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Mansoor S, Hamid S, Tuan TT, Park JE, Chung YS. Advance computational tools for multiomics data learning. Biotechnol Adv 2024; 77:108447. [PMID: 39251098 DOI: 10.1016/j.biotechadv.2024.108447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial role in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.
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Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Thai Thanh Tuan
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea; Multimedia Communications Laboratory, University of Information Technology, Ho Chi Minh city 70000, Vietnam; Multimedia Communications Laboratory, Vietnam National University, Ho Chi Minh city 70000, Vietnam
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju, Jeju-do, Republic of Korea.
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea.
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2
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Bell TN, Kusi-Appiah AE, Tocci V, Lyu P, Zhu L, Zhu F, Van Winkle D, Cao H, Singh MS, Lenhert S. Scalable lipid droplet microarray fabrication, validation, and screening. PLoS One 2024; 19:e0304736. [PMID: 38968248 PMCID: PMC11226032 DOI: 10.1371/journal.pone.0304736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/16/2024] [Indexed: 07/07/2024] Open
Abstract
High throughput screening of small molecules and natural products is costly, requiring significant amounts of time, reagents, and operating space. Although microarrays have proven effective in the miniaturization of screening for certain biochemical assays, such as nucleic acid hybridization or antibody binding, they are not widely used for drug discovery in cell culture due to the need for cells to internalize lipophilic drug candidates. Lipid droplet microarrays are a promising solution to this problem as they are capable of delivering lipophilic drugs to cells at dosages comparable to solution delivery. However, the scalablility of the array fabrication, assay validation, and screening steps has limited the utility of this approach. Here we take several new steps to scale up the process for lipid droplet array fabrication, assay validation in cell culture, and drug screening. A nanointaglio printing process has been adapted for use with a printing press. The arrays are stabilized for immersion into aqueous solution using a vapor coating process. In addition to delivery of lipophilic compounds, we found that we are also able to encapsulate and deliver a water-soluble compound in this way. The arrays can be functionalized by extracellular matrix proteins such as collagen prior to cell culture as the mechanism for uptake is based on direct contact with the lipid delivery vehicles rather than diffusion of the drug out of the microarray spots. We demonstrate this method for delivery to 3 different cell types and the screening of 92 natural product extracts on a microarray covering an area of less than 0.1 cm2. The arrays are suitable for miniaturized screening, for instance in high biosafety level facilities where space is limited and for applications where cell numbers are limited, such as in functional precision medicine.
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Affiliation(s)
- Tracey N. Bell
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Aubrey E. Kusi-Appiah
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Vincent Tocci
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Pengfei Lyu
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Lei Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - David Van Winkle
- Department of Physics, Florida State University, Tallahassee, Florida, United States of America
| | - Hongyuan Cao
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Mandip S. Singh
- College of Pharmacy and Pharmaceutical Science, Florida A&M University, Tallahassee, Florida, United States of America
| | - Steven Lenhert
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
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Sytu MRC, Cho DH, Hahm JI. Self-Assembled Block Copolymers as a Facile Pathway to Create Functional Nanobiosensor and Nanobiomaterial Surfaces. Polymers (Basel) 2024; 16:1267. [PMID: 38732737 PMCID: PMC11085100 DOI: 10.3390/polym16091267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Block copolymer (BCP) surfaces permit an exquisite level of nanoscale control in biomolecular assemblies solely based on self-assembly. Owing to this, BCP-based biomolecular assembly represents a much-needed, new paradigm for creating nanobiosensors and nanobiomaterials without the need for costly and time-consuming fabrication steps. Research endeavors in the BCP nanobiotechnology field have led to stimulating results that can promote our current understanding of biomolecular interactions at a solid interface to the never-explored size regimes comparable to individual biomolecules. Encouraging research outcomes have also been reported for the stability and activity of biomolecules bound on BCP thin film surfaces. A wide range of single and multicomponent biomolecules and BCP systems has been assessed to substantiate the potential utility in practical applications as next-generation nanobiosensors, nanobiodevices, and biomaterials. To this end, this Review highlights pioneering research efforts made in the BCP nanobiotechnology area. The discussions will be focused on those works particularly pertaining to nanoscale surface assembly of functional biomolecules, biomolecular interaction properties unique to nanoscale polymer interfaces, functionality of nanoscale surface-bound biomolecules, and specific examples in biosensing. Systems involving the incorporation of biomolecules as one of the blocks in BCPs, i.e., DNA-BCP hybrids, protein-BCP conjugates, and isolated BCP micelles of bioligand carriers used in drug delivery, are outside of the scope of this Review. Looking ahead, there awaits plenty of exciting research opportunities to advance the research field of BCP nanobiotechnology by capitalizing on the fundamental groundwork laid so far for the biomolecular interactions on BCP surfaces. In order to better guide the path forward, key fundamental questions yet to be addressed by the field are identified. In addition, future research directions of BCP nanobiotechnology are contemplated in the concluding section of this Review.
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Affiliation(s)
- Marion Ryan C. Sytu
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
| | - David H. Cho
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA;
| | - Jong-in Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
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Ma H, Murphy C, Loscher CE, O’Kennedy R. Autoantibodies - enemies, and/or potential allies? Front Immunol 2022; 13:953726. [PMID: 36341384 PMCID: PMC9627499 DOI: 10.3389/fimmu.2022.953726] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/24/2022] [Indexed: 08/13/2023] Open
Abstract
Autoantibodies are well known as potentially highly harmful antibodies which attack the host via binding to self-antigens, thus causing severe associated diseases and symptoms (e.g. autoimmune diseases). However, detection of autoantibodies to a range of disease-associated antigens has enabled their successful usage as important tools in disease diagnosis, prognosis and treatment. There are several advantages of using such autoantibodies. These include the capacity to measure their presence very early in disease development, their stability, which is often much better than their related antigen, and the capacity to use an array of such autoantibodies for enhanced diagnostics and to better predict prognosis. They may also possess capacity for utilization in therapy, in vivo. In this review both the positive and negative aspects of autoantibodies are critically assessed, including their role in autoimmune diseases, cancers and the global pandemic caused by COVID-19. Important issues related to their detection are also highlighted.
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Affiliation(s)
- Hui Ma
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Caroline Murphy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - Richard O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Research, Development and Innovation, Qatar Foundation, Doha, Qatar
- Hamad Bin Khalifa University, Doha, Qatar
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5
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Li X, Zhang X, Shi X, Shi H, Wang Z, Peng C. Review in isothermal amplification technology in food microbiological detection. Food Sci Biotechnol 2022; 31:1501-1511. [PMID: 36119387 PMCID: PMC9469833 DOI: 10.1007/s10068-022-01160-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 11/04/2022] Open
Abstract
Food-borne diseases caused by microbial contamination have always been a matter of great concern to human beings. Hence, the research on these problems has never stopped. With the development of microorganism amplification technology, more and more detection methods have come into our vision. However, traditional detection technologies presents more or less drawbacks, such as complicated operation, low accuracy, low sensitivity, long-time detection, and so on. Therefore, more convenient, accurate, and sensitive measurement for the microorganism are needed. Isothermal amplification technology is one of the alternative approach containing the above mentioned advantages. This work mainly summarizes the principles of loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA) which belong to isothermal amplification. Meanwhile, the application of LAMP and RCA in food microorganism detection is introduced.
