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SanchesTrevizol J, Dionizio A, Delgado AQ, Ventura TMO, da Silva Ribeiro CF, Rabelo Buzalaf N, Bosqueiro JR, Buzalaf MAR. Optimized protocol for shotgun label-free proteomic analysis of pancreatic islets. Biol Methods Protoc 2024; 9:bpae003. [PMID: 38405023 PMCID: PMC10893585 DOI: 10.1093/biomethods/bpae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
Pancreatic islets are crucial in diabetes research. Consequently, this protocol aims at optimizing both the protein-extraction process and the proteomic analysis via shotgun methods for pancreatic islets. Six protocols were tested, combining three types of chemical extraction with two mechanical extraction methods. Furthermore, two protocols incorporated a surfactant to enhance enzymatic cleavage. The steps involved extraction and concentration of protein, protein quantification, reduction, alkylation, digestion, purification and desalination, sample concentration to ∼1 µl, and proteomic analysis using the mass spectrometer. The most effective protocol involves either a milder chemical extraction paired with a more intensive mechanical process, or a more robust chemical extraction paired with a gentle mechanical process, tailored to the sample's characteristics. Additionally, it was observed that the use of a surfactant proved ineffective for these types of samples. Protocol 5 was recently used with success to examine metabolic changes in pancreatic islets of non-obese diabetic mice exposed to low doses of fluoride ions (F-) and the primary pathways altered by the treatment.
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Affiliation(s)
- Juliana SanchesTrevizol
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | | | | | | | - Nathalia Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - José Roberto Bosqueiro
- Department of Physical Education, Faculty of Science, São Paulo State University, Bauru, São Paulo, Brazil
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Behera RN, Bisht VS, Giri K, Ambatipudi K. Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment. Proteomics Clin Appl 2023; 17:e2300016. [PMID: 37259687 DOI: 10.1002/prca.202300016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.
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Affiliation(s)
- Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vinod S Bisht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldeep Giri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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3
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Han T, Cong H, Yu B, Shen Y. Application of peptide biomarkers in life analysis based on liquid chromatography-mass spectrometry technology. Biofactors 2022; 48:725-743. [PMID: 35816279 DOI: 10.1002/biof.1875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/18/2022] [Indexed: 12/11/2022]
Abstract
Biomedicine is developing rapidly in the 21st century. Among them, the qualitative and quantitative analysis of peptide biomarkers is of considerable importance for the diagnosis and therapy of diseases and the quality evaluation of drugs and food. The identification and quantitative analysis of peptides have been going on for decades. Traditionally, immunoassays or biological assays are generally used to quantify peptides in biological matrices. However, the selectivity and sensitivity of these methods cannot meet the requirements of the application. The separation and analysis technique of liquid chromatography-mass spectrometry (LC-MS) supplies a reliable alternative. In contrast to immunoassays, LC-MS methods are capable of providing the analytical prowess necessary to satisfy the demands of peptide biomarker research in the life sciences arena. This review article provides a historical account of the in-roads made by LC-MS technology for the detection of peptide biomarkers in the past 10 years, with the focus on the qualification/quantification developments and their applications.
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Affiliation(s)
- Tingting Han
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
| | - Hailin Cong
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, China
| | - Bing Yu
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
- State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, China
| | - Youqing Shen
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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Nienhaus K, Xue Y, Shang L, Nienhaus GU. Protein adsorption onto nanomaterials engineered for theranostic applications. NANOTECHNOLOGY 2022; 33:262001. [PMID: 35294940 DOI: 10.1088/1361-6528/ac5e6c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The key role of biomolecule adsorption onto engineered nanomaterials for therapeutic and diagnostic purposes has been well recognized by the nanobiotechnology community, and our mechanistic understanding of nano-bio interactions has greatly advanced over the past decades. Attention has recently shifted to gaining active control of nano-bio interactions, so as to enhance the efficacy of nanomaterials in biomedical applications. In this review, we summarize progress in this field and outline directions for future development. First, we briefly review fundamental knowledge about the intricate interactions between proteins and nanomaterials, as unraveled by a large number of mechanistic studies. Then, we give a systematic overview of the ways that protein-nanomaterial interactions have been exploited in biomedical applications, including the control of protein adsorption for enhancing the targeting efficiency of nanomedicines, the design of specific protein adsorption layers on the surfaces of nanomaterials for use as drug carriers, and the development of novel nanoparticle array-based sensors based on nano-bio interactions. We will focus on particularly relevant and recent examples within these areas. Finally, we conclude this topical review with an outlook on future developments in this fascinating research field.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe, Germany
| | - Yumeng Xue
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an, 710072, People's Republic of China
| | - Li Shang
- State Key Laboratory of Solidification Processing, Center for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi'an, 710072, People's Republic of China
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), D-76344 Eggenstein-Leopoldshafen, Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology (KIT), D-76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States of America
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5
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Uddin MS, Kabir MT, Rahman MS, Behl T, Jeandet P, Ashraf GM, Najda A, Bin-Jumah MN, El-Seedi HR, Abdel-Daim MM. Revisiting the Amyloid Cascade Hypothesis: From Anti-Aβ Therapeutics to Auspicious New Ways for Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21165858. [PMID: 32824102 PMCID: PMC7461598 DOI: 10.3390/ijms21165858] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/03/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disorder related to age, characterized by the cerebral deposition of fibrils, which are made from the amyloid-β (Aβ), a peptide of 40–42 amino acids. The conversion of Aβ into neurotoxic oligomeric, fibrillar, and protofibrillar assemblies is supposed to be the main pathological event in AD. After Aβ accumulation, the clinical symptoms fall out predominantly due to the deficient brain clearance of the peptide. For several years, researchers have attempted to decline the Aβ monomer, oligomer, and aggregate levels, as well as plaques, employing agents that facilitate the reduction of Aβ and antagonize Aβ aggregation, or raise Aβ clearance from brain. Unluckily, broad clinical trials with mild to moderate AD participants have shown that these approaches were unsuccessful. Several clinical trials are running involving patients whose disease is at an early stage, but the preliminary outcomes are not clinically impressive. Many studies have been conducted against oligomers of Aβ which are the utmost neurotoxic molecular species. Trials with monoclonal antibodies directed against Aβ oligomers have exhibited exciting findings. Nevertheless, Aβ oligomers maintain equivalent states in both monomeric and aggregation forms; so, previously administered drugs that precisely decrease Aβ monomer or Aβ plaques ought to have displayed valuable clinical benefits. In this article, Aβ-based therapeutic strategies are discussed and several promising new ways to fight against AD are appraised.
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Affiliation(s)
- Md. Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka 1213, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka 1207, Bangladesh
- Correspondence: ; Tel.: +880-171-022-0110
| | - Md. Tanvir Kabir
- Department of Pharmacy, BRAC University, Dhaka 1212, Bangladesh;
| | - Md. Sohanur Rahman
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India;
| | - Philippe Jeandet
- Research Unit, Induced Resistance and Plant Bioprotection, EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims CEDEX 2, France;
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Agnieszka Najda
- Laboratory of Quality of Vegetables and Medicinal Plants, Department of Vegetable Crops and Medicinal Plants, University of Life Sciences in Lublin, 15 Akademicka Street, 20-950 Lublin, Poland;
| | - May N. Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia;
| | - Hesham R. El-Seedi
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China;
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 23 Uppsala, Sweden
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Koom 32512, Egypt
| | - Mohamed M. Abdel-Daim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
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Mercer C, Jones A, Rusling JF, Leech D. Multiplexed Electrochemical Cancer Diagnostics With Automated Microfluidics. ELECTROANAL 2019; 31:208-211. [PMID: 32390709 PMCID: PMC7207070 DOI: 10.1002/elan.201800632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/26/2018] [Indexed: 01/08/2023]
Abstract
Microfluidic platforms can lead to miniaturisation, increased throughput and reduced reagent consumption, particularly when the processes are automated. Here, a programmable microcontroller is used for automation of a microfluidic platform configured to electrochemically determine the levels of 8 proteins simultaneously in complex liquid samples. The platform system is composed of a programmable Arduino microcontroller that controls inexpensive valve actuators, pump, magnetic stirrer and electronic display. The programmable microcontroller results in repeatable timing for each step in a complex assay protocol, such as sandwich immunoassays. Application of the platform is demonstrated using a multiplexed electrochemical immunoassay based on capture at the electrode surface of magnetic particles labelled with horseradish peroxidase and detection antibody. The multiplexed assay protocol is completed in less than 30 mins and results in detection of eight proteins associated with prostate cancer. The approach presented can be used to automate and simplify high-throughput screening campaigns, such as detection of multiple biomarkers in patient samples.
