1
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Yang M, Wu E, Tang W, Qian J, Zhan C. Interplay between nanomedicine and protein corona. J Mater Chem B 2021; 9:6713-6727. [PMID: 34328485 DOI: 10.1039/d1tb01063h] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanomedicine is recognized as a promising agent for diverse biomedical applications; however, its safety and efficiency in clinical practice remains to be enhanced. A priority issue is the protein corona (PC), which imparts unique biological identities to prototype and determines the actual biological functions in biological fluids. Decades of work has already illuminated abundant considerations that influence the composition of the protein corona. Thereinto, the physical assets of nanomedicines (e.g., size and shape, surface properties, nanomaterials) and the biological environment collectively play fundamental roles in shaping the PC, including the types and quantities of plasma proteins. The properties of nanomedicines are dependent on certain factors. This review aims to explore the applications of nanomedicines by regulating their interplay with PC.
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Affiliation(s)
- Min Yang
- Department of Pharmacology, School of Basic Medical Sciences & Center of Medical Research and Innovation, Shanghai Pudong Hospital & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200032, P. R. China.
| | - Ercan Wu
- MOE Key Laboratory of Smart Drug Delivery, School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Wenjing Tang
- MOE Key Laboratory of Smart Drug Delivery, School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Jun Qian
- MOE Key Laboratory of Smart Drug Delivery, School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Changyou Zhan
- Department of Pharmacology, School of Basic Medical Sciences & Center of Medical Research and Innovation, Shanghai Pudong Hospital & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200032, P. R. China. and MOE Key Laboratory of Smart Drug Delivery, School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
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2
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Chantada-Vázquez MDP, García Vence M, Serna A, Núñez C, Bravo SB. SWATH-MS Protocols in Human Diseases. Methods Mol Biol 2021; 2259:105-141. [PMID: 33687711 DOI: 10.1007/978-1-0716-1178-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of molecular biomarkers for human diseases is one of the most important disciplines in translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and depth needed to succeed in this task. In this chapter, we show different sample processing methods (major protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several proteins in different types of samples (serum/plasma, saliva, urine, tears).
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Affiliation(s)
| | - María García Vence
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | | | - Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain.
| | - Susana B Bravo
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain.
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3
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Identification of a Profile of Neutrophil-Derived Granule Proteins in the Surface of Gold Nanoparticles after Their Interaction with Human Breast Cancer Sera. NANOMATERIALS 2020; 10:nano10061223. [PMID: 32586001 PMCID: PMC7353125 DOI: 10.3390/nano10061223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/09/2020] [Accepted: 06/19/2020] [Indexed: 12/29/2022]
Abstract
It is well known that the interaction of a nanomaterial with a biological fluid leads to the formation of a protein corona (PC) surrounding the nanomaterial. Using standard blood analyses, alterations in protein patterns are difficult to detect. PC acts as a “nano-concentrator” of serum proteins with affinity for nanoparticles’ surface. Consequently, characterization of PC could allow detection of otherwise undetectable changes in protein concentration at an early stage of a disease, such as breast cancer (BC). Here, we employed gold nanoparticles (AuNPsdiameter: 10.02 ± 0.91 nm) as an enrichment platform to analyze the human serum proteome of BC patients (n = 42) and healthy controls (n = 42). Importantly, the analysis of the PC formed around AuNPs after their interaction with serum samples of BC patients showed a profile of proteins that could differentiate breast cancer patients from healthy controls. These proteins developed a significant role in the immune and/or innate immune system, some of them being neutrophil-derived granule proteins. The analysis of the PC also revealed serum proteome alterations at the subtype level.