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Fu H, Zhang C, Wang Y, Chen G. Advances in multiplex molecular detection technologies for harmful algae. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:43745-43757. [PMID: 35449333 DOI: 10.1007/s11356-022-20269-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
As the eutrophication of natural water bodies becomes more and more serious, the frequency of outbreaks of harmful algal blooms (HABs) mainly formed by harmful algae also increases. HABs have become a global ecological problem that poses a serious threat to human health and food safety. Therefore, it is extremely important to establish methods that can rapidly detect harmful algal species for early warning of HABs. The traditional morphology-based identification method is inefficient and inaccurate. In recent years, the rapid development of molecular biology techniques has provided new ideas for the detection of harmful algae and has become a research hotspot. The current molecular detection methods for harmful algal species mainly include fluorescence in situ hybridization, sandwich hybridization, and quantitative PCR (qPCR), but all of these methods can only detect single harmful algal species at a time. The establishment of methods for the simultaneous detection of multiple harmful algal species has become a new trend in the development of molecular detection technology because various harmful algal species may coexist in the natural water environment. The established molecular techniques for multiple detections of harmful algae mainly include gene chip, multiplex PCR, multiplex qPCR, massively parallel sequencing, antibody chip, and multiple isothermal amplification. This review mainly focuses on the principles, advantages and disadvantages, application progress, and application prospects of these multiple detection technologies, aiming at providing effective references not only for the fisheries but also for economic activities, environment, and human health.
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Affiliation(s)
- Hanyu Fu
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Chunyun Zhang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Yuanyuan Wang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China
| | - Guofu Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, People's Republic of China.
- School of Environment, Harbin Institute of Technology, Harbin, 150009, People's Republic of China.
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Zhou X, Yang CT, Xu Q, Lou Z, Xu Z, Thierry B, Gu N. Gold Nanoparticle Probe-Assisted Antigen-Counting Chip Using SEM. ACS APPLIED MATERIALS & INTERFACES 2019; 11:6769-6776. [PMID: 30676729 DOI: 10.1021/acsami.8b19055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Currently, it remains challenging to count protein-biomarker molecules present in a small droplet of biological samples. Herein, we propose a gold nanoparticle (GNP) probe-assisted sandwich-counting strategy that relies on a GNP probe, an antibody-functionalized chip to "count" antigen molecules using a scanning electron microscope. Both standard carcinoembryonic antigen (CEA) and two real CEA-related tumor samples (tumor tissues and serum) were assayed to demonstrate the proof-of-concept of the counting strategy. Results show that our method is excellently correlative with enzyme-linked immuno-sorbent assay (ELISA) that is widely used in clinics for antigen or antibody detection and the limit of detection of our enumeration strategy reaches down to 0.045 ng/mL, which is ∼40 times more sensitive than the conventional ELISA. Therefore, our GNP probe-assisted sandwich-counting strategy has the potential to be used for quantification of protein biomarkers at ultralow concentrations in early tumor specimens and detection of target proteins in much diluted concentrations.
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Affiliation(s)
- Xin Zhou
- Institute of Comparative Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China , Yangzhou University , Yangzhou 225009 , China
| | - Chih-Tsung Yang
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, Mawson Lakes Campus , University of South Australia , South Australia 5095 , Australia
| | - Qiaoshu Xu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210009 , China
| | - Zhichao Lou
- College of Materials Science and Engineering , Nanjing Forestry University , Nanjing 210037 , China
| | - Zhengfeng Xu
- Center of Medical Genetics , Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University , Nanjing 210029 , China
| | - Benjamin Thierry
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, Mawson Lakes Campus , University of South Australia , South Australia 5095 , Australia
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210009 , China
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Abstract
The technique of surface-enhanced laser desorption/ionization time-of-flight SELDI-TOF mass spectrometry could be used to establish serum or plasma proteomic profiles in esophageal adenocarcinoma. The protein profiles in patients may be used to predict survival and monitor response to chemotherapy in patients with esophageal adenocarcinoma. Here, a protocol for sample preparation from esophageal adenocarcinoma, analysis of proteomic profiles, and collection of protein fractions for identification of significant peaks is presented.
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Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018; 47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.
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Affiliation(s)
- Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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Pagano G, Johnson C, Hahn DC, Arsenault RJ. A new tool for studying waterfowl immune and metabolic responses: Molecular level analysis using kinome profiling. Ecol Evol 2018; 8:8537-8546. [PMID: 30250721 PMCID: PMC6144969 DOI: 10.1002/ece3.4370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/16/2018] [Accepted: 06/15/2018] [Indexed: 01/03/2023] Open
Abstract
Here, we describe the design of an Anas-specific kinome peptide array that can be used to study the immunometabolic responses of mallard and American black duck to pathogens, contaminants, and environmental stress. The peptide arrays contain 2,642 unique phosphorylate-able peptide sequences representing 1,900 proteins. These proteins cover a wide array of metabolic and immunological processes, and 758 Gene Ontology Biological processes are statistically significantly represented on the duck peptide array of those 164 contain the term "metabolic" and 25 "immune." In addition, we conducted a comparison of mallard to American black duck at a genetic and proteomic level. Our results show a significant genomic and proteomic overlap between these two duck species, so that we have designed a cross-reactive peptide array capable of studying both species. This is the first reported development of a wildlife species-specific kinome peptide array.
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Affiliation(s)
- Giovanni Pagano
- Center for Bioinformatics and Computational BiologyUniversity of DelawareNewarkDelaware
| | - Casey Johnson
- Department of Animal and Food SciencesUniversity of DelawareNewarkDelaware
| | | | - Ryan J. Arsenault
- Department of Animal and Food SciencesUniversity of DelawareNewarkDelaware
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Ch'ng ACW, Hamidon NHB, Konthur Z, Lim TS. Magnetic Nanoparticle-Based Semi-Automated Panning for High-Throughput Antibody Selection. Methods Mol Biol 2018; 1701:301-319. [PMID: 29116512 DOI: 10.1007/978-1-4939-7447-4_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The application of recombinant human antibodies is growing rapidly mainly in the field of diagnostics and therapeutics. To identify antibodies against a specific antigen, panning selection is carried out using different display technologies. Phage display technology remains the preferred platform due to its robustness and efficiency in biopanning experiments. There are both manual and semi-automated panning selections using polystyrene plastic, magnetic beads, and nitrocellulose as the immobilizing solid surface. Magnetic nanoparticles allow for improved antigen binding due to their large surface area. The Kingfisher Flex magnetic particle processing system was originally designed to aid in RNA, DNA, and protein extraction using magnetic beads. However, the system can be programmed for antibody phage display panning. The automation allows for a reduction in human error and improves reproducibility in between selections with the preprogrammed movements. The system requires minimum human intervention to operate; however, human intervention is needed for post-panning steps like phage rescue. In addition, polyclonal and monoclonal ELISA can be performed using the semi-automated platform to evaluate the selected antibody clones. This chapter will summarize the suggested protocol from the panning stage till the monoclonal ELISA evaluation. Other than this, important notes on the possible optimization and troubleshooting are also included at the end of this chapter.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Analytical Biochemistry Research Centre, Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Nurul Hamizah Binti Hamidon
- Analytical Biochemistry Research Centre, Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Zoltán Konthur
- Max Planck Institute of Colloids and Interfaces, Mühlenberg 1, 14476, Potsdam, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia. .,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, Penang, Malaysia.
