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Zhao Z, Wang C, Zhao J, Li Y, Zhang S, Dong J, Zuo H, Ou J, Deng N, Bian Y. Immobilized PAD4 enzyme on magnetic nanoparticles for screening natural inhibitors from traditional Chinese medicines. Talanta 2024; 278:126492. [PMID: 38955099 DOI: 10.1016/j.talanta.2024.126492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/15/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
Dysregulation of peptidyl arginine deiminase 4 (PAD4) is involved in a variety of diseases including rheumatoid arthritis (RA) and Alzheimer's disease (AD), and it has emerged as potential and promising therapeutic target. However, no PAD4 inhibitor is ready for clinical use. Immobilized enzyme screening technology has gained increasing attention due to its low cost, reusability, easy separation from the reaction mixture, and resistance to changes in environmental conditions. In this study, PAD4 was immobilized on the magnetic nanoparticles (MNP) to prolong its activity stability, and a simple and rapid screening strategy of traditional Chinese medicine inhibitors based on immobilized PAD4 was established. The PAD4 enzyme was immobilized on magnetic nanoparticles (MNP) via Schiff base reaction using glutaraldehyde (GA) as crosslinking agent. Compared with free PAD4, the resulting MNP@GA@PAD4 exhibited an enhanced tolerance to temperature and storage stability, and its reusability was greatly improved with 66 % of initial enzyme activity after being recycled 10 times. The inhibitory activity of the immobilized PAD4 was assessed using two known PAD4 inhibitors GSK484 and BB-Cl-amidine. The semi-maximum inhibitory concentrations (IC50) of GSK484 and BB-Cl-amidine for MNP@GA@PAD4 were 1.00 and 0.97 μM, respectively, for free PAD4 were 0.64 and 0.85 μM, respectively. Finally, the MNP@GA@PAD4 was employed to rapid screen of natural PAD4 inhibitors from forty traditional Chinese medicines (TCMs). Under the same conditions, the controlled experiment was conducted with free PAD4. The screening results of TCMs inhibitors on MNP@GA@PAD4 and free PAD4 were similar, the alcohol extracts of Cinnamomi Cortex and Caryophylli Flos had significant inhibitory effects on PAD4 enzyme activity. The IC50 values of Cinnamomi Cortex extract for MNP@GA@PAD4 and free PAD4 were determined as 27 and 48 μg/mL, respectively. The IC50 values of Caryophylli Flos extracts for MNP@GA@PAD4 and free PAD4 were determined as 48 and 32 μg/mL, respectively. For the first time, this study proposed a method to immobilize PAD4 on magnetic materials, and developed a rapid, reusable and feasible strategy to screening natural PAD4 inhibitors from TCMs.
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Affiliation(s)
- Zeyuan Zhao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Chenyang Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Juanjuan Zhao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Yanfeng Li
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Shengxiang Zhang
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Jianhui Dong
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Haiyue Zuo
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Junjie Ou
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China
| | - Nan Deng
- Instrumental Analysis Center, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, PR China.
| | - Yangyang Bian
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, PR China.
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Ji C, Li J, Mei J, Su W, Dai H, Li F, Liu P. Advanced Nanomaterials for the Diagnosis and Treatment of Renal Cell Carcinoma. ADVANCED NANOBIOMED RESEARCH 2022. [DOI: 10.1002/anbr.202200079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Chen Ji
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Junru Li
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Junyang Mei
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Weiran Su
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Huili Dai
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Fengqin Li
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200032 China
- Central Laboratory Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
- Micro-Nano Research and Diagnosis Center RenJi Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
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Nickerson JL, Doucette AA. Maximizing Cumulative Trypsin Activity with Calcium at Elevated Temperature for Enhanced Bottom-Up Proteome Analysis. BIOLOGY 2022; 11:biology11101444. [PMID: 36290348 PMCID: PMC9598648 DOI: 10.3390/biology11101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Simple Summary Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Abstract Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.