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4
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Del Pilar Chantada-Vázquez M, López AC, Vence MG, Vázquez-Estévez S, Acea-Nebril B, Calatayud DG, Jardiel T, Bravo SB, Núñez C. Proteomic investigation on bio-corona of Au, Ag and Fe nanoparticles for the discovery of triple negative breast cancer serum protein biomarkers. J Proteomics 2019; 212:103581. [PMID: 31731051 DOI: 10.1016/j.jprot.2019.103581] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/14/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022]
Abstract
Nowadays, there are no targeted therapeutic modalities for triple negative breast cancer (TNBC). This disease is associated with poor prognosis and worst clinical outcome because of the aggressive nature of the tumor, delayed diagnosis, and non-specific symptoms in the early stages. Therefore, identification of novel specific TNBC serum biomarkers for screening and therapeutic purposes remains an urgent clinical requirement. New user-friendly and cheap methods for biomarker identification are needed, and nanotechnology offers new opportunities. When dispersed in blood, nanoparticles (NPs) are covered by a protein shell termed "protein corona" (PC). While alterations in protein patterns are challeging to detect by conventional blood analyses, PC acts as a "nano-concentrator" of serum proteins with affinity for NPs' surface. So, the characterization of PC could allow the detection of otherwise undetectable changes in protein concentration at an early stage of the disease or after chemotherapy or surgery. To explore this research idea, serum samples from 8 triple negative breast cancer (TNBC) patients and 8 patients without malignancy were allowed to interact with gold nanoparticles (AuNPs: 10.02 ± 0.91 nm), silver nanoparticles (AgNPs: 9.73 ± 1.70 nm) and magnetic nanoparticles (MNPs: (9.30 ± 0.67 nm). Here, in order to identify biomarker candidates in serum of TNBC patients, these nanomaterials were combined with electrophoretic separation (SDS-PAGE) to performed qualitative and quantitative comparisons of the serum proteomes of TNBC patients (n = 8) and healthy controls (n = 8) by liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis. The results were validated through a sequential window acquisition of all theoretical mass spectra (SWATH) analysis, performed in total serum samples (patients and controls) using this approach as a multiple reaction monitoring (MRM) analysis. SIGNIFICANCE: It is well known that several proteins presented in human serum are important biomarkers for the diagnosis or prognosis of different diseases, as triple negative breast cancer (TNBC). Determining how nanomaterials as gold nanoparticles (AuNPs: 10.02 ± 0.91 nm), silver nanoparticles (AgNPs: 9.73 ± 1.70 nm) and magnetic nanoparticles (MNPs: (9.30 ± 0.67 nm) interact with human serum will assist not only in understanding their effects on the biological system (biocompability and toxicity), but also to obtain information for developing novel nanomaterials with high specificity and selectivity towards proteins with an important biological function (prognostic and diagnostic protein biomarkers).
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Affiliation(s)
| | - Antonio Castro López
- Breast Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain
| | - María García Vence
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Sergio Vázquez-Estévez
- Oncology Division, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain
| | - Benigno Acea-Nebril
- Department of Surgery, Breast Unit, Complexo Hospitalario Universitario A Coruña (CHUAC), SERGAS, A Coruña, Spain
| | - David G Calatayud
- Department of Electroceramics, Instituto de Cerámica y Vidrio-CSIC, Kelsen 5, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Teresa Jardiel
- Department of Electroceramics, Instituto de Cerámica y Vidrio-CSIC, Kelsen 5, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Susana B Bravo
- Proteomic Unit, Instituto de Investigaciones Sanitarias-IDIS, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain.
| | - Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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5
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Potential clinical applications of the personalized, disease-specific protein corona on nanoparticles. Clin Chim Acta 2019; 501:102-111. [PMID: 31678275 DOI: 10.1016/j.cca.2019.10.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023]
Abstract
Nanoscale objects lose their original identity once in contact with biological fluids and get a new biological identity, referred to as a protein corona (PC). The PC modifies many of the physicochemical properties of nanoparticles (NPs), including surface charge, size, and aggregation state. These changes, in turn, affect the biological fate of NPs, including their biodistribution, pharmacokinetics, and therapeutic efficacy. It is well known that even small differences in the composition of a protein source (e.g., plasma and serum) can considerably change the composition of the corona formed on the surface of the same NPs. Recently, it has been shown that the PC is intensely affected by the patient's specific disease. Consequently, the same nanomaterial incubated with proteins of biological fluids belonging to patients with different pathologies adsorbs protein coronas with different compositions, giving rise to the concept of the personalized protein corona (PPC). Herein, we review recent advances on the topic of PPC, with a particular focus on their clinical significance.