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12
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Zhang X, Hu H. Investigating and characterizing the binding activity of the immobilized calmodulin to calmodulin-dependent protein kinase I binding domain with atomic force microscopy. Chem Cent J 2017; 11:128. [PMID: 29214517 PMCID: PMC5718999 DOI: 10.1186/s13065-017-0360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/30/2017] [Indexed: 12/03/2022] Open
Abstract
Protein–protein interactions are responsible for many biological processes, and the study of how proteins undergo a conformational change induced by other proteins in the immobilized state can help us to understand a protein’s function and behavior, empower the current knowledge on molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. In this study, a bottom-up approach was utilized to fabricate micro/nanometer-scale protein patterns. One cysteine mutated calmodulin (CaM), as a model protein, was immobilized on thiol-terminated pattern surfaces. Atomic Force Microscopy (AFM) was then employed as a tool to investigate the interactions between CaM and CaM kinase I binding domain, and show that the immobilized CaM retains its activity to interact with its target protein. Our work demonstrate the potential of employing AFM to the research and assay works evolving surface-based protein–protein interactions biosensors, bioelectronics or drug screening.
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Affiliation(s)
- Xiaoning Zhang
- College of Biotechnology, Southwest University, Chongqing, 400715, China.
| | - Hongmei Hu
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan, 316021, China
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Wang L, Hu YQ, Zhao ZJ, Zhang HY, Gao B, Lu WG, Xu XL, Lin XS, Wang JP, Jie Q, Luo ZJ, Yang L. Screening and validation of serum protein biomarkers for early postmenopausal osteoporosis diagnosis. Mol Med Rep 2017; 16:8427-8433. [PMID: 28983612 DOI: 10.3892/mmr.2017.7620] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 07/27/2017] [Indexed: 11/06/2022] Open
Abstract
Postmenopausal osteoporosis is one of the most prominent worldwide public health problems and the morbidity is increasing with the aging population. It has been demonstrated that early diagnosis and intervention delay the disease progression and improve the outcome. Therefore, searching for biomarkers that are able to identify postmenopausal women at high risk for developing osteoporosis is an effective way to improve the quality of life of patients, and alleviate social and economic burdens. In the present study, a protein array was used to identify potential biomarkers. The bone mineral densities of 10 rats were dynamically measured in an ovariectomized model by micro‑computed tomography assessment, and the early stage of osteoporosis was defined. Through the protein array‑based screening, the expression levels of six serum protein biomarkers in ovariectomized rats were observed to alter at the initiation stage of the postmenopausal osteoporosis. Fractalkine, tissue inhibitor of metalloproteinases‑1 and monocyte chemotactic protein‑1 were finally demonstrated to be increased in the serum of eight enrolled postmenopausal osteoporosis patients using ELISA assay and were correlated with the severity of progressive bone loss. These biomarkers may be explored as potential early biomarkers to readily evaluate and diagnose postmenopausal osteoporosis in the clinic.
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Affiliation(s)
- Long Wang
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Ya-Qian Hu
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Zhuo-Jie Zhao
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Hong-Yang Zhang
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Bo Gao
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Wei-Guang Lu
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xiao-Long Xu
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xi-Sheng Lin
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jin-Peng Wang
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Qiang Jie
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Zhuo-Jing Luo
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Liu Yang
- Institute of Orthopedic Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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14
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Masuda M, Yamada T. Signaling pathway profiling using reverse-phase protein array and its clinical applications. Expert Rev Proteomics 2017. [PMID: 28621158 DOI: 10.1080/14789450.2017.1344101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Increased accessibility to next-generation sequencing within the last decade has led to a paradigm shift in cancer treatment from one-size-fits-all medicine to precision medicine providing therapeutic strategies tailored to the requirements of individual patients. However, the effect of even the most successful agent yet tested is only transient, and durable efficacy has yet to be achieved. Genome- and transcriptome-based approaches cannot fully predict the diversity of protein expression patterns or post-translational modifications that directly contribute to cancer pathogenesis and physiology. This underscores the need for concordant proteomic analysis in the next stage of precision medicine. Areas covered: This review begins with an overview of the recent advances and trends in precision medicine that currently rely on genomics, and highlights the utility of antibody-based reverse-phase protein array (RPPA) technology as a proteomic tool in this context. Expert commentary: RPPA is well suited for pharmacodynamics analysis in view of its ability to precisely map signaling status using limited amounts of clinical samples. In addition, the cost-effectiveness and rapid turn-around time of the RPPA platform offer a substantial advantage over existing molecular profiling technologies in clinical settings.
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Affiliation(s)
- Mari Masuda
- a Division of Chemotherapy and Clinical Research , National Cancer Center Research Institute , Tokyo , Japan
| | - Tesshi Yamada
- a Division of Chemotherapy and Clinical Research , National Cancer Center Research Institute , Tokyo , Japan
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15
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Patterned surfaces for biological applications: A new platform using two dimensional structures as biomaterials. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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16
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Gade AM, Meadows MK, Ellington AD, Anslyn EV. Differential array sensing for cancer cell classification and novelty detection. Org Biomol Chem 2017; 15:9866-9874. [DOI: 10.1039/c7ob02174g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of semi-specific peptides reported in the literature to bind various epitopes on cell surfaces were used in a differential sensing array to pattern cell line identity.
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Affiliation(s)
| | | | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Eric V. Anslyn
- Department of Chemistry
- The University of Texas at Austin
- Austin
- USA
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17
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Lin F, Li Z, Hua Y, Lim YP. Proteomic profiling predicts drug response to novel targeted anticancer therapeutics. Expert Rev Proteomics 2016; 13:411-20. [PMID: 26954459 DOI: 10.1586/14789450.2016.1164043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Most recently approved anti-cancer drugs by the US FDA are targeted therapeutic agents and this represents an important trend for future anticancer therapy. Unlike conventional chemotherapy that rarely considers individual differences, it is crucial for targeted therapies to identify the beneficial subgroup of patients for the treatment. Currently, genomics and transcriptomics are the major 'omic' analytics used in studies of drug response prediction. However, proteomic profiling excels both in its advantages of directly detecting an instantaneous dynamic of the whole proteome, which contains most current diagnostic markers and therapeutic targets. Moreover, proteomic profiling improves understanding of the mechanism for drug resistance and helps finding optimal combination therapy. This article reviews the recent success of applications of proteomic analytics in predicting the response to targeted anticancer therapeutics, and discusses the potential avenues and pitfalls of proteomic platforms and techniques used most in the field.