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Bilal M, Iqbal HM, Adil SF, Shaik MR, Abdelgawad A, Hatshan MR, Khan M. Surface-coated magnetic nanostructured materials for robust bio-catalysis and biomedical applications-A review. J Adv Res 2022; 38:157-177. [PMID: 35572403 PMCID: PMC9091734 DOI: 10.1016/j.jare.2021.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Enzymes based bio-catalysis has wide range of applications in various chemical and biological processes. Thus, the process of enzymes immobilization on suitable support to obtain highly active and stable bio-catalysts has great potential in industrial applications. Particularly, surface-modified magnetic nanomaterials have garnered a special interest as versatile platforms for biomolecules/enzyme immobilization. AIM OF REVIEW This review spotlights recent progress in the immobilization of various enzymes onto surface-coated multifunctional magnetic nanostructured materials and their derived nano-constructs for multiple applications. Conclusive remarks, technical challenges, and insightful opinions on this field of research which are helpful to expand the application prospects of these materials are also given with suitable examples. KEY SCIENTIFIC CONCEPTS OF REVIEW Nanostructured materials, including surface-coated magnetic nanoparticles have recently gained immense significance as suitable support materials for enzyme immobilization, due to their large surface area, unique functionalities, and high chemical and mechanical stability. Besides, magnetic nanoparticles are less expensive and offers great potential in industrial applications due to their easy recovery and separation form their enzyme conjugates with an external magnetic field. Magnetic nanoparticles based biocatalytic systems offer a wide-working temperature, pH range, increased storage and thermal stabilities. So far, several studies have documented the application of a variety of surface modification and functionalization techniques to circumvent the aggregation and oxidation of magnetic nanoparticles. Surface engineering of magnetic nanoparticles (MNPs) helps to improve the dispersion stability, enhance mechanical and physicochemical properties, upgrade the surface activity and also increases enzyme immobilization capabilities and biocompatibility of the materials. However, several challenges still need to be addressed, such as controlled synthesis of MNPs and clinical aspects of these materials require consistent research from multidisciplinary scientists to realize its practical applications.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Corresponding authors.
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Syed Farooq Adil
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Mohammed Rafi Shaik
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
- Corresponding authors.
| | - Abdelatty Abdelgawad
- Department of Industrial Engineering, College of Engineering, King Saud University, P.O. Box 800, Riyadh 11421, Kingdom of Saudi Arabia
| | - Mohammad Rafe Hatshan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Mujeeb Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
- Corresponding authors.
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Immobilization Techniques on Bioprocesses: Current Applications Regarding Enzymes, Microorganisms, and Essential Oils. FOOD BIOPROCESS TECH 2022. [DOI: 10.1007/s11947-022-02780-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nuti S, Fernández-Lodeiro C, Fernández-Lodeiro J, Fernández-Lodeiro A, Pérez-Juste J, Pastoriza-Santos I, LaGrow AP, Schraidt O, Luis Capelo-Martínez J, Lodeiro C. Polyallylamine assisted synthesis of 3D branched AuNPs with plasmon tunability in the vis-NIR region as refractive index sensitivity probes. J Colloid Interface Sci 2022; 611:695-705. [PMID: 34979340 DOI: 10.1016/j.jcis.2021.12.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/14/2021] [Accepted: 12/07/2021] [Indexed: 02/08/2023]
Abstract
This paper describes the synthesis of highly branched gold nanoparticles (AuNPs) through a facile seeded growth approach using poly(allylamine hydrochloride) (PAH) as shape inducing agent. The obtained branched AuNPs present highly tunable optical properties in the Vis-NIR region from ca. 560 nm to 1260 nm. We controlled the morphology, and therefore the optical response, of the NPs by either changing the gold salt to seeds ratio or by fine-tuning the solution pH. We proposed that the formation of size-dependent PAH-AuCl4- aggregates as demonstrated by dynamic light scattering measurements, together with pH-dependent gold salt speciation might be responsible for the branched morphology. Advanced electron microscopy techniques demonstrated the polycrystalline nature of the AuNPs and facilitated a better understanding of branched morphology. Additionally, the refractive index sensitivity estimated by the inflection point of the Localized Surface Plasmon Resonance (LSPR) band can be controlled by tuning the nanoparticle branching. Furthermore, the versatility of the PAH chemistry allowed the easy functionalization of the synthesized NPs.
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Affiliation(s)
- Silvia Nuti
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica Campus, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2829-516 Caparica, Portugal
| | - Carlos Fernández-Lodeiro
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas Marcosende, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Javier Fernández-Lodeiro
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica Campus, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2829-516 Caparica, Portugal.
| | - Adrián Fernández-Lodeiro
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica Campus, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2829-516 Caparica, Portugal
| | - Jorge Pérez-Juste
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas Marcosende, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Isabel Pastoriza-Santos
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas Marcosende, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36310 Vigo, Spain
| | - Alec P LaGrow
- International Iberian Nanotechnology Laboratory, Braga 4715-330, Portugal
| | - Oliver Schraidt
- International Iberian Nanotechnology Laboratory, Braga 4715-330, Portugal
| | - José Luis Capelo-Martínez
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica Campus, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2829-516 Caparica, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Group, LAQV@REQUIMTE, Chemistry Department, NOVA School of Science and Technology, NOVA University Lisbon, Caparica Campus, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Rua dos Inventores, Madam Parque, Caparica Campus, 2829-516 Caparica, Portugal.