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Affiliation(s)
- Conan Mercer
- School of Chemistry, and Ryan Institute National University of Ireland Galway University Road, Galway
| | - Abby Jones
- Department of Chemistry University of Connecticut Storrs, CT 06269, USA
| | - James F. Rusling
- School of Chemistry, and Ryan Institute National University of Ireland Galway University Road, Galway
- Department of Chemistry University of Connecticut Storrs, CT 06269, USA
- Institute of Materials Science University of Connecticut Storrs, CT 06269, USA
- Department of Surgery, and Neag Cancer Center UConn Health Farmington, CT 06032, USA
| | - Dónal Leech
- School of Chemistry, and Ryan Institute National University of Ireland Galway University Road, Galway
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Masood A, Benabdelkamel H, Alfadda AA. Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity. High Throughput 2018; 7:ht7030027. [PMID: 30213114 PMCID: PMC6164994 DOI: 10.3390/ht7030027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography in combination with mass spectrometry, for high-throughput protein identification. These studies have applied proteomics to comprehensive biochemical profiling and comparison studies while using different tissues and biological fluids from patients to demonstrate the physiological or pathological adaptations within their proteomes. Further investigations into these proteome-wide alterations will enable us to not only understand the disease pathophysiology, but also to determine signature proteins that can serve as biomarkers for obesity and related diseases. This review examines the different proteomic techniques used to study human obesity and discusses its successful applications along with its technical limitations.
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Affiliation(s)
- Afshan Masood
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia.
| | - Hicham Benabdelkamel
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia.
| | - Assim A Alfadda
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia.
- Department of Medicine, College of Medicine, King Saud University, P.O. Box 2925 (38), Riyadh 11461, Saudi Arabia.
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Golizeh M, Melendez-Pena CE, Ward BJ, Saeed S, Santamaria C, Conway B, Cooper C, Klein MB, Ndao M. Proteomic fingerprinting in HIV/HCV co-infection reveals serum biomarkers for the diagnosis of fibrosis staging. PLoS One 2018; 13:e0195148. [PMID: 29608613 PMCID: PMC5880398 DOI: 10.1371/journal.pone.0195148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/16/2018] [Indexed: 12/18/2022] Open
Abstract
Background Hepatic complications of hepatitis C virus (HCV), including fibrosis and cirrhosis are accelerated in human immunodeficiency virus (HIV)-infected individuals. Although, liver biopsy remains the gold standard for staging HCV-associated liver disease, this test can result in serious complications and is subject to sampling errors. These challenges have prompted a search for non-invasive methods for liver fibrosis staging. To this end, we compared serum proteome profiles at different stages of fibrosis in HIV/HCV co- and HCV mono-infected patients using surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS). Methods Sera from 83 HIV/HCV co- and 68 HCV mono-infected subjects in 4 stages of fibrosis were tested. Sera were fractionated, randomly applied to protein chip arrays (IMAC, CM10 and H50) and spectra were generated at low and high laser intensities. Results Sixteen biomarkers achieved a p value < 0.01 (ROC values > 0.75 or < 0.25) predictive of fibrosis status in co-infected individuals and 14 in mono infected subjects. Five of these candidate biomarkers contributed to both mono- and co-infected subjects. Candidate diagnostic algorithms were created to distinguish between non-fibrotic and fibrotic individuals using a panel of 4 biomarker peaks. Conclusion These data suggest that SELDI MS profiling can identify diagnostic serum biomarkers for fibrosis that are both common and distinct in HIV/HCV co-infected and HCV mono-infected individuals.
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Affiliation(s)
- Makan Golizeh
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Brian J. Ward
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Sahar Saeed
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, Quebec, Canada
| | - Cynthia Santamaria
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Brian Conway
- Vancouver Infectious Diseases Center, Vancouver, British Columbia, Canada
| | - Curtis Cooper
- The Ottawa Hospital-General Campus, Ottawa, Ontario, Canada
| | - Marina B. Klein
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, Quebec, Canada
| | - Momar Ndao
- Program in Infectious Diseases and Immunity in Global Health, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- National Reference Centre for Parasitology, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- * E-mail:
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Lim J, Cho J, Paik Y, Chang Y, Kim H. Diagnostic Application of Serum Proteomic Patterns in Gastric Cancer Patients by ProteinChip Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Int J Biol Markers 2018; 22:281-6. [DOI: 10.1177/172460080702200407] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is one of the currently used techniques to identify biomarkers for cancers. This study was planned to establish a system to accurately distinguish gastric cancer patients by using SELDI-TOF-MS. A total of 100 serum samples obtained from 60 individuals with gastric cancer and 40 healthy individuals were screened. Protein expression profiles were expressed on CM10 ProteinChip arrays and analyzed. Peak intensities were analyzed with the Biomarker Wizard software to identify peaks showing significantly different intensities between normal and cancer groups. Classification analysis and construction of decision trees were done with the Biomarker Pattern software 5.0. Seventeen protein peaks showed significant differences between the two groups. The decision tree which gave the highest discrimination included four peaks at mass 5,919, 8,583, 10,286, and 13,758 as splitters. The sensitivity and specificity for classification of the decision tree were 96.7% (58/60) and 97.5% (39/40), respectively. When the protein biomarker pattern was tested on a blinded test set, it yielded a sensitivity of 93.3% (28/30) and a specificity of 90% (18/20). These results suggest that serum protein profiling by the SELDI system may distinguish gastric cancer patients from healthy controls with relatively high sensitivity and specificity.