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Affiliation(s)
- Fan Lin
- a Department of Cell Biology , Nanjing Medical University , Nanjing , China.,b Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Zilin Li
- b Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Yunfen Hua
- c College of Pharmaceutical Science, Zhejiang University of Technology , Hangzhou , China
| | - Yoon Pin Lim
- b Department of Biochemistry , Yong Loo Lin School of Medicine, National University of Singapore , Singapore.,d Bioinformatics Institute, Agency for Science and Technology , Singapore.,e NUS Graduate School of Integrative Sciences and Technology , Singapore
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18
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Duncan MW, Hunsucker SW. Proteomics as a Tool for Clinically Relevant Biomarker Discovery and Validation. Exp Biol Med (Maywood) 2016; 230:808-17. [PMID: 16339745 DOI: 10.1177/153537020523001105] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The excitement associated with clinical applications of proteomics was initially focused on its potential to serve as a vehicle for both biomarker discovery and drug discovery and routine clinical sample analysis. Some approaches were thought to be able to “identify” mass spectral characteristics that distinguished between control and disease samples, and thereafter it was believed that the same tool could be employed to screen samples in a high-throughput clinical setting. However, this has been difficult to achieve, and the early promise is yet to be fully realized. While we see an important place for mass spectrometry in drug and biomarker discovery, we believe that alternative strategies will prove more fruitful for routine analysis. Here we discuss the power and versatility of 2D gels and mass spectrometry in the discovery phase of biomarker work but argue that it is better to rely on immunochemical methods for high-throughput validation and routine assay applications.
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Affiliation(s)
- Mark W Duncan
- Department of Pediatrics, Section of Pulmonary Medicine, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
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19
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Ghazanfari L, Lenhert S. Screening of Lipid Composition for Scalable Fabrication of Solvent-Free Lipid Microarrays. FRONTIERS IN MATERIALS 2016; 3:55. [PMID: 29333429 PMCID: PMC5761732 DOI: 10.3389/fmats.2016.00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Liquid microdroplet arrays on surfaces are a promising approach to the miniaturization of laboratory processes such as high-throughput screening. The fluid nature of these droplets poses unique challenges and opportunities in their fabrication and application, particularly for the scalable integration of multiple materials over large areas and immersion into cell culture solution. Here, we use pin spotting and nanointaglio printing to screen a library of lipids and their mixtures for their compatibility with these fabrication processes, as well as stability upon immersion into aqueous solution. More than 200 combinations of natural and synthetic oils composed of fatty acids, triglycerides, and hydrocarbons were tested for their pin-spotting and nanointaglio print quality and their ability to contain the fluorescent compound tetramethylrhodamine B isothiocyanate (TRITC) upon immersion in water. A combination of castor oil and hexanoic acid at the ratio of 1:1 (w/w) was found optimal for producing reproducible patterns that are stable upon immersion into water. This method is capable of large-scale nanomaterials integration.
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20
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Huang L, Aryal GH, Tam-Chang SW, Publicover NG, Hunter KW. Self-assembled biosensor with universal reporter and dual-quenchers for detection of unlabelled nucleic acids. Analyst 2016; 141:1376-82. [PMID: 26757447 DOI: 10.1039/c5an02094h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A novel biosensor with universal reporter and dual quenchers was developed for rapid, sensitive, selective, and inexpensive detection of unlabelled nucleic acids. The biosensor is based on a single-strand DNA stem-loop motif with an extended universal reporter-binding region, a G-base rich stem region, and a universal address-binding region. The self-assembly of these stem-loop probes with fluorescence labeled universal reporter and a universal address region conjugated to gold nanoparticles forms the basis of a biosensor for DNA or microRNA targets in solution. The introduction of dual quenchers (G-base quenching and gold surface plasmon resonance-induced quenching) significantly reduces the fluorescence background to as low as 12% of its original fluorescence intensity and hence enhances the detection limit to 0.01 picomoles without signal ampilication.
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Affiliation(s)
- Liming Huang
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Gyan H Aryal
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Suk-Wah Tam-Chang
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Nelson G Publicover
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Kenneth W Hunter
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
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21
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Differential Protein Expression Profiles in Glaucomatous Trabecular Meshwork: An Evaluation Study on a Small Primary Open Angle Glaucoma Population. Adv Ther 2016; 33:252-67. [PMID: 26820987 PMCID: PMC4769730 DOI: 10.1007/s12325-016-0285-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Primary open angle glaucoma (POAG) is a progressive optic neuropathy characterized by impaired aqueous outflow and extensive remodeling in the trabecular meshwork (TM). The aim of this study was to characterize and compare the expression patterns of selected proteins belonging to the tissue remodeling, inflammation and growth factor pathways in ex vivo glaucomatous and post-mortem TMs using protein-array analysis. METHODS TM specimens were collected from 63 white subjects, including 40 patients with glaucoma and 23 controls. Forty POAG TMs were collected at the time of surgery and 23 post-mortem specimens were from non-glaucomatous donor sclerocorneal tissues. Protein profiles were evaluated using a chip-based array consisting of 60 literature-selected antibodies. RESULTS A different expression of some factors was observed in POAG TMs with respect to post-mortem specimens, either in abundance (interleukin [IL]10, IL6, IL5, IL7, IL12, IL3, macrophage inflammatory protein [MIP]1δ/α, vascular endothelial growth factor [VEGF], transforming growth factor beta 1 [TGFβ1], soluble tumor necrosis factor receptor I [sTNFRI]) or in scarcity (IL16, IL18, intercellular adhesion molecule 3 [ICAM3], matrix metalloproteinase-7 [MMP7], tissue inhibitor of metalloproteinase 1 [TIMP1]). MMP2, MMP7, TGFβ1, and VEGF expressions were confirmed by Western blot, zymography, and polymerase chain reaction. No difference in protein profile expression was detected between glaucomatous subtypes. CONCLUSION The analysis of this small TM population highlighted some proteins linked to POAG, some previously reported and others of new detection (IL7, MIPs, sTNFαRI). A larger POAG population is required to select promising disease-associated biomarker candidates. FUNDING This study was partially supported by the Fondazione Roma, the Italian Ministry of Health and the "National 5xMille 2010 tax donation to IRCCS-G.B. Bietti Foundation".
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22
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Krizkova S, Heger Z, Zalewska M, Moulick A, Adam V, Kizek R. Nanotechnologies in protein microarrays. Nanomedicine (Lond) 2015; 10:2743-55. [PMID: 26039143 DOI: 10.2217/nnm.15.81] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.
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Affiliation(s)
- Sona Krizkova
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Zbynek Heger
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Marta Zalewska
- Department of Biomedical & Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland, European Union
| | - Amitava Moulick
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Vojtech Adam
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Rene Kizek
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
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23
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Romanov V, Davidoff SN, Miles AR, Grainger DW, Gale BK, Brooks BD. A critical comparison of protein microarray fabrication technologies. Analyst 2015; 139:1303-26. [PMID: 24479125 DOI: 10.1039/c3an01577g] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
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Affiliation(s)
- Valentin Romanov
- Wasatch Microfluidics, LLC, 825 N. 300 W., Suite C325, Salt Lake City, UT, USA.