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6
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del Pilar Chantada-Vázquez M, López AC, Bravo SB, Vázquez-Estévez S, Acea-Nebril B, Núñez C. Proteomic analysis of the bio-corona formed on the surface of (Au, Ag, Pt)-nanoparticles in human serum. Colloids Surf B Biointerfaces 2019; 177:141-148. [DOI: 10.1016/j.colsurfb.2019.01.056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/15/2019] [Accepted: 01/26/2019] [Indexed: 12/13/2022]
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7
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Núñez C, Estévez SV, del Pilar Chantada M. Inorganic nanoparticles in diagnosis and treatment of breast cancer. J Biol Inorg Chem 2018; 23:331-345. [DOI: 10.1007/s00775-018-1542-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/04/2018] [Indexed: 12/26/2022]
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8
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Jorge S, Araújo J, Pimentel-Santos F, Branco JC, Santos HM, Lodeiro C, Capelo J. Unparalleled sample treatment throughput for proteomics workflows relying on ultrasonic energy. Talanta 2018; 178:1067-1076. [DOI: 10.1016/j.talanta.2017.07.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/22/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
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Jagadeesan KK, Ekström S. MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis. SLAS DISCOVERY 2017; 22:1246-1252. [PMID: 28825969 DOI: 10.1177/2472555217727517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recently, mass spectrometry (MS) has emerged as an important tool for high-throughput screening (HTS) providing a direct and label-free detection method, complementing traditional fluorescent and colorimetric methodologies. Among the various MS techniques used for HTS, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) provides many of the characteristics required for high-throughput analyses, such as low cost, speed, and automation. However, visualization and analysis of the large datasets generated by HTS MALDI-MS can pose significant challenges, especially for multiparametric experiments. The datasets can be generated fast, and the complexity of the experimental data (e.g., screening many different sorbent phases, the sorbent mass, and the load, wash, and elution conditions) makes manual data analysis difficult. To address these challenges, a comprehensive informatics tool called MALDIViz was developed. This tool is an R-Shiny-based web application, accessible independently of the operating system and without the need to install any program locally. It has been designed to facilitate easy analysis and visualization of MALDI-MS datasets, comparison of multiplex experiments, and export of the analysis results to high-quality images.
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Affiliation(s)
| | - Simon Ekström
- 1 Department of Biomedical Engineering, Lund University, Lund, Sweden
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10
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de Jesus JR, da Silva Fernandes R, de Souza Pessôa G, Raimundo IM, Arruda MAZ. Depleting high-abundant and enriching low-abundant proteins in human serum: An evaluation of sample preparation methods using magnetic nanoparticle, chemical depletion and immunoaffinity techniques. Talanta 2017; 170:199-209. [PMID: 28501159 DOI: 10.1016/j.talanta.2017.03.091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/16/2017] [Accepted: 03/29/2017] [Indexed: 02/07/2023]
Abstract
The efficiency of three different depletion methods to remove the most abundant proteins, enriching those human serum proteins with low abundance is checked to make more efficient the search and discovery of biomarkers. These methods utilize magnetic nanoparticles (MNPs), chemical reagents (sequential application of dithiothreitol and acetonitrile, DTT/ACN), and commercial apparatus based on immunoaffinity (ProteoMiner, PM). The comparison between methods shows significant removal of abundant protein, remaining in the supernatant at concentrations of 4.6±0.2, 3.6±0.1, and 3.3±0.2µgµL-1 (n=3) for MNPs, DTT/ACN and PM respectively, from a total protein content of 54µgµL-1. Using GeLC-MS/MS analysis, MNPs depletion shows good efficiency in removing high molecular weight proteins (>80kDa). Due to the synergic effect between the reagents DTT and ACN, DTT/ACN-based depletion offers good performance in the depletion of thiol-rich proteins, such as albumin and transferrin (DTT action), as well as of high molecular weight proteins (ACN action). Furthermore, PM equalization confirms its efficiency in concentrating low-abundant proteins, decreasing the dynamic range of protein levels in human serum. Direct comparison between the treatments reveals 72 proteins identified when using MNP depletion (43 of them exclusively by this method), but only 20 proteins using DTT/ACN (seven exclusively by this method). Additionally, after PM treatment 30 proteins were identified, seven exclusively by this method. Thus, MNPs and DTT/ACN depletion can be simple, quick, cheap, and robust alternatives for immunochemistry-based protein depletion, providing a potential strategy in the search for disease biomarkers.