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Kruszewska J, Zajda J, Matczuk M. How to effectively prepare a sample for bottom-up proteomic analysis of nanoparticle protein corona? A critical review. Talanta 2021; 226:122153. [PMID: 33676702 DOI: 10.1016/j.talanta.2021.122153] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 02/08/2023]
Abstract
Since the interest in the biomedical applications of inorganic nanoparticles (NPs) has rapidly grown over the last decades, there is a need for a thorough characterization of bio-nano interactions. NPs introduced to the body (mostly intravenously) encounter plasma proteins, that instantly create a so-called "protein corona" on the NPs surface, giving the nanomaterial a new biological identity. Type of the proteins that interact with NPs may affect the in vivo fate of NPs. For that reason, it is particularly important to establish analytical methods capable of corona protein identification. Bottom-up proteomics is most often used for that purpose. A crucial part of the experiment is sample preparation, as it is already proven that different protocols may lead to distinct results. This review is aimed at providing a characterization of two main stages of sample preparation: separation of NPs with protein corona from the unbound proteins and the digestion of corona proteins. Separation techniques such as centrifugation, magnetic separation, and chromatography and three digestion methods (in-gel, in-solution, and on-particle) are described with special emphasis paid on their advantages and disadvantages as well as their influence on the result of identification. This paper also indicates the need for standardization of protein corona identification protocols, as some of the proteins may be preferentially detected while applying a particular digestion procedure.
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Affiliation(s)
- Joanna Kruszewska
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland
| | - Joanna Zajda
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland
| | - Magdalena Matczuk
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664, Warsaw, Poland.
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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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Liu Y, Zhang W, Han B, Zhang L, Zhou P. Changes in bioactive milk serum proteins during milk powder processing. Food Chem 2020; 314:126177. [DOI: 10.1016/j.foodchem.2020.126177] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
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Jorge S, Pereira K, López-Fernández H, LaFramboise W, Dhir R, Fernández-Lodeiro J, Lodeiro C, Santos HM, Capelo-Martínez JL. Ultrasonic-assisted extraction and digestion of proteins from solid biopsies followed by peptide sequential extraction hyphenated to MALDI-based profiling holds the promise of distinguishing renal oncocytoma from chromophobe renal cell carcinoma. Talanta 2019; 206:120180. [PMID: 31514886 DOI: 10.1016/j.talanta.2019.120180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
A novel analytical approach is proposed to discriminate between solid biopsies of chromophobe renal cell carcinoma (chRCC) and renal oncocytoma (RO). The method comprises the following steps: (i) ultrasonic extraction of proteins from solid biopsies, (ii) protein depletion with acetonitrile, (iii) ultrasonic assisted in-solution digestion using magnetic nanoparticle with immobilized trypsin, (iv) C18 tip-based preconcentration of peptides, (v) sequential extraction of the peptides with ACN, (vi) MALDI-snapshot of the extracts and (vii) investigation of the extract containing the most discriminating features using high resolution mass spectrometry. With this approach we have been able to differentially cluster renal oncocytoma and chromophobe renal cell carcinoma and identified 18 proteins specific to chromophobe and seven unique to renal oncocytoma. Chromophobes express proteins associated with ATP function (ATP5I & 5E; VATE1 & G2; ADT2), glycolysis (PGK1) and neuromedin whilst oncocytomas express ATP5H, ATPA, DEPD7 and TRIPB thyroid receptor interacting protein.
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Affiliation(s)
- Susana Jorge
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - Kevin Pereira
- PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - Hugo López-Fernández
- ESEI -Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain; CINBIO -Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312, Vigo, Spain; Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Rúa Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - William LaFramboise
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Rajiv Dhir
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Javier Fernández-Lodeiro
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - Carlos Lodeiro
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - Hugo M Santos
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal
| | - Jose L Capelo-Martínez
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Park, Rua dos Inventores, 2825-152, Caparica, Portugal.
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