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24
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Rosenberg JM, Utz PJ. Protein microarrays: a new tool for the study of autoantibodies in immunodeficiency. Front Immunol 2015; 6:138. [PMID: 25904912 PMCID: PMC4387933 DOI: 10.3389/fimmu.2015.00138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/12/2015] [Indexed: 12/19/2022] Open
Abstract
Autoimmunity is highly coincident with immunodeficiency. In a small but growing number of primary immunodeficiencies, autoantibodies are diagnostic of a given disease and implicated in disease pathogenesis. In order to improve our understanding of the role of autoantibodies in immunodeficiencies and to discover novel autoantibodies, new proteomic tools are needed. Protein microarrays have the ability to screen for reactivity to hundreds to many thousands of unique autoantigens simultaneously on a single chip using minimal serum input. Here, we review different types of protein microarrays and how they can be useful in framing the study of primary and secondary immunodeficiencies.
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Affiliation(s)
- Jacob M Rosenberg
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine , Stanford, CA , USA
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine , Stanford, CA , USA ; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine , Stanford, CA , USA
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25
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Leary TF, Manafirasi S, Maldarelli C. Mass transfer in the biomolecular binding of a target against probe molecules on the surface of microbeads sequestered in wells in a microfluidic cell. LAB ON A CHIP 2015; 15:459-77. [PMID: 25408192 DOI: 10.1039/c4lc01185f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Diagnostic tools which screen the binding interactions of a protein target against a display of biomolecular probes to identify molecules which bind the target are central to cell proteomic studies, and to diagnostic assays. Here, we study a microfluidic design for screening interactions in which the probe molecules are hosted on microbeads sequestered in wells arranged at the bottom of a microfluidic flow channel. Assays are undertaken by streaming an analyte solution with a fluorescently labelled target through the cell, and identifying the fluorescing beads. Numerical simulations are first constructed for the analyte flow over the microbeads in the well array, and the increase in the target concentration on the microbead surface. The binding profile is expressed as a function of the ratio of the convective to the diffusive transport rates (Peclet number or Pe), and the ratio of the kinetic to the diffusive rates (Damkohler number, Da). For any Pe, as Da becomes small enough, the transport is determined by the intrinsic kinetic binding rate. As Pe increases, a thin concentration boundary layer develops over the top surface of the microbead because of the convective flow, and target binds more rapidly. However, the relatively stagnant layers of liquid in the well provide a diffusion barrier which slows the target transport, and for any Da and Pe the transport is slower than equivalent patches of probes arranged on the channel wall. Experiments are also undertaken at high Pe, using the binding of fluorescently labelled NeutrAvidin as a target to probes of its binding partner, biotin, on the microbead surface. The binding profile is compared to the simulations to measure the kinetic rate constant, and this comparison shows that the transport in the cell is not kinetically limited because of the diffusion barriers created by the stagnant liquid layer in the well. Simulations and experiments on microbeads which are only partially recessed in the well demonstrate an increase in the mass transfer rate as more of the microbead surface intersects the flow and the diffusion limitation due to the stagnant layer of liquid surrounding the bottom part of the microbead is minimized.
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Affiliation(s)
- Thomas F Leary
- Levich Institute and Department of Chemical Engineering, The City College of the City University of New York, New York, New York 10031, USA.
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26
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Masuda M, Yamada T. Signaling pathway profiling by reverse-phase protein array for personalized cancer medicine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:651-7. [PMID: 25448010 DOI: 10.1016/j.bbapap.2014.10.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/01/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Abstract
Deregulation of intracellular signaling through accumulation of genetic alterations is a hallmark of cancer. In the past few decades, concerted and systematic efforts have been made to identify key genetic alterations and to develop therapeutic agents targeting active signaling molecules. However, the efficacy of molecular therapeutics often varies among individuals, and precise mapping of active molecules in individual patients is now considered an essential for therapy optimization. Reverse-phase protein array or microarray (RPPA or RPPM) is an emerging antibody-based highly quantitative proteomic technology, especially suitable for profiling of expression and modification of signaling proteins in low abundance. Because the supply of clinical materials is often limited, RPPA technology is highly advantageous for clinical proteomics in view of its high sensitivity as well as accurate quantification. RPPA has now begun to be incorporated into various clinical trials employing molecular-targeted therapeutics. In this article we review and discuss the application of RPPA technology in the fields of basic, preclinical, and clinical research. The RPPA Global Workshop was recently launched to accelerate the exchange of rapidly expanding knowledge of this fascinating technology among academic laboratories and industries worldwide. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Mari Masuda
- Division of Chemotherapy and Clinical Research, Translational Research Group, National Cancer Center Research Institute, Tokyo, Japan
| | - Tesshi Yamada
- Division of Chemotherapy and Clinical Research, Translational Research Group, National Cancer Center Research Institute, Tokyo, Japan.
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27
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Kwak JW, Jeong H, Han SH, Kim Y, Son SM, Mook-Jung I, Hwang D, Park JW. Phosphokinase antibody arrays on dendron-coated surface. PLoS One 2014; 9:e96456. [PMID: 24802362 PMCID: PMC4011796 DOI: 10.1371/journal.pone.0096456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 04/08/2014] [Indexed: 12/04/2022] Open
Abstract
Monitoring protein phosphorylation at the cellular level is important to understand the intracellular signaling. Among the phosphoproteomics methods, phosphokinase antibody arrays have emerged as preferred tools to measure well-characterized phosphorylation in the intracellular signaling. Here, we present a dendron-coated phosphokinase antibody array (DPA) in which the antibodies are immobilized on a dendron-coated glass slide. Self-assembly of conically shaped dendrons well-controlled in size and structure resulted in precisely controlled lateral spacing between the immobilized phosphosite-specific antibodies, leading to minimized steric hindrance and improved antigen-antibody binding kinetics. These features increased sensitivity, selectivity, and reproducibility in measured amounts of protein phosphorylation. To demonstrate the utility of the DPA, we generated the phosphorylation profiles of brain tissue samples obtained from Alzheimer's disease (AD) model mice. The analysis of the profiles revealed signaling pathways deregulated during the course of AD progression.
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Affiliation(s)
- Ju-Won Kwak
- Department of Chemistry, POSTECH, Pohang, Republic of Korea
| | - Hyobin Jeong
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
| | - Sun-Ho Han
- Department of Biochemistry and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Youngkyu Kim
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
| | - Sung Min Son
- Department of Biochemistry and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
- * E-mail: (IM-J); (DH); (JWP)
| | - Daehee Hwang
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Republic of Korea
- Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu, Republic of Korea
- * E-mail: (IM-J); (DH); (JWP)
| | - Joon Won Park
- Department of Chemistry, POSTECH, Pohang, Republic of Korea
- * E-mail: (IM-J); (DH); (JWP)
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Abstract
Breast cancer is one of the major public health problems of the Western world. Recent advances in genomics and gene expression-profiling approaches have enriched our understanding of this heterogeneous disease. However, progress in functional proteomics in breast cancer research has been relatively slow. Allied with genomics, the functional proteomics approach will be important in improving diagnosis through better classification of breast cancer and in predicting prognosis and response to different therapies, including chemotherapy, hormonal therapy, and targeted therapy. In this review, we will present functional proteomic approaches with a focus on the recent clinical implications of utilizing the reverse-phase protein array platform in breast cancer research.