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Affiliation(s)
- Jemmyson Romário de Jesus
- Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil
| | - Rafael da Silva Fernandes
- Group for Instrumentation and Automation in Analytical Chemistry - GIA Institute of Chemistry, University of Campinas - UNICAMP
| | - Gustavo de Souza Pessôa
- Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil
| | - Ivo Milton Raimundo
- Group for Instrumentation and Automation in Analytical Chemistry - GIA Institute of Chemistry, University of Campinas - UNICAMP
| | - Marco Aurélio Zezzi Arruda
- Spectrometry, Sample Preparation and Mechanization Group - GEPAM, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas - UNICAMP, Campinas, Brazil.
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11
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Fernández-Lodeiro J, Rodríguez-González B, Santos HM, Bertolo E, Capelo JL, Dos Santos AA, Lodeiro C. Unraveling the Organotellurium Chemistry Applied to the Synthesis of Gold Nanomaterials. ACS OMEGA 2016; 1:1314-1325. [PMID: 31457198 PMCID: PMC6640781 DOI: 10.1021/acsomega.6b00309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/05/2016] [Indexed: 06/10/2023]
Abstract
Long-term preservation of the properties of gold nanoparticles in both solution and the dry powder form can be difficult. We have overcome this challenge by using organotellurium derivatives as both reducing agents and stabilizers in the synthesis of gold nanoparticles. This new synthetic protocol takes advantage of the photochemical and oxidative properties of diphenyl ditelluride (Ph2Te2), which, so far, have never been exploited in the synthesis of gold nanoparticles. The Au/Te core/shell (inorganic/organic) hybrid nanomaterial can be obtained in a one-step reaction, using only Ph2Te2 and HAuCl4. By modifying the reaction conditions, different resonance conditions of the gold core are achieved due to the formation of external shells with different thicknesses. The organotellurium shell can be easily removed by resuspension of the nanoparticles in environmentally friendly solvents, such as water or ethanol, making the Au core available for subsequent applications. A mechanism for the formation of core/shell nanoparticles has also been discussed.
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Affiliation(s)
- Javier Fernández-Lodeiro
- BIOSCOPE
Group, UCIBIO@REQUIMTE, Chemistry Department, Faculty of Science and
Technology, University NOVA of Lisbon, Caparica 2829-516, Portugal
- ProteoMass
Scientific Society, Faculty of
Science and Technology, Madan Parque, Building VI, Office 23, Campus de Caparica, Caparica 2829-516, Portugal
- Instituto
de Química, Universidade de São
Paulo, Av. Prof. Lineu
Prestes, 748, CxP.26077, São Paulo 05508-000, Brazil
| | - Benito Rodríguez-González
- Scientific
and Technological Research Assistance Centre (CACTI), University of
Vigo, Lagoas-Marcosende, Vigo 36310, Spain
| | - Hugo M. Santos
- BIOSCOPE
Group, UCIBIO@REQUIMTE, Chemistry Department, Faculty of Science and
Technology, University NOVA of Lisbon, Caparica 2829-516, Portugal
- ProteoMass
Scientific Society, Faculty of
Science and Technology, Madan Parque, Building VI, Office 23, Campus de Caparica, Caparica 2829-516, Portugal
| | - Emilia Bertolo
- Biomolecular
Research Group, School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, U.K.
