for sensitive detection of urothelial tumor cells. Cancer Med 2019; 9:290-301. [PMID: 31709750 PMCID: PMC6943141 DOI: 10.1002/cam4.2655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
Background Early detection of urothelial carcinoma (UC) by noninvasive diagnostic methods with high accuracy is still underscored. This study aimed to develop a noninvasive assay incorporating both enrichment of urine exfoliated cells and immunoassays for UC detection. Methods Polystyrene dishes were exposed to oxygen plasma and modified with 3‐aminopropyltriethoxysilane to prepare amine‐functionalized nanostructured substrates (NS). Performance characterization of NS was evaluated by atomic force microscope and X‐ray photoelectron spectroscopy. Urine exfoliated cells were captured by NS and then immunostained to detect urinary tumor cells (UTCs), which was called UTC assay. The receiver operating characteristic (ROC) curve, area under ROC curve (AUC), and Youden index were used to find the cutoff value of UTC assay. ROC analysis and McNemar test were used to compare the diagnostic accuracy of UTC assay with cytology. Kappa test was used to analyze the agreement of UTC assay and cytology with pathological diagnosis. Results Nanostructured substrates had good cell binding yields of nucleated cells and tumor cells. CK20+CD45−CD11b− cells were considered as UTCs. UTC number ≥ 1 per sample could be considered as a positive result. By AUC and Kappa analysis, UTC assay showed good performance in UC detection. McNemar test demonstrated that UTC assay had a superior sensitivity even in low‐grade subgroup and a similar specificity compared to cytology in UC diagnosis. Conclusions Nanostructured substrates could be used to enrich the exfoliated cells from urine samples. UTC assay with NS has the potential to play a role in UC detection. The value of this assay still needs additional validation by large, multi‐center studies.
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Affiliation(s)
- Xin Wang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Yuanyuan Gu
- PerMed Biomedicine Institute, Shanghai, China
| | - Shiwei Zhang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Gangqiang Li
- Department of Pathology, Naval Characteristic Medical Center, Shanghai, China
| | - Tianyao Liu
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Tianwei Wang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Haixiang Qin
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Bo Jiang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Lin Zhu
- PerMed Biomedicine Institute, Shanghai, China
| | - Yajun Li
- PerMed Biomedicine Institute, Shanghai, China
| | - Haozhi Lei
- PerMed Biomedicine Institute, Shanghai, China
| | - Ming Li
- Department of Pathology, The Affiliated Suzhou Municipal Hospital of Nanjing Medical University, Suzhou, China
| | - Qun Zhang
- PerMed Biomedicine Institute, Shanghai, China
| | - Rong Yang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
| | - Feng Fang
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Hongqian Guo
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, China
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Wiśniewski JR. Filter Aided Sample Preparation - A tutorial. Anal Chim Acta 2019; 1090:23-30. [PMID: 31655642 DOI: 10.1016/j.aca.2019.08.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/08/2023]
Abstract
Filter Aided Sample Preparation (FASP) is a widely used protein processing technique in "bottom-up" proteomics. Its popularity reflects the key features of the method: its applicability to a variety of sample types and the high quality of the released peptides. Successful application of FASP requires optimized properties of sample lysate and its amount, use of ultrafiltration units with membranes having large molecular mass cut-offs and well selected conditions for protein digestion. In contrast to the majority of sample preparation methods, FASP allows digestion of proteins with a variety of enzymes and a straightforward monitoring of protein-to-peptide conversion. A unique feature of FASP is the possibility to cleave proteins in a consecutive way using several proteases and to separate peptide fractions. Understanding principles of the method gives guidance in applying FASP to different types of samples in optimization of conditions of the FASP-workflow.
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Affiliation(s)
- Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
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