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Affiliation(s)
- Young Kwang Chae
- Division of Cancer Medicine and Departments of Breast Medical Oncology and Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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29
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Abstract
This review describes the worldwide situation of visceral and tegumentary leishmaniasis with an emphasis on diagnosis, including methods for the detection of antibodies, antigens, parasite DNA and of skin testing. The advantages and problems of each method are discussed and the need for a rapid, sensitive and low-cost diagnostic method for use in field conditions is highlighted. Recent advances in Leishmania genome sequencing, the use of DNA microarrays and protein microarray methodologies and their potential use for leishmaniasis diagnosis are presented.
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Affiliation(s)
- Carlos Alberto P Tavares
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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30
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Govender P, Baugh JA, Pennington SR, Dunn MJ, Donnelly SC. Role of proteomics in the investigation of pulmonary fibrosis. Expert Rev Proteomics 2014; 4:379-88. [PMID: 17552922 DOI: 10.1586/14789450.4.3.379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pulmonary fibrosis arises as a consequence of aberrant remodeling and defective repair mechanisms within the lung. This destructive process is the cause of much of the morbidity and mortality in many pulmonary disorders. Unfortunately, therapeutic options are limited. A significant advancement in the management of patients with pulmonary fibrosis would be the identification of biomarkers for diagnosis, prognosis and prediction of patient response to therapy. Bronchoalveolar lavage is an ideal tissue target for the discovery of these potential biomarkers in pulmonary fibrosis. Integrative approaches using both gel- and mass spectrometry-based proteomic workflows will allow full coverage of this complex proteome, thereby unlocking this potential information as a clinical tool to aid diagnosis and guide treatment for individual patients with pulmonary fibrosis.
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Affiliation(s)
- Praveen Govender
- University College Dublin, School of Medicine & Medical Science, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
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31
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Abstract
Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis.
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Affiliation(s)
- Andrew N Stephens
- University of Sydney, Department of Molecular & Microbial Biosciences, NSW, Australia.
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32
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Liang F, Clarke N, Patel P, Loncar M, Quan Q. Scalable photonic crystal chips for high sensitivity protein detection. OPTICS EXPRESS 2013; 21:32306-12. [PMID: 24514823 DOI: 10.1364/oe.21.032306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Scalable microfabrication technology has enabled semiconductor and microelectronics industries, among other fields. Meanwhile, rapid and sensitive bio-molecule detection is increasingly important for drug discovery and biomedical diagnostics. In this work, we designed and demonstrated that photonic crystal sensor chips have high sensitivity for protein detection and can be mass-produced with scalable deep-UV lithography. We demonstrated label-free detection of carcinoembryonic antigen from pg/mL to μg/mL, with high quality factor photonic crystal nanobeam cavities.
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Stangner T, Wagner C, Singer D, Angioletti-Uberti S, Gutsche C, Dzubiella J, Hoffmann R, Kremer F. Determining the specificity of monoclonal antibody HPT-101 to tau-peptides with optical tweezers. ACS NANO 2013; 7:11388-11396. [PMID: 24279833 DOI: 10.1021/nn405303u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Optical tweezers-assisted dynamic force spectroscopy is employed to investigate specific receptor-ligand interactions on the level of single binding events. In particular, we analyze binding of the phosphorylation-specific monoclonal antibody (mAb) HPT-101 to synthetic tau-peptides with two potential phosphorylation sites (Thr231 and Ser235), being the most probable markers for Alzheimer's disease. Whereas the typical interpretation of enzyme-linked immunosorbent assay (ELISA) suggests that this monoclonal antibody binds exclusively to the double-phosphorylated tau-peptide, we show here by DFS that the specificity of only mAb HPT-101 is apparent. In fact, binding occurs also to each sort of monophosphorylated peptide. Therefore, we characterize the unbinding process by analyzing the measured rupture force distributions, from which the lifetime of the bond without force τ0, its characteristic length xts, and the free energy of activation ΔG are extracted for the three mAb/peptide combinations. This information is used to build a simple theoretical model to predict features of the unbinding process for the double-phosphorylated peptide purely based on data on the monophosphorylated ones. Finally, we introduce a method to combine binding and unbinding measurements to estimate the relative affinity of the bonds. The values obtained for this quantity are in accordance with ELISA, showing how DFS can offer important insights about the dynamic binding process that are not accessible with this common and widespread assay.
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Affiliation(s)
- Tim Stangner
- Department of Experimental Physics I, Leipzig University , Linnéstraße 5, D-04103 Leipzig, Germany
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34
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Pre-absorbed immunoproteomics: a novel method for the detection of bacterial surface proteins. Methods Mol Biol 2013; 1061:113-21. [PMID: 23963933 DOI: 10.1007/978-1-62703-589-7_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Bacterial surface proteins are often investigated as potential vaccine candidates and biomarkers of virulence. In this chapter, a novel method for identifying bacterial surface proteins is presented, which combines immunoproteomic with immunoserologic techniques. Immunoproteomics, involving the separation of proteins by two-dimensional electrophoresis (2-DE) and Western blotting, has become an increasingly popular method for identifying immunoreactive proteins. In conventional serological technique, cross-absorption is a powerful method used to minimize cross reaction during agglutination assays. The serum pre-absorption process in our method was developed from cross-absorption but modified to remove antibodies that recognized bacterial surface antigens, thereby generating pre-absorbed sera. These pre-absorbed sera were used in Western blotting after 2-DE to find bacterial surface protein antigens. This new method has been proven to be a useful tool for identifying surface proteins, and aid in the development of new vaccine subunits and disease diagnostics.
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Moussavi-Harami SF, Annis DS, Ma W, Berry SM, Coughlin EE, Strotman LN, Maurer LM, Westphall MS, Coon JJ, Mosher DF, Beebe DJ. Characterization of molecules binding to the 70K N-terminal region of fibronectin by IFAST purification coupled with mass spectrometry. J Proteome Res 2013; 12:3393-404. [PMID: 23750785 DOI: 10.1021/pr400225p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Fibronectin (Fn) is a large glycoprotein present in plasma and extracellular matrix and is important for many processes. Within Fn the 70 kDa N-terminal region (70k-Fn) is involved in cell-mediated Fn assembly, a process that contributes to embryogenesis, development, and platelet thrombus formation. In addition, major human pathogens including Staphlycoccus aureus and Streptococcus pyogenes bind the 70k-Fn region by a novel form of protein-protein interaction called β-zipper formation, facilitating bacterial spread and colonization. Knowledge of blood plasma and platelet proteins that interact with 70k-Fn by β-zipper formation is incomplete. In the current study, we aimed to characterize these proteins through affinity purification. For this affinity purification, we used a novel purification technique termed immiscible filtration assisted by surface tension (IFAST). The foundation of this technology is immiscible phase filtration, using a magnet to draw paramagnetic particle (PMP)-bound analyte through an immiscible barrier (oil or organic solvent) that separates an aqueous sample from an aqueous eluting buffer. The immiscible barrier functions to remove unbound proteins via exclusion rather than dilutive washing used in traditional isolation methods. We identified 31 interactors from plasma, of which only seven were previously known to interact with Fn. Furthermore, five proteins were identified to interact with 70k-Fn from platelet lysate, of which one was previously known. These results demonstrate that IFAST offers advantages for proteomic studies of interacting molecules in that the technique requires small sample volumes, can be done with high enough throughput to sample multiple interaction conditions, and is amenable to exploratory mass spectrometric and confirmatory immuno-blotting read-outs.