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Affiliation(s)
- J.Y. Lim
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - J.Y. Cho
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - Y.H. Paik
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - Y.S. Chang
- Department of Internal Medicine, Yonsei Yongdong Cancer Center, Yonsei University College of Medicine, Seoul
| | - H.G. Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul - South Korea
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Röthlisberger S, Pedroza-Diaz J. Urine protein biomarkers for detection of cardiovascular disease and their use for the clinic. Expert Rev Proteomics 2017; 14:1091-1103. [DOI: 10.1080/14789450.2017.1394188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sarah Röthlisberger
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
| | - Johanna Pedroza-Diaz
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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Biron D, Nedelkov D, Missé D, Holzmuller P. Proteomics and Host–Pathogen Interactions. GENETICS AND EVOLUTION OF INFECTIOUS DISEASES 2017. [PMCID: PMC7149668 DOI: 10.1016/b978-0-12-799942-5.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Zhang F, Xu C, Ning L, Hu F, Shan G, Chen H, Yang M, Chen W, Yu J, Xu G. Exploration of Serum Proteomic Profiling and Diagnostic Model That Differentiate Crohn's Disease and Intestinal Tuberculosis. PLoS One 2016; 11:e0167109. [PMID: 27997555 PMCID: PMC5173341 DOI: 10.1371/journal.pone.0167109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/07/2016] [Indexed: 01/30/2023] Open
Abstract
AIM To explore the diagnostic models of Crohn's disease (CD), Intestinal tuberculosis (ITB) and the differential diagnostic model between CD and ITB by analyzing serum proteome profiles. METHODS Serum proteome profiles from 30 CD patients, 21 ITB patients and 30 healthy controls (HCs) were analyzed by using weak cationic magnetic beads combined with MALDI-TOF-MS technique to detect the differentially expressed proteins of serum samples. Three groups were made and compared accordingly: group of CD patients and HCs, group of ITB patients and HCs, group of CD patients and ITB patients. Wilcoxon rank sum test was used to screen the ten most differentiated protein peaks (P < 0.05). Genetic algorithm combining with support vector machine (SVM) was utilized to establish the optimal diagnostic models for CD, ITB and the optimal differential diagnostic model between CD and ITB. The predictive effects of these models were evaluated by Leave one out (LOO) cross validation method. RESULTS There were 236 protein peaks differently expressed between group of CD patients and HCs, 305 protein peaks differently expressed between group of ITB patients and HCs, 332 protein peaks differently expressed between group of CD patients and ITB patients. Ten most differentially expressed peaks were screened out between three groups respectively (P < 0.05) to establish diagnostic models and differential diagnostic model. A diagnostic model comprising of four protein peaks (M/Z 4964, 3029, 2833, 2900) can well distinguish CD patients and HCs, with a specificity and sensitivity of 96.7% and 96.7% respectively. A diagnostic model comprising four protein peaks (M/Z 3030, 2105, 2545, 4210) can well distinguish ITB patients and HCs, with a specificity and sensitivity of 93.3% and 95.2% respectively. A differential diagnostic model comprising three potential biomarkers protein peaks (M/Z 4267, 4223, 1541) can well distinguish CD patients and ITB patients, with a specificity and sensitivity of 76.2% and 80.0% respectively. Among the eleven protein peaks from the diagnostic models and differential diagnostic model, two have been successfully purified and identified, Those two peaks were M/Z 2900 from the diagnostic model between CD and HCs and M/Z 1541 from the differential diagnostic model between CD and ITB. M/Z 2900 was identified as appetite peptide, M/Z 1541 was identified as Lysyl oxidase-like 2 (LOXL-2). CONCLUSION The differently expressed protein peaks analyzed by serum proteome with weak cationic magnetic beads combined MALDI-TOF-MS technique can effectively distinguish CD patients and HCs, ITB patients and HCs, CD patients and ITB patients. The diagnostic model between CD patients and HCs consisting of four protein peaks (M/Z 4964, 3029, 2833, 2900), the diagnostic model between ITB patients and HCs comprising four protein peaks (M/Z 3030, 2105, 2545, 4210) and the differential diagnostic model between CD patients and ITB patients comprising three protein peaks (M/Z 4267, 4223, 1541) had high specificity and sensitivity and can contribute to diagnoses of CD, ITB and the differential diagnosis between CD and ITB. Two proteins from the diagnostic model of CD and the differential diagnostic model between CD and ITB were identified. Further experiments are required using a larger cohort of samples.
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Affiliation(s)
- Fenming Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chengfu Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Longgui Ning
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Fengling Hu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Guodong Shan
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Hongtan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Ming Yang
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Wenguo Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jiekai Yu
- Department of Tumor Research Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Guoqiang Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- * E-mail:
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Tracing the voyage of SELDI-TOF MS in cancer biomarker discovery and its current depreciation trend – need for resurrection? Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
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Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
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Plasma biosignature and brain pathology related to persistent cognitive impairment in late-life depression. Mol Psychiatry 2015; 20:594-601. [PMID: 25092249 PMCID: PMC4494754 DOI: 10.1038/mp.2014.76] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/19/2014] [Accepted: 06/06/2014] [Indexed: 02/03/2023]
Abstract
Cognitive impairment is highly prevalent among individuals with late-life depression (LLD) and tends to persist even after successful treatment. The biological mechanisms underlying cognitive impairment in LLD are complex and likely involve abnormalities in multiple pathways, or 'cascades,' reflected in specific biomarkers. Our aim was to evaluate peripheral (blood-based) evidence for biological pathways associated with cognitive impairment in older adults with LLD. To this end, we used a data-driven comprehensive proteomic analysis (multiplex immunoassay including 242 proteins), along with measures of structural brain abnormalities (gray matter atrophy and white matter hyperintensity volume via magnetic resonance imaging), and brain amyloid-β (Aβ) deposition (PiB-positron emission tomography). We analyzed data from 80 older adults with remitted major depression (36 with mild cognitive impairment (LLD+MCI) and 44 with normal cognitive (LLD+NC)) function. LLD+MCI was associated with differential expression of 24 proteins (P<0.05 and q-value <0.30) related mainly to the regulation of immune-inflammatory activity, intracellular signaling, cell survival and protein and lipid homeostasis. Individuals with LLD+MCI also showed greater white matter hyperintensity burden compared with LLD+NC (P=0.015). We observed no differences in gray matter volume or brain Aβ deposition between groups. Machine learning analysis showed that a group of three proteins (Apo AI, IL-12 and stem cell factor) yielded accuracy of 81.3%, sensitivity of 75% and specificity of 86.4% in discriminating participants with MCI from those with NC function (with an averaged cross-validation accuracy of 76.3%, sensitivity of 69.4% and specificity of 81.8% with nested cross-validation considering the model selection bias). Cognitive impairment in LLD seems to be related to greater cerebrovascular disease along with abnormalities in immune-inflammatory control, cell survival, intracellular signaling, protein and lipid homeostasis, and clotting processes. These results suggest that individuals with LLD and cognitive impairment may be more vulnerable to accelerated brain aging and shed light on possible mediators of their elevated risk for progression to dementia.
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Agarwal S, Ghanty P, Pal NR. Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer’s disease. Bioinformatics 2015; 31:2505-13. [DOI: 10.1093/bioinformatics/btv173] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 03/22/2015] [Indexed: 01/23/2023] Open
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Pedroza-Díaz J, Röthlisberger S. Advances in urinary protein biomarkers for urogenital and non-urogenital pathologies. Biochem Med (Zagreb) 2015; 25:22-35. [PMID: 25672464 PMCID: PMC4401308 DOI: 10.11613/bm.2015.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/14/2014] [Indexed: 01/18/2023] Open
Abstract
The discovery of protein biomarkers that reflect the biological state of the body is of vital importance to disease management. Urine is an ideal source of biomarkers that provides a non-invasive approach to diagnosis, prognosis and prediction of diseases. Consequently, the study of the human urinary proteome has increased dramatically over the last 10 years, with many studies being published. This review focuses on urinary protein biomarkers that have shown potential, in initial studies, for diseases affecting the urogenital tract, specifically chronic kidney disease and prostate cancer, as well as other non-urogenital pathologies such as breast cancer, diabetes, atherosclerosis and osteoarthritis. PubMed was searched for peer-reviewed literature on the subject, published in the last 10 years. The keywords used were "urine, biomarker, protein, and/or prostate cancer/breast cancer/chronic kidney disease/diabetes/atherosclerosis/osteoarthritis". Original studies on the subject, as well as a small number of reviews, were analysed including the strengths and weaknesses, and we summarized the performance of biomarkers that demonstrated potential. One of the biggest challenges found is that biomarkers are often shared by several pathologies so are not specific to one disease. Therefore, the trend is shifting towards implementing a panel of biomarkers, which may increase specificity. Although there have been many advances in urinary proteomics, these have not resulted in similar advancements in clinical practice due to high costs and the lack of large data sets. In order to translate these potential biomarkers to clinical practice, vigorous validation is needed, with input from industry or large collaborative studies.