| | - José Luis Capelo
- BIOSCOPE
Group, UCIBIO@REQUIMTE, Chemistry Department, Faculty of Science and
Technology, University NOVA of Lisbon, Caparica 2829-516, Portugal
- ProteoMass
Scientific Society, Faculty of
Science and Technology, Madan Parque, Building VI, Office 23, Campus de Caparica, Caparica 2829-516, Portugal
| | - Alcindo A. Dos Santos
- Instituto
de Química, Universidade de São
Paulo, Av. Prof. Lineu
Prestes, 748, CxP.26077, São Paulo 05508-000, Brazil
| | - Carlos Lodeiro
- BIOSCOPE
Group, UCIBIO@REQUIMTE, Chemistry Department, Faculty of Science and
Technology, University NOVA of Lisbon, Caparica 2829-516, Portugal
- ProteoMass
Scientific Society, Faculty of
Science and Technology, Madan Parque, Building VI, Office 23, Campus de Caparica, Caparica 2829-516, Portugal
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12
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Núñez C, Capelo JL, Igrejas G, Alfonso A, Botana LM, Lodeiro C. An overview of the effective combination therapies for the treatment of breast cancer. Biomaterials 2016; 97:34-50. [PMID: 27162073 DOI: 10.1016/j.biomaterials.2016.04.027] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 04/05/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022]
Abstract
Breast cancer (BC) is generally classified based on the receptors overexpressed on the cell nucleus, which include hormone receptors such as progesterone (PR) and estrogen (ER), and HER2. Triple-negative breast cancer (TNBC) is a type of cancer that lacks any of these three types of receptor proteins (ER/PR/HER2). Tumor cells exhibit drug resistant phenotypes that decrease the efficacy of chemotherapeutic treatments. Generally, drug resistance has a genetic basis that is caused by an abnormal gene expression, nevertheless, there are several types of drug resistance: efflux pumps reducing the cellular concentration of the drug, alterations in membrane lipids that reduce cellular uptake, increased or altered drug targets, metabolic alteration of the drug, inhibition of apoptosis, repair of the damaged DNA, and alteration of the cell cycle checkpoints. The use of "combination therapy" is recognized as an efficient solution to treat human diseases, in particular, breast cancer. In this review, we give examples of different nanocarriers used to co-deliver multiple therapeutics (chemotherapeutic agent and nucleic acid) to drug-resistant tumor cells, and lastly, we give our recommendations for the future directions for the co-delivery treatments.
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Affiliation(s)
- Cristina Núñez
- Pharmacology Deparment, Faculty of Veterinary, University of Santiago de Compostela, 27002, Lugo, Spain; C4O Group, Research Unit UCIBIO-REQUIMTE, 2829-516, Caparica, Portugal.
| | - José Luis Capelo
- BIOSCOPE Group, UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182, Caparica, Portugal
| | - Gilberto Igrejas
- C4O Group, Research Unit UCIBIO-REQUIMTE, 2829-516, Caparica, Portugal; Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Amparo Alfonso
- Pharmacology Deparment, Faculty of Veterinary, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Luis M Botana
- Pharmacology Deparment, Faculty of Veterinary, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Carlos Lodeiro
- BIOSCOPE Group, UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182, Caparica, Portugal.
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13
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de Jesus JR, Pessôa GDS, Sussulini A, Martínez JLC, Arruda MAZ. Proteomics strategies for bipolar disorder evaluation: From sample preparation to validation. J Proteomics 2016; 145:187-196. [PMID: 27113133 DOI: 10.1016/j.jprot.2016.04.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 02/06/2023]
Abstract
Bipolar disorder (BD) is a complex and costly psychiatric disorder, which affects one hundred million people worldwide. Due to its heterogeneity, correct BD diagnosis is still a challenge. In order to overcome this issue, different bioanalytical strategies have been proposed in the literature recently. Among these strategies, proteomic approaches have arisen as some of the most promising in the area. Thus, recent applications suggest protein profiles to further refine the proteome of BD as well as the discovery of novel protein biomarkers to facilitate diagnostics. In this review, the state-of-art of proteomic research in BD is summarized. Furthermore, important aspects of proteomics for understanding of BD, such as sample type and size, sampling, sample preparation, gel-based and gel-free proteomics, proteomic quantitative and protein validation are overviewed.