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Chandrasekhar S, Iyer LK, Panchal JP, Topp EM, Cannon JB, Ranade VV. Microarrays and microneedle arrays for delivery of peptides, proteins, vaccines and other applications. Expert Opin Drug Deliv 2013; 10:1155-70. [PMID: 23662940 DOI: 10.1517/17425247.2013.797405] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Peptide and protein microarray and microneedle array technology provides direct information on protein function and potential drug targets in drug discovery and delivery. Because of this unique ability, these arrays are well suited for protein profiling, drug target identification/validation and studies of protein interaction, biochemical activity, immune responses, clinical prognosis and diagnosis and for gene, protein and drug delivery. AREAS COVERED The aim of this review is to describe and summarize past and recent developments of microarrays in their construction, characterization and production and applications of microneedles in drug delivery. The scope and limitations of various technologies in this respect are discussed. EXPERT OPINION This article offers a review of microarray/microneedle technologies and possible future directions in targeting and in the delivery of pharmacologically active compounds for unmet needs in biopharmaceutical research. A better understanding of the production and use of microarrays and microneedles for delivery of peptides, proteins and vaccines is needed.
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Affiliation(s)
- Saradha Chandrasekhar
- Purdue University, Department of Industrial and Physical Pharmacy, West Lafayette, IN 47907, USA
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Li Q, Jain MR, Chen W, Li H. A multidimensional approach to an in-depth proteomics analysis of transcriptional regulators in neuroblastoma cells. J Neurosci Methods 2013; 216:118-27. [PMID: 23558336 DOI: 10.1016/j.jneumeth.2013.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/21/2013] [Accepted: 03/24/2013] [Indexed: 12/13/2022]
Abstract
The dynamic regulation of transcriptional events is fundamental to many aspects of neuronal cell functions. However, proteomics methods have not been routinely used in global neuroproteomics analyses of transcriptional regulators because they are much less abundant than the "house-keeping" proteins in cells and tissues. Recent improvements in both biochemical preparations of nuclear proteins and detection sensitivities of proteomics technologies have made the global analysis of nuclear transcriptional regulators possible. We report here an optimised neuroproteomic method for the analysis of transcriptional regulators in the nuclear extracts of SHSY-5Y neuroblastoma cells by combining an improved nuclear protein extraction procedure with multidimensional peptide separation approaches. We found that rigorous removal of cytoplasmic proteins and solubilisation of DNA-associated proteins improved the number of nuclear proteins identified. Furthermore, we discovered that multidimensional peptide separations by either strong cation exchange (SCX) chromatography or electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) analysis detected more than 1800 nuclear proteins, which constitutes one of the largest datasets of nuclear proteins reported for a neuronal cell. Thus, in-depth analysis of transcriptional regulators for studying neurological diseases are increasingly feasible.
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Affiliation(s)
- Qing Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, 205 S. Orange Avenue, F-1226, Newark, NJ 07103, USA
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Staquicini FI, Pasqualini R, Arap W. Ligand-directed profiling: applications to target drug discovery in cancer. Expert Opin Drug Discov 2013; 4:51-9. [PMID: 23480336 DOI: 10.1517/17460440802628152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Generation of targeted therapy remains a major challenge in medicine. The development of drugs that can discriminate between tumor cells and non-malignant cells would improve efficacy and reduce general side effects. Phage display allows identification of specific supramolecular complexes that can target therapeutic compounds or imaging agents, both in vitro and in vivo. The use of phage display to identify molecules expressed on the surface of human cancer cells without bias, as well as to provide initial steps toward identification of a ligand/receptor-based map of the human microvasculature, has broad implications for drug discovery in general, especially for cancer therapy. OBJECTIVE/METHOD In this review, we discuss the use of phage display technology as a ligand-directed targeting strategy and its applications to drug discovery. CONCLUSION Compared to other existing drug discovery platforms, phage display technology has the advantage to provide valuable clues pointing to target proteins in an unbiased biological context. The result from various display library screenings indicates that in many cases the selected peptide motifs mimic biological ligands. Analysis of peptide motifs targeting a receptor provides a basis for rational drug design of targeted peptidomimetics.
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Affiliation(s)
- Fernanda I Staquicini
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA +1 713 792 3872 ; +1 713 745 0201 ;
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Yuk JS, Guignon EF, Lynes MA. Highly sensitive grating coupler-based surface plasmon-coupled emission (SPCE) biosensor for immunoassay. Analyst 2013; 138:2576-82. [DOI: 10.1039/c3an00135k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Feron D, Charlier C, Gourain V, Garderet L, Coste-Burel M, Le Pape P, Weigel P, Jacques Y, Hermouet S, Bigot-Corbel E. Multiplexed infectious protein microarray immunoassay suitable for the study of the specificity of monoclonal immunoglobulins. Anal Biochem 2012; 433:202-9. [PMID: 23103342 DOI: 10.1016/j.ab.2012.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 08/24/2012] [Accepted: 10/06/2012] [Indexed: 11/16/2022]
Abstract
Enzyme-linked immunosorbent assays (ELISAs) used to detect antibodies specific for common infectious agents such as Epstein-Barr virus (EBV), cytomegalovirus (CMV), Toxoplasma gondii (T. gondii), and hepatitis C virus (HCV) are time-consuming and require large volumes of samples, which restrict their use. We propose a new assay based on a multiplexed infectious protein (MIP) microarray combining different epitopes representative of the four germs. Antigens and lysates were printed on nitrocellulose slides to constitute the microarray. First, the microarray was incubated with human serum samples. Then, the suitability of the microarray for analysis of the specificity of purified monoclonal immunoglobulin (mc Ig) was assessed using serum and mc Ig of HCV-positive patients. Bound human immunoglobulin G (IgG) was detected using fluorescently labeled secondary antibodies, and the signals were quantified. Results obtained in serum samples with the new MIP microarray immunoassay were compared with ELISAs; we observed concordances of 95% for EBV, 93% for CMV, 91% for T. gondii, and 100% for HCV. Regarding purified mc Ig of HCV-positive patients, 3 of 3 recognized antigens printed on the microarray. Hence, the novel EBV/CMV/T. gondii/HCV MIP microarray allows simultaneous diagnosis of polyclonal and monoclonal immune response to infectious diseases using very small volume samples.