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Affiliation(s)
- Johanna Pedroza-Díaz
- Instituto Tecnologico Metropolitano, Facultad de Ciencias Exactas y Aplicadas, Medellin, Colombia
| | - Sarah Röthlisberger
- Instituto Tecnologico Metropolitano, Facultad de Ciencias Exactas y Aplicadas, Medellin, Colombia
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Fania C, Sogno I, Vasso M, Torretta E, Leone R, Bruno A, Consonni P, Albini A, Gelfi C. A PSA-guided approach for a better diagnosis of prostatic adenocarcinoma based on MALDI profiling and peptide identification. Clin Chim Acta 2014; 439:42-9. [PMID: 25312866 DOI: 10.1016/j.cca.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is the second cause of mortality in men worldwide. The prostate-specific antigen (PSA) test is routinely adopted in diagnosis; nevertheless more reliable biomarkers are continuously under investigation by monitoring the release of molecules into the bloodstream. The serum protein profiles appear to provide cancer-specific fingerprints that help to discriminate patients (especially with low PSA level) from controls, improving the performance of existing clinical tests. METHODS Samples from healthy controls and PCa patients with low (≤4 ng/mL) and high PSA (>4 ng/mL) levels were analyzed by MALDI profiling, and by a multi fractionation approach coupled to ESI-MS for peaks identification. RESULTS MALDI profiling achieved to detect 10 and 14 changed peaks (p-value <0.05), respectively, in PCa patients with low and high PSA versus controls. In particular, a peak identified as C3f fragment, resulted overexpressed in low PSA PCa patients. CONCLUSIONS PSA test, coupled to MALDI profiling, is able to detect changes, specifically related to PCa, in low molecular weight protein range. Furthermore, for the first time in prostate cancer research, the identification and quantification of the small peptide C3f appears to be relevant for the detection of false negatives, providing an additive diagnostic power to PSA (p<0.01) and suggesting its use in clinical tests.
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Affiliation(s)
- Chiara Fania
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy; IRCCS Policlinico San Donato, Piazza Edmondo Malan, San Donato Milanese, Milan 20097, Italy.
| | - Ilaria Sogno
- Istituto di Ricovero e Cura a Carattere Scientifico MultiMedica, via Fantoli 16/15, Milan 20138, Italy.
| | - Michele Vasso
- Istituto di Bioimmagini e Fisiologia Molecolare (IBFM)-CNR, C.da Pietrapollastra-Pisciotto, Cefalù, Palermo 90015, Italy.
| | - Enrica Torretta
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy; IRCCS Policlinico San Donato, Piazza Edmondo Malan, San Donato Milanese, Milan 20097, Italy.
| | - Roberta Leone
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy.
| | - Antonino Bruno
- Istituto di Ricovero e Cura a Carattere Scientifico MultiMedica, via Fantoli 16/15, Milan 20138, Italy.
| | - Paolo Consonni
- Istituto di Ricovero e Cura a Carattere Scientifico MultiMedica, via Fantoli 16/15, Milan 20138, Italy.
| | - Adriana Albini
- IRCCS Tecnologie Avanzate e Modelli Assistenziali in Oncologia - Arcispedale Santa Maria Nuova, Viale Umberto I 50, Reggio Emilia 42123, Italy.
| | - Cecilia Gelfi
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi Di Milano, Via F.lli Cervi 93, Segrate, Milan 20090, Italy; IRCCS Policlinico San Donato, Piazza Edmondo Malan, San Donato Milanese, Milan 20097, Italy; Istituto di Bioimmagini e Fisiologia Molecolare (IBFM)-CNR, Via F.lli Cervi 93, Segrate, Milan 20090, Italy.
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20
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Xin YN, Geng N, Lin ZH, Cui YZ, Duan HP, Zhang M, Xuan SY. Serum complement C3f and fibrinopeptide A are potential novel diagnostic biomarkers for non-alcoholic fatty liver disease: a study in Qingdao Twins. PLoS One 2014; 9:e108132. [PMID: 25250770 PMCID: PMC4176972 DOI: 10.1371/journal.pone.0108132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 08/25/2014] [Indexed: 01/20/2023] Open
Abstract
Aims To compare the different serum peptidome patterns between twins with and without non-alcoholic fatty liver disease (NAFLD) in order to help understand the pathogenesis of NAFLD and to identify potential diagnostic and therapeutic targets. Methods The peptidomics patterns of 63 cases with NAFLD were compared with their twin healthy controls in Qingdao, China. Peptides between 800Da and 3500Da were captured and concentrated using C18 reversed-phase columns, followed by MALDI-TOF mass spectrometry. The sequences of peptides associated with NAFLD were further identified by MALDI-TOF-TOF. Further validation studies were conducted. One hundred additional serum samples were detected by commercially available ELISA kits to calculate the concentrations of complement C3f and fibrinopeptide A, respectively. The differences of these two peptides in the NAFLD and control groups were compared using SPSS 17.0, respectively. Results Compared with healthy controls, eleven peaks (861.1, 877.07, 904.5, 1206.57, 1350.64, 1518.7, 1690.9, 1777.94, 2931.29, 3190.4, 3261.4) were up-regulated and 7 peaks (942.44, 1020.47, 1060.06, 1211.7, 1263.63, 1449.76, 2768.3) were down-regulated in the NAFLD group. Two peptides derived from complement C3f and fibrinopeptide A, respectively, had the highest ROC values indistinguishing NAFLD cases from their normal controls. In the validation group, the concentrations of complement C3f and fibrinopeptide A (1466.929±78.306 pg/ml, 4.189±0.326 ng/ml, respevtively) in NAFLD group was higher than in control group (complement C3f 1159.357±99.624 pg/ml, FPA 3.039±0.483 ng/ml; P<0.05). Conclusions In this study, we established apeptidomics pattern that could help distinguish NAFLD patients from their twin controls. The differently-regulated peptides identified in our study may be potential diagnostic markers or therapeutic targets for NAFLD.
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Affiliation(s)
- Yong-Ning Xin
- Qingdao Municipal Hospital, Qingdao, Shandong Province, PR China
| | - Ning Geng
- School of Medicine, Qingdao University, Qingdao, Shandong Province, PR China
| | - Zhong-Hua Lin
- Qingdao Municipal Hospital, Qingdao, Shandong Province, PR China
| | - Ya-Zhou Cui
- Key Laboratory of Ministry of Health for Biotech-Drug, Key Laboratory for Modern Medicine and Technology of Shandong Province, Shandong Medicinal Biotechnology Center, Shandong Academy of Medical Sciences, Jinan, PR China
| | - Hai-Ping Duan
- Qingdao Municipal Centers for Disease Control and Prevention, Qingdao, Shandong Province, PR China
| | - Mei Zhang
- Qingdao Municipal Hospital, Qingdao, Shandong Province, PR China
| | - Shi-Ying Xuan
- Qingdao Municipal Hospital, Qingdao, Shandong Province, PR China
- * E-mail:
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Redzic JS, Ung TH, Graner MW. Glioblastoma extracellular vesicles: reservoirs of potential biomarkers. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2014; 7:65-77. [PMID: 24634586 PMCID: PMC3952682 DOI: 10.2147/pgpm.s39768] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glioblastoma multiforme (GBM) is the most frequent and most devastating of the primary central nervous system tumors, with few patients living beyond 2 years postdiagnosis. The damage caused by the disease and our treatments for the patients often leave them physically and cognitively debilitated. Generally, GBMs appear after very short clinical histories and are discovered by imaging (using magnetic resonance imaging [MRI]), and the diagnosis is validated by pathology, following surgical resection. The treatment response and diagnosis of tumor recurrence are also tracked by MRI, but there are numerous problems encountered with these monitoring modalities, such as ambiguous interpretation and forms of pseudoprogression. Diagnostic, prognostic, and predictive biomarkers would be an immense boon in following treatment schemes and in determining recurrence, which often requires an invasive intracranial biopsy to verify imaging data. Extracellular vesicles (EVs) are stable, membrane-enclosed, virus-sized particles released from either the cell surface or from endosomal pathways that lead to the systemic release of EVs into accessible biofluids, such as serum/plasma, urine, cerebrospinal fluid, and saliva. EVs carry a wide variety of proteins, nucleic acids, lipids, and other metabolites, with many common features but with enough individuality to be able to identify the cell of origin of the vesicles. These components, if properly interrogated, could allow for the identification of tumor-derived EVs in biofluids, indicating tumor progression, relapse, or treatment failure. That knowledge would allow clinicians to continue with treatment regimens that were actually effective or to change course if the therapies were failing. Here, we review the features of GBM EVs, in terms of EV content and activities that may lead to the use of EVs as serially accessible biomarkers for diagnosis and treatment response in neuro-oncology.