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Affiliation(s)
- Jemmyson Romário de Jesus
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil; UCIBIO-REQUIMTE, Chemistry Department, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Gustavo de Souza Pessôa
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil
| | - Alessandra Sussulini
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil
| | - José Luis Capelo Martínez
- UCIBIO-REQUIMTE, Chemistry Department, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Caparica, Portugal; ProteoMass Scientific Society, MadanPark, Rua dos Inventores s/n, Monte de Caparica, Caparica, Portugal
| | - Marco Aurélio Zezzi Arruda
- Spectrometry, Sample Preparation and Mechanization Group, GEPAM, University of Campinas (UNICAMP), Campinas, Brazil; National Institute of Science and Technology for Bioanalytics, University of Campinas (UNICAMP), Campinas, Brazil.
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14
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Abdelhamid HN, Wu HF. Gold nanoparticles assisted laser desorption/ionization mass spectrometry and applications: from simple molecules to intact cells. Anal Bioanal Chem 2016; 408:4485-502. [DOI: 10.1007/s00216-016-9374-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/29/2015] [Accepted: 01/28/2016] [Indexed: 01/05/2023]
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15
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López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M. Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. BMC Bioinformatics 2015; 16:318. [PMID: 26437641 PMCID: PMC4595311 DOI: 10.1186/s12859-015-0752-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills. RESULTS Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Mass-Up software allows data preprocessing, as well as subsequent analysis including (i) biomarker discovery, (ii) clustering, (iii) biclustering, (iv) three-dimensional PCA visualization and (v) classification of large sets of spectra data. CONCLUSIONS Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at http://sing.ei.uvigo.es/mass-up.
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Affiliation(s)
- H López-Fernández
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
| | - H M Santos
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica, Setubal, Portugal.
| | - J L Capelo
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica, Setubal, Portugal.
| | - F Fdez-Riverola
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
| | - D Glez-Peña
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
| | - M Reboiro-Jato
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
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López-Cortés R, Formigo J, Reboiro-Jato M, Fdez-Riverola F, Blanco FJ, Lodeiro C, Oliveira E, Capelo JL, Santos HM. A methodological approach based on gold-nanoparticles followed by matrix assisted laser desorption ionization time of flight mass spectrometry for the analysis of urine profiling of knee osteoarthritis. Talanta 2015; 150:638-45. [PMID: 26838453 DOI: 10.1016/j.talanta.2015.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
The aim of this work is to develop a nanoparticle-based methodology to find out biomarkers of diagnostic for knee osteoarthritis, KOA, through the use of matrix assisted laser desorption ionization time-of-flight-based mass spectrometry profiling. Urine samples used for this study were obtained from KOA patients (42 patients), patients with prosthesis (58 patients), and controls (36 individuals) with no history of joint disease. Gold-nano particle MALDI-based urine profiling was optimized and then applied over the 136 individuals. Jaccard index and 10 different classifiers over MALDI MS datasets were used to find out potential biomarkers. Then, the specificity and sensitivity of the method were evaluated. The presence of ten m/z signals as potential biomarkers in the healthy versus non-healthy approach suggests that patients (KOA and prosthesis) are differentiable from the healthy volunteers through profiling. The automatic diagnostic study confirmed these preliminary conclusions. The sensitivity and the specificity for the urine profiling criteria here reported, achieved by the C4.5 classifier, is 97% and 69% respectively. Thus, it is confirmed the utility of the method proposed in this work as an additional fast, non-expensive and robust test for KOA diagnostic. When the proposed method is compared with those used in common practice it is found that sensitivity is the highest, thus with a low false negative rate for diagnostic KOA patients in the population studied. Specificity is lower but in the range accepted for diagnostic objectives.
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Affiliation(s)
- Rubén López-Cortés
- Facultade de Bioloxia, Departamento de Bioquímica, Xenética e Inmunoloxía, Grupo de Biomarcadores Moleculares, Universidade de Vigo, Campus Lagoas-Marcosende E36310, Vigo, Spain
| | - Jacobo Formigo
- Department of Physical Medicine and Rehabilitation, Complexo Hospitalario Universitario de Ourense, Spain
| | - Miguel Reboiro-Jato
- SING Group, Informatics Department, Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain
| | - Florentino Fdez-Riverola
- SING Group, Informatics Department, Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain
| | - Francisco J Blanco
- Servicio de Reumatología, Unidad de Proteómica, ProteoRed/ISCIII, INIBIC-Hospital Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Carlos Lodeiro
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Elisabete Oliveira
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - J L Capelo
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal.
| | - H M Santos
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal.