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Affiliation(s)
- Jasmina S Redzic
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Timothy H Ung
- Department of Neurosurgery, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Michael W Graner
- Department of Neurosurgery, School of Medicine, University of Colorado Denver, Aurora, CO, USA
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22
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Fitzsimons NJ, Sun L, Moul JW. Medical technologies for the diagnosis of prostate cancer. Expert Rev Med Devices 2014; 4:227-39. [PMID: 17359227 DOI: 10.1586/17434440.4.2.227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Prostate cancer is an extremely prevalent problem, especially in our aging population. The prostate-specific antigen test has revolutionized prostate cancer screening. Significant advances have been made in the usage of prostate-specific antigen and its derivatives, biomarkers, diagnostic imaging techniques, biopsy strategy, biopsy needle design and anesthetic agents. Further improvement in prostate cancer detection hinges on the development of an imaging technique that is tumor specific and sensitive to biological aggressiveness.
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Affiliation(s)
- Nicholas J Fitzsimons
- Division of Urologic Surgery and Duke Prostate Center, Duke University Medical Center, Durham, NC 27710, USA.
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de Roos B. Proteomic analysis of human plasma and blood cells in nutritional studies: development of biomarkers to aid disease prevention. Expert Rev Proteomics 2014; 5:819-26. [DOI: 10.1586/14789450.5.6.819] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Patel S. Role of Proteomics in Biomarker Discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:39-75. [DOI: 10.1016/b978-0-12-800168-4.00003-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Nagnan-Le Meillour P, Vercoutter-Edouart AS, Hilliou F, Le Danvic C, Lévy F. Proteomic Analysis of Pig (Sus scrofa) Olfactory Soluble Proteome Reveals O-Linked-N-Acetylglucosaminylation of Secreted Odorant-Binding Proteins. Front Endocrinol (Lausanne) 2014; 5:202. [PMID: 25538681 PMCID: PMC4257092 DOI: 10.3389/fendo.2014.00202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 11/13/2014] [Indexed: 11/13/2022] Open
Abstract
The diversity of olfactory binding proteins (OBPs) is a key point to understand their role in molecular olfaction. Since only few different sequences were characterized in each mammalian species, they have been considered as passive carriers of odors and pheromones. We have explored the soluble proteome of pig nasal mucus, taking benefit of the powerful tools of proteomics. Combining two-dimensional electrophoresis, mass spectrometry, and western-blot with specific antibodies, our analyses revealed for the first time that the pig nasal mucus is mainly composed of secreted OBP isoforms, some of them being potentially modified by O-GlcNAcylation. An ortholog gene of the glycosyltransferase responsible of the O-GlcNAc linking on extracellular proteins in Drosophila and Mouse (EOGT) was amplified from tissues of pigs of different ages and sex. The sequence was used in a phylogenetic analysis, which evidenced conservation of EOGT in insect and mammalian models studied in molecular olfaction. Extracellular O-GlcNAcylation of secreted OBPs could finely modulate their binding specificities to odors and pheromones. This constitutes a new mechanism for extracellular signaling by OBPs, suggesting that they act as the first step of odor discrimination.
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Affiliation(s)
- Patricia Nagnan-Le Meillour
- UMR 8576, USC-Unité de Glycobiologie Structurale et Fonctionnelle, INRA, CNRS, Université de Lille 1 , Villeneuve d'Ascq , France
| | | | - Frédérique Hilliou
- UMR 7254, UMR 1355 Institut Sophia Agrobiotech, INRA, CNRS, Université de Nice Sophia Antipolis , Sophia Antipolis , France
| | - Chrystelle Le Danvic
- Unité de Glycobiologie Structurale et Fonctionnelle, Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale (UNCEIA) , Villeneuve d'Ascq , France
| | - Frédéric Lévy
- UMR 7247, UMR 85 Unité de Physiologie de la Reproduction et des Comportements, INRA, CNRS, Université François Rabelais, Haras Nationaux , Nouzilly , France
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Signal amplification strategy for sensitive immunoassay of prostate specific antigen (PSA) based on ferrocene incorporated polystyrene spheres. Anal Chim Acta 2013; 793:19-25. [DOI: 10.1016/j.aca.2013.07.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 07/19/2013] [Accepted: 07/25/2013] [Indexed: 12/13/2022]
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Kossowska B, Dudka I, Gancarz R, Antonowicz-Juchniewicz J. Application of classic epidemiological studies and proteomics in research of occupational and environmental exposure to lead, cadmium and arsenic. Int J Hyg Environ Health 2013; 216:1-7. [DOI: 10.1016/j.ijheh.2012.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/16/2012] [Accepted: 03/07/2012] [Indexed: 10/28/2022]
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ZHAO JING, BO BING, YIN YONGMEI, LI GENXI. GOLD NANOPARTICLES-BASED BIOSENSORS FOR BIOMEDICAL APPLICATION. ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1793984412300087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gold nanoparticles are the most extensively studied nanomaterials for biomedical application due to their unique properties, such as rapid and simple synthesis, large surface area, strong adsorption ability and facile conjugation to various biomolecules. The remarkable photophysical properties of gold nanoparticles have provided plenty of opportunities for the preparation of gold nanoparticles-based optical biosensors, while the excellent biocompatibility, conductivity, catalytic properties and large surface-to-volume ratio have facilitated the application of gold nanoparticles in the construction of electrochemical biosensors. In this review, we mainly detail the gold nanoparticles-based optical and electrochemical biosensors for biomedical application in the recent two years, which have exhibited greatly enhanced analytical performances in the detection of DNA, proteins and some important small molecules.
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Affiliation(s)
- JING ZHAO
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - BING BO
- Department of Oncology, The First Affiliated, Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - YONG-MEI YIN
- Department of Oncology, The First Affiliated, Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - GEN-XI LI
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Department of Biochemistry and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P. R. China
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Chang WC, Hsu PI, Chen YY, Hsiao M, Lu PJ, Chen CH. Observation of peptide differences between cancer and control in gastric juice. Proteomics Clin Appl 2012; 2:55-62. [PMID: 21136779 DOI: 10.1002/prca.200780066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Biomarkers for various diseases have been extensively searched for the past 5 years. Nevertheless, most efforts were focused on the search for protein biomarkers from serum samples. In this work, we tried to look for peptide biomarkers from gastric juice samples with MALDI-TOF-MS. More than 200 gastric juice samples from healthy people, gastric ulcer patients, duodenal ulcer patients, and cancer patients were examined. There were clear pattern differences of mass spectra among samples from healthy people and patients with different gastric diseases. We found five peptides for gastric cancer diagnosis with high sensitivity and specificity. Sequences of these five peptides, including two pepsinogen fragments, leucine zipper protein fragment, albumin fragment, and α-1-antitrypsin fragment, have been identified by mass spectrometric analysis and immuno-deplete assay with antibodies.
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Affiliation(s)
- Wei-Chao Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Tan HT, Lee YH, Chung MCM. Cancer proteomics. MASS SPECTROMETRY REVIEWS 2012; 31:583-605. [PMID: 22422534 DOI: 10.1002/mas.20356] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/16/2011] [Accepted: 11/16/2011] [Indexed: 05/31/2023]
Abstract
Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early-stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high-throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology.
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Affiliation(s)
- Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Di Carlo M, Giacomazza D, San Biagio PL. Alzheimer's disease: biological aspects, therapeutic perspectives and diagnostic tools. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:244102. [PMID: 22595372 DOI: 10.1088/0953-8984/24/24/244102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia among older people. Dementia is an irreversible brain disorder that seriously affects a person's ability to carry out daily activities. It is characterized by loss of cognitive functioning and behavioral abilities, to such an extent that it interferes with the daily life and activities of the affected patients. Although it is still unknown how the disease process begins, it seems that brain damage starts a decade or more before problems become evident. Scientific data seem to indicate that changes in the generation or the degradation of the amyloid-b peptide (Aβ) lead to the formation of aggregated structures that are the triggering molecular events in the pathogenic cascade of AD. This review summarizes some characteristic features of Aβ misfolding and aggregation and how cell damage and death mechanisms are induced by these supramolecular and toxic structures. Further, some interventions for the early diagnosis of AD are described and in the last part the potential therapeutic strategies adoptable to slow down, or better block, the progression of the pathology are reported.
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Affiliation(s)
- M Di Carlo
- Istituto di Biomedicina ed Immunologia Molecolare (IBIM), CNR, Palermo, Italy.
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Liu Y, Liu Y, Feng H, Wu Y, Joshi L, Zeng X, Li J. Layer-by-layer assembly of chemical reduced graphene and carbon nanotubes for sensitive electrochemical immunoassay. Biosens Bioelectron 2012; 35:63-68. [DOI: 10.1016/j.bios.2012.02.007] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/02/2012] [Accepted: 02/06/2012] [Indexed: 01/05/2023]
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Clarke MSF. Proteomic analysis of skeletal muscle tissue using SELDI-TOF MS: application to disuse atrophy. Methods Mol Biol 2012; 818:131-141. [PMID: 22083821 DOI: 10.1007/978-1-61779-418-6_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Skeletal muscle atrophy in response to disuse/unloading is a complex adaptation that involves many components of the muscle tissue. The underlying mechanisms that initiate and control the loss of muscle tissue during this response, especially contractile proteins located within the myofibers, are as yet unclear. One approach capable of distinguishing protein changes specifically associated with disuse/unloading-induced skeletal muscle atrophy is to compare the proteomic profiles of similar muscles between control, unloaded/atrophied, and unloaded/"atrophy-protected" experimental conditions. By utilizing a subtractive proteomic analysis approach, those proteins specifically modulated during the atrophic response can be identified and discriminated from those associated with disuse in general. We here describe the use of SELDI-TOF MS coupled with micro-scale preparative ion-exchange chromatography to detect proteins potentially specifically associated with the atrophic response in rat skeletal muscle.
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Affiliation(s)
- Mark S F Clarke
- Department of Health and Human Performance, University of Houston, Houston, TX, USA.
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Suzuki S, Yamayoshi Y, Nishimuta A, Tanigawara Y. S100A10 protein expression is associated with oxaliplatin sensitivity in human colorectal cancer cells. Proteome Sci 2011; 9:76. [PMID: 22206547 PMCID: PMC3317844 DOI: 10.1186/1477-5956-9-76] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 12/30/2011] [Indexed: 12/27/2022] Open
Abstract
Background Individual responses to oxaliplatin (L-OHP)-based chemotherapy remain unpredictable. The objective of our study was to find candidate protein markers for tumor sensitivity to L-OHP from intracellular proteins of human colorectal cancer (CRC) cell lines. We performed expression difference mapping (EDM) analysis of whole cell lysates from 11 human CRC cell lines with different sensitivities to L-OHP by using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), and identified a candidate protein by liquid chromatography/mass spectrometry ion trap time-of-flight (LCMS-IT-TOF). Results Of the qualified mass peaks obtained by EDM analysis, 41 proteins were differentially expressed in 11 human colorectal cancer cell lines. Among these proteins, the peak intensity of 11.1 kDa protein was strongly correlated with the L-OHP sensitivity (50% inhibitory concentrations) (P < 0.001, R2 = 0.80). We identified this protein as Protein S100-A10 (S100A10) by MS/MS ion search using LCMS-IT-TOF. We verified its differential expression and the correlation between S100A10 protein expression levels in drug-untreated CRC cells and their L-OHP sensitivities by Western blot analyses. In addition, S100A10 protein expression levels were not correlated with sensitivity to 5-fluorouracil, suggesting that S100A10 is more specific to L-OHP than to 5-fluorouracil in CRC cells. S100A10 was detected in cell culture supernatant, suggesting secretion out of cells. Conclusions By proteomic approaches including SELDI technology, we have demonstrated that intracellular S100A10 protein expression levels in drug-untreated CRC cells differ according to cell lines and are significantly correlated with sensitivity of CRC cells to L-OHP exposure. Our findings provide a new clue to searching predictive markers of the response to L-OHP, suggesting that S100A10 is expected to be one of the candidate protein markers.
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Affiliation(s)
- Sayo Suzuki
- Department of Clinical Pharmacokinetics and Pharmacodynamics, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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Chen HS, Liu M, Shi LJ, Zhao JL, Zhang CP, Lin LQ, Liu Y, Zhang SJ, Jin JC, Wang L, Shen BZ, Liu JR. Effects of Raspberry Phytochemical Extract on Cell Proliferation, Apoptosis, and Serum Proteomics in a Rat Model. J Food Sci 2011; 76:T192-8. [PMID: 22417609 DOI: 10.1111/j.1750-3841.2011.02373.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hong-Sheng Chen
- Treatment Center of Oncology, the Fourth Affiliated Hospital of Harbin Medical Univ., 37 YiYuan Street, NanGang District, Harbin 150001, PR China
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A renewable and ultrasensitive electrochemiluminescence immunosenor based on magnetic RuL@SiO2-Au~RuL-Ab2 sandwich-type nano-immunocomplexes. SENSORS 2011; 11:7749-62. [PMID: 22164043 PMCID: PMC3231728 DOI: 10.3390/s110807749] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/20/2011] [Accepted: 07/21/2011] [Indexed: 11/17/2022]
Abstract
An ultrasensitive and renewable electrochemiluminescence (ECL) immunosensor was developed for the detection of tumor markers by combining a newly designed trace tag and streptavidin-coated magnetic particles (SCMPs). The trace tag (RuL@SiO(2)-Au~RuL-Ab2) was prepared by loading Ru(bpy)(3)(2+)(RuL)-conjuged secondary antibodies (RuL-Ab2) on RuL@SiO(2) (RuL-doped SiO(2)) doped Au (RuL@SiO(2)-Au). To fabricate the immunosensor, SCMPs were mixed with biotinylated AFP primary antibody (Biotin-Ab1), AFP, and RuL@SiO2-Au~RuL-Ab2 complexes, then the resulting SCMP/Biotin-Ab1/AFP/RuL@SiO2-Au~RuL-Ab2 (SBAR) sandwich-type immunocomplexes were absorbed on screen printed carbon electrode (SPCE) for detection. The immunocomplexes can be easily washed away from the surface of the SPCE when the magnetic field was removed, which made the immunosensor reusable. The present immunosensor showed a wide linear range of 0.05-100 ng mL(-1) for detecting AFP, with a low detection limit of 0.02 ng mL(-1) (defined as S/N = 3). The method takes advantage of three properties of the immunosensor: firstly, the RuL@SiO(2)-Au~RuL-Ab2 composite exhibited dual amplification since SiO(2) could load large amount of reporter molecules (RuL) for signal amplification. Gold particles could provide a large active surface to load more reporter molecules (RuL-Ab2). Accordingly, through the ECL response of RuL and tripropylamine (TPA), a strong ECL signal was obtained and an amplification analysis of protein interaction was achieved. Secondly, the sensor is renewable because the sandwich-type immunocomplexes can be readily absorbed or removed on the SPCE's surface in a magnetic field. Thirdly, the SCMP modified probes can perform the rapid separation and purification of signal antibodies in a magnetic field. Thus, the present immunosensor can simultaneously realize separation, enrichment and determination. It showed potential application for the detection of AFP in human sera.