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Bonn F, Bartel J, Büttner K, Hecker M, Otto A, Becher D. Picking vanished proteins from the void: how to collect and ship/share extremely dilute proteins in a reproducible and highly efficient manner. Anal Chem 2014; 86:7421-7. [PMID: 24987932 DOI: 10.1021/ac501189j] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Successful proteome analyses of highly dilute samples are strongly dependent on optimized workflows considering especially sample preparation prior to highly sensitive mass spectrometric analysis. Various methods are available for enrichment of proteome samples, each characterized by specific advantages and disadvantages limiting their general application as a method of choice. Here we suggest an optimized universal protocol ensuring reproducibility and effective enrichment of dilute samples by commercial affinity beads. By comparably assessing the performance of the new protocol with selected standard enrichment techniques, we show the seamless application of the enrichment in common mass spectrometry based proteomic workflows. Further, novel applications are suggested including a facile storage and shipping of desiccated, trapped proteome samples at ambient temperatures and usage of the affinity beads for gel-free proteomic approaches.
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Affiliation(s)
- Florian Bonn
- Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald , Friedrich-Ludwig-Jahn-Strasse 15, 17487 Greifswald, Germany
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Fernández-Lodeiro A, Fernández-Lodeiro J, Núñez C, Bastida R, Capelo JL, Lodeiro C. Polyamine ligand-mediated self-assembly of gold and silver nanoparticles into chainlike structures in aqueous solution: towards new nanostructured chemosensors. ChemistryOpen 2013; 2:200-7. [PMID: 24551567 PMCID: PMC3892197 DOI: 10.1002/open.201300023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Indexed: 01/11/2023] Open
Abstract
Polyamine ligands are very versatile compounds due to their water solubility and flexibility. In the present work, we have exploited the binding ability of a polyamine molecular linker (L (2-)) bearing different functional groups, which favors the self-assembling of silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs) into 1D nanochains in aqueous solution. The chainlike assemblies of AuNPs and AgNPs were structurally stable for a long period of time, during which their characteristic optical properties remained unchanged. The mechanism of AuNPs and AgNPs chain assembly associated with the induction of electric dipole-dipole interactions arising from the partial ligand exchange of surface-adsorbed citrate ions by (L (2-)) was investigated. UV/Vis spectrophotometry and transmission electron microscopy (TEM) were used to determine timedependent structural changes associated with formation of the 1D nanoparticle structures. Finally, the sensing of Hg(2+) in aqueous solution using AgNPs@(L)(2-) and AuNPs@(L)(2-) assemblies was also carried out in aqueous solution.
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Affiliation(s)
- Adrián Fernández-Lodeiro
- BIOSCOPE Group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon 2829-516, Monte da Caparica (Portugal) E-mail: @fct.unl.pt
| | - Javier Fernández-Lodeiro
- BIOSCOPE Group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon 2829-516, Monte da Caparica (Portugal) E-mail: @fct.unl.pt
| | - Cristina Núñez
- BIOSCOPE Group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon 2829-516, Monte da Caparica (Portugal) E-mail: @fct.unl.pt ; Ecology Research Group, Department of Geographical and Life Sciences, Canterbury Christ Church University CT1 1QU, Canterbury (UK)
| | - Rufina Bastida
- Inorganic Chemistry Department, Faculty of Chemistry, University of Santiago de Compostela 15782 Santiago de Compostela (Spain)
| | - José Luis Capelo
- BIOSCOPE Group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon 2829-516, Monte da Caparica (Portugal) E-mail: @fct.unl.pt
| | - Carlos Lodeiro
- BIOSCOPE Group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon 2829-516, Monte da Caparica (Portugal) E-mail: @fct.unl.pt
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