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Juhász G, Földi I, Penke B. Systems biology of Alzheimer's disease: How diverse molecular changes result in memory impairment in AD. Neurochem Int 2011; 58:739-50. [DOI: 10.1016/j.neuint.2011.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 01/19/2011] [Accepted: 02/10/2011] [Indexed: 01/13/2023]
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The application of SELDI-TOF-MS in clinical diagnosis of cancers. J Biomed Biotechnol 2011; 2011:245821. [PMID: 21687541 PMCID: PMC3114543 DOI: 10.1155/2011/245821] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/30/2011] [Indexed: 12/24/2022] Open
Abstract
Cancer diagnosis is important, and the early diagnosis of cancers could predict a more successful treatment. The proteomic studies emerged to be useful in combined analyses of samples from patients and provide more accurate diagnosis when compared to the single-factor-based diagnosis. In recent years, cancer detection with surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS) is flourishing and brought significant progress in this area. This paper summarizes some recent results with this technique for cancer diagnosis.
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Xu S, Liu Y, Wang T, Li J. Positive Potential Operation of a Cathodic Electrogenerated Chemiluminescence Immunosensor Based on Luminol and Graphene for Cancer Biomarker Detection. Anal Chem 2011; 83:3817-23. [DOI: 10.1021/ac200237j] [Citation(s) in RCA: 319] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shoujiang Xu
- Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- College of Materials Science and Engineering, and Key Laboratory for Micro−Nano Optoelectronic Devices of Ministry of Education, Hunan University, Changsha 410082, China
| | - Yang Liu
- Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Taihong Wang
- College of Materials Science and Engineering, and Key Laboratory for Micro−Nano Optoelectronic Devices of Ministry of Education, Hunan University, Changsha 410082, China
| | - Jinghong Li
- Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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Jensen GC, Krause CE, Sotzing GA, Rusling JF. Inkjet-printed gold nanoparticle electrochemical arrays on plastic. Application to immunodetection of a cancer biomarker protein. Phys Chem Chem Phys 2011; 13:4888-94. [PMID: 21212889 DOI: 10.1039/c0cp01755h] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Electrochemical detection combined with nanostructured sensor surfaces offers potentially low-cost, high-throughput solutions for detection of clinically significant proteins. Inkjet printing offers an inexpensive non-contact fabrication method for microelectronics that is easily adapted for incorporating into protein immunosensor devices. Herein we report the first direct fabrication of inkjet-printed gold nanoparticle arrays, and apply them to electrochemical detection of the cancer biomarker interleukin-6 (IL-6) in serum. The gold nanoparticle ink was printed on a flexible, heat resistant polyimide Kapton substrate and subsequently sintered to create eight-electrode arrays costing <0.2 euro per array. The inkjet-printed working electrodes had reproducible surface areas with RSD <3%. Capture antibodies for IL-6 were linked onto the eight-electrode array, and used in sandwich immunoassays. A biotinylated secondary antibody with 16-18 horseradish peroxidase labels was used, and detection was achieved by hydroquinone-mediated amperometry. The arrays provided a clinically relevant detection limit of 20 pg mL(-1) in calf serum, sensitivity of 11.4 nA pg(-1) cm(-2), and a linear dynamic range of 20-400 pg mL(-1).
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269-3060, USA
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41
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. MASS SPECTROMETRY REVIEWS 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
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42
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Zhang B, Barekati Z, Kohler C, Radpour R, Asadollahi R, Holzgreve W, Zhong XY. Proteomics and biomarkers for ovarian cancer diagnosis. Appl Biochem Biotechnol 2010; 168:910-6. [PMID: 20689132 DOI: 10.1007/s12010-012-9829-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 07/05/2012] [Indexed: 12/13/2022]
Abstract
Ovarian cancer remains a leading cause of death from gynecological malignancy. Early diagnosis is the most important determinant of survival. Current diagnostic tools have had very limited success in early detection. In recent years, the advancing techniques for proteomics have accelerated the discovery of ovarian cancer biomarkers. Numerous proteomics-based molecular biomarkers/panels have been identified and hold great potential for diagnostic applications, but they need further development and validation. This article reviews recently published data on the diagnosis of ovarian cancer with proteomics, including the major proteomics technologies and promising strategies for biomarker discovery and development.
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Affiliation(s)
- Bei Zhang
- Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
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43
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Fish DJ, Brewood GP, Kim JS, Garbett NC, Chaires JB, Benight AS. Statistical analysis of plasma thermograms measured by differential scanning calorimetry. Biophys Chem 2010; 152:184-90. [DOI: 10.1016/j.bpc.2010.09.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 09/22/2010] [Accepted: 09/22/2010] [Indexed: 11/26/2022]
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44
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Humpel C. Identifying and validating biomarkers for Alzheimer's disease. Trends Biotechnol 2010; 29:26-32. [PMID: 20971518 PMCID: PMC3016495 DOI: 10.1016/j.tibtech.2010.09.007] [Citation(s) in RCA: 287] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/28/2010] [Accepted: 09/28/2010] [Indexed: 12/13/2022]
Abstract
The identification and validation of biomarkers for diagnosing Alzheimer's disease (AD) and other forms of dementia are increasingly important. To date, ELISA measurement of β-amyloid(1–42), total tau and phospho-tau-181 in cerebrospinal fluid (CSF) is the most advanced and accepted method to diagnose probable AD with high specificity and sensitivity. However, it is a great challenge to search for novel biomarkers in CSF and blood by using modern potent methods, such as microarrays and mass spectrometry, and to optimize the handling of samples (e.g. collection, transport, processing, and storage), as well as the interpretation using bioinformatics. It seems likely that only a combined analysis of several biomarkers will define a patient-specific signature to diagnose AD in the future.
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Affiliation(s)
- Christian Humpel
- Laboratory of Psychiatry and Experimental Alzheimer's Research, Department of Psychiatry and Psychotherapy, Innsbruck Medical University, Anichstr. 35, A-6020 Innsbruck, Austria.
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Rusling JF, Kumar CV, Gutkind JS, Patel V. Measurement of biomarker proteins for point-of-care early detection and monitoring of cancer. Analyst 2010; 135:2496-511. [PMID: 20614087 DOI: 10.1039/c0an00204f] [Citation(s) in RCA: 355] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This critical review evaluates progress toward viable point-of-care protein biomarker measurements for cancer detection and diagnostics. The ability to measure panels of specific, selective cancer biomarker proteins in physicians' surgeries and clinics has the potential to revolutionize cancer detection, monitoring, and therapy. The dream envisions reliable, cheap, automated, technically undemanding devices that can analyze a patient's serum or saliva in a clinical setting, allowing on-the-spot diagnosis. Existing commercial products for protein assays are reliable in laboratory settings, but have limitations for point-of-care applications. A number of ultrasensitive immunosensors and some arrays have been developed, many based on nanotechnology. Multilabel detection coupled with high capture molecule density in immunosensors and arrays seems to be capable of detecting a wide range of protein concentrations with sensitivity ranging into the sub pg mL(-1) level. Multilabel arrays can be designed to detect both high and ultralow abundance proteins in the same sample. However, only a few of the newer ultrasensitive methods have been evaluated with real patient samples, which is key to establishing clinical sensitivity and selectivity.
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Affiliation(s)
- James F Rusling
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA.
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46
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Munge BS, Fisher J, Millord LN, Krause CE, Dowd RS, Rusling JF. Sensitive electrochemical immunosensor for matrix metalloproteinase-3 based on single-wall carbon nanotubes. Analyst 2010; 135:1345-50. [PMID: 20358056 PMCID: PMC2923849 DOI: 10.1039/c0an00028k] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel electrochemical immunosensor for the detection of matrix metalloproteinase-3 (MMP-3), a cancer biomarker protein, based on vertically aligned single-wall carbon nanotube (SWCNT) arrays is presented. Detection was based on a sandwich immunoassay consisting of horseradish peroxidase (14-16 labels) conjugated to a secondary antibody and/or a polymer bead loaded with multi-enzyme labels. Performance was optimized by effective minimization of non-specific binding (NSB) events using Bovine serum albumin (BSA), Tween-20 and optimization of the primary antibody and secondary antibody concentrations. Results provided a detection limit of 0.4 ng mL(-1) (7.7 pM) for the 14-16 label sensor protocol and 4 pg mL(-1) (77 fM) using a multiply enzyme labeled polymeric bead amplification strategy in 10 microL of calf serum. This immunosensor based on SWCNT arrays offers great promise for a rapid, simple, cost-effective method for clinical screening of cancer biomarkers for point-of-care diagnosis.
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Affiliation(s)
- Bernard S Munge
- Salve Regina University, Department of Chemistry, Newport, Rhode Island 02840-4192, USA.
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47
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Malhotra R, Patel V, Vaqué JP, Gutkind JS, Rusling JF. Ultrasensitive electrochemical immunosensor for oral cancer biomarker IL-6 using carbon nanotube forest electrodes and multilabel amplification. Anal Chem 2010; 82:3118-23. [PMID: 20192182 PMCID: PMC2854872 DOI: 10.1021/ac902802b] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Squamous cell carcinomas of head and neck (HNSCC) are associated with immune, inflammatory, and angiogenic responses involving interleukin-6 (IL-6). This article reports an ultrasensitive electrochemical immunosensor for human IL-6 and proof-of-concept studies of IL-6 detection in HNSCC cells. Single wall carbon nanotube (SWNT) forests with attached capture antibodies (Ab(1)) for IL-6 were used in an electrochemical sandwich immunoassay protocol using enzyme label horseradish peroxidase (HRP) to measure very low (
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Affiliation(s)
- Ruchika Malhotra
- Department of Chemistry and Institute of Materials Science, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA
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48
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Ndao M, Spithill TW, Caffrey R, Li H, Podust VN, Perichon R, Santamaria C, Ache A, Duncan M, Powell MR, Ward BJ. Identification of novel diagnostic serum biomarkers for Chagas' disease in asymptomatic subjects by mass spectrometric profiling. J Clin Microbiol 2010; 48:1139-49. [PMID: 20071547 PMCID: PMC2849606 DOI: 10.1128/jcm.02207-09] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 12/26/2009] [Accepted: 01/07/2010] [Indexed: 01/10/2023] Open
Abstract
More than 10 million people are thought to be infected with Trypanosoma cruzi, primarily in the Americas. The clinical manifestations of Chagas' disease (CD) are variable, but most subjects remain asymptomatic for decades. Only 15 to 30% eventually develop terminal complications. All current diagnostic tests have limitations. New approaches are needed for blood bank screening as well as for improved diagnosis and prognosis. Sera from subjects with asymptomatic CD (n = 131) were compared to those from uninfected controls (n = 164) and subjects with other parasitic diseases (n = 140), using protein array mass spectrometry. To identify biomarkers associated with CD, sera were fractionated by anion-exchange chromatography and bound to two commercial ProteinChip array chemistries: WCX2 and IMAC3. Multiple candidate biomarkers were found in CD sera (3 to 75.4 kDa). Algorithms employing 3 to 5 of these biomarkers achieved up to 100% sensitivity and 98% specificity for CD. The biomarkers most useful for diagnosis were identified and validated. These included MIP1 alpha, C3a anaphylatoxin, and unusually truncated forms of fibronectin, apolipoprotein A1 (ApoA1), and C3. An antipeptide antiserum against the 28.9-kDa C terminus of the fibronectin fragment achieved good specificity (90%) for CD in a Western blot format. We identified full-length ApoA1 (28.1 kDa), the major structural and functional protein component of high-density lipoprotein (HDL), as an important negative biomarker for CD, and relatively little full-length ApoA1 was detected in CD sera. This work provides proof of principle that both platform-dependent (i.e., mass spectrometry-based) and platform-independent (i.e., Western blot) tests can be generated using high-throughput mass profiling.
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Affiliation(s)
- Momar Ndao
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada.
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49
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Proteomic analysis of porcine saliva. Vet J 2010; 187:356-62. [PMID: 20093058 DOI: 10.1016/j.tvjl.2009.12.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 12/19/2009] [Accepted: 12/22/2009] [Indexed: 01/17/2023]
Abstract
Saliva contains a number of proteins that may be useful as biomarkers of health and disease and can be easily obtained from large numbers of animals in a non-invasive, stress-free way. The objective of this study was to explore the protein composition of porcine saliva from 10 specific pathogen free pigs using first one-dimensional SDS-PAGE and then two-dimensional electrophoresis and mass spectrometry. A reference proteome pattern for porcine saliva was established with the identification of 13 different, mainly saliva-specific, proteins. These reference data will facilitate the investigation of salivary proteins potentially altered in disease and could serve as novel diagnostic biomarkers.
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50
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Diagnosis of parasitic diseases: old and new approaches. Interdiscip Perspect Infect Dis 2009; 2009:278246. [PMID: 20069111 PMCID: PMC2804041 DOI: 10.1155/2009/278246] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 08/29/2009] [Indexed: 12/28/2022] Open
Abstract
Methods for the diagnosis of infectious diseases have stagnated in the last 20–30 years. Few major advances in clinical diagnostic testing have been made since the introduction of PCR, although new technologies are being investigated. Many tests that form the backbone of the “modern” microbiology laboratory are based on very old and labour-intensive technologies such as microscopy for malaria. Pressing needs include more rapid tests without sacrificing sensitivity, value-added tests, and point-of-care tests for both high- and low-resource settings. In recent years, research has been focused on alternative methods to improve the diagnosis of parasitic diseases. These include immunoassays, molecular-based approaches, and proteomics using mass spectrometry platforms technology. This review summarizes the progress in new approaches in parasite diagnosis and discusses some of the merits and disadvantages of these tests.
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