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Affiliation(s)
- Delphine Feron
- INSERM UMR892/CNRS UMR6299, Institut de Recherche Thérapeutique, Université de Nantes, 44007 Nantes Cedex 1, France
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Díez P, Dasilva N, González-González M, Matarraz S, Casado-Vela J, Orfao A, Fuentes M. Data Analysis Strategies for Protein Microarrays. MICROARRAYS 2012; 1:64-83. [PMID: 27605336 PMCID: PMC5003438 DOI: 10.3390/microarrays1020064] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/13/2012] [Accepted: 07/31/2012] [Indexed: 01/22/2023]
Abstract
Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation.
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Affiliation(s)
- Paula Díez
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Juan Casado-Vela
- Translational Oncology Unit, Instituto de Investigaciones Biomédicas 'Alberto Sols', Spanish National Research Council (CSIC-UAM), 28029 Madrid, Spain.
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
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Cunningham BT, Zangar RC. Photonic crystal enhanced fluorescence for early breast cancer biomarker detection. JOURNAL OF BIOPHOTONICS 2012; 5:617-28. [PMID: 22736539 PMCID: PMC3844005 DOI: 10.1002/jbio.201200037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/23/2012] [Accepted: 04/30/2012] [Indexed: 05/05/2023]
Abstract
Photonic crystal surfaces offer a compelling platform for improving the sensitivity of surface-based fluorescent assays used in disease diagnostics. Through the complementary processes of photonic crystal enhanced excitation and enhanced extraction, a periodic dielectric-based nanostructured surface can simultaneously increase the electric field intensity experienced by surface-bound fluorophores and increase the collection efficiency of emitted fluorescent photons. Through the ability to inexpensively fabricate photonic crystal surfaces over substantial surface areas, they are amenable to single-use applications in biological sensing, such as disease biomarker detection in serum. In this review, we will describe the motivation for implementing high-sensitivity, multiplexed biomarker detection in the context of breast cancer diagnosis. We will summarize recent efforts to improve the detection limits of such assays though the use of photonic crystal surfaces. Reduction of detection limits is driven by low autofluorescent substrates for photonic crystal fabrication, and detection instruments that take advantage of their unique features.
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Affiliation(s)
- Brian T Cunningham
- Department of Electrical and Computer Engineering, Department of Bioengineering University of Illinois at Urbana-Champaign, USA.
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Kelly P, Paulin F, Lamont D, Baker L, Clearly S, Exon D, Thompson A. Pre-treatment plasma proteomic markers associated with survival in oesophageal cancer. Br J Cancer 2012; 106:955-61. [PMID: 22294182 PMCID: PMC3305965 DOI: 10.1038/bjc.2012.15] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background: The incidence of oesophageal adenocarcinoma is increasing worldwide but survival remains poor. Neoadjuvant chemotherapy can improve survival, but prognostic and predictive biomarkers are required. This study built upon preclinical approaches to identify prognostic plasma proteomic markers in oesophageal cancer. Methods: Plasma samples collected before and during the treatment of oesophageal cancer and non-cancer controls were analysed by surface-enhanced laser desorption/ionisation time-of-flight (SELDI-TOF) mass spectroscopy (MS). Protein peaks were identified by MS in tryptic digests of purified fractions. Associations between peak intensities obtained in the spectra and clinical endpoints (survival, disease-free survival) were tested by univariate (Fisher's exact test) and multivariate analysis (binary logistic regression). Results: Plasma protein peaks were identified that differed significantly (P<0.05, ANOVA) between the oesophageal cancer and control groups at baseline. Three peaks, confirmed as apolipoprotein A-I, serum amyloid A and transthyretin, in baseline (pre-treatment) samples were associated by univariate and multivariate analysis with disease-free survival and overall survival. Conclusion: Plasma proteins can be detected prior to treatment for oesophageal cancer that are associated with outcome and merit testing as prognostic and predictive markers of response to guide chemotherapy in oesophageal cancer.
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Affiliation(s)
- P Kelly
- Dundee Cancer Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK.
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Liu X, Wu Y, Gao Y, Wang J, Li Z, Han J, Jin G, Ma H. Tuning the surface chemistry of iPDMS for improved protein microarray performance. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16572d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Zhang W, Liu G, Tang F, Shao J, Lu Y, Bao Y, Yao H, Lu C. Pre-absorbed immunoproteomics: a novel method for the detection of Streptococcus suis surface proteins. PLoS One 2011; 6:e21234. [PMID: 21713002 PMCID: PMC3119691 DOI: 10.1371/journal.pone.0021234] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 05/24/2011] [Indexed: 11/19/2022] Open
Abstract
Streptococcus suis serotype 2 (SS2) is a zoonotic pathogen that can cause infections in pigs and humans. Bacterial surface proteins are often investigated as potential vaccine candidates and biomarkers of virulence. In this study, a novel method for identifying bacterial surface proteins is presented, which combines immunoproteomic and immunoserologic techniques. Critical to the success of this new method is an improved procedure for generating two-dimensional electrophoresis gel profiles of S. suis proteins. The S. suis surface proteins identified in this study include muramidase-released protein precursor (MRP) and an ABC transporter protein, while MRP is thought to be one of the main virulence factors in SS2 located on the bacterial surface. Herein, we demonstrate that the ABC transporter protein can bind to HEp-2 cells, which strongly suggests that this protein is located on the bacterial cell surface and may be involved in pathogenesis. An immunofluorescence assay confirmed that the ABC transporter is localized to the bacterial outer surface. This new method may prove to be a useful tool for identifying surface proteins, and aid in the development of new vaccine subunits and disease diagnostics.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Guangjin Liu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Fang Tang
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jing Shao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yan Lu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yinli Bao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Huochun Yao
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Chengping Lu
- Key Laboratory of Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Woo JR, Lim DK, Nam JM. Minimally stable nanoparticle-based colorimetric assay for simple, rapid, and sensitive antibody structure and activity evaluation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:648-655. [PMID: 21308990 DOI: 10.1002/smll.201002080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Indexed: 05/30/2023]
Abstract
A gold nanoparticle-based colorimetric antibody structure and activity evaluation method is developed without using complicated and expensive instrumentation. In this assay, a minimum number of antibodies to stabilize nanoparticles are conjugated to gold nanoparticles to prepare minimally stable nanoparticle probes, and the addition of salt rapidly induced particle aggregation and a color change of the solution from red to blue (25-min assay time). It is found that the solution color change is affected by the degree of structural denaturation of antibodies, and the conformational change of antibodies affects the modification of antibodies to nanoparticles and particle stability. Importantly, the colorimetric method can be applied to different types of antibodies (IgG, IgA, and IgM) and it shows comparable or better structural sensitivity than conventional circular dichroism spectroscopy. Moreover, immunoassay results show that these structural changes of antibodies are highly correlated with their antigen-binding activities. Rapid particle aggregation and high structural sensitivity are achieved in this assay because particles are modified with a minimum number of antibodies to stabilize particles in solution. This nanoparticle-based colorimetric method could be useful in evaluating the structural and activity changes of an array of antibodies in an easy, rapid, and sensitive manner.
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Affiliation(s)
- Jung-Reem Woo
- Department of Chemistry, Seoul National University, 599 Gwanak-ro, Sillim-dong, Gwanak-gu,Seoul, 151-747, South Korea
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Abstract
Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer, diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics, proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as high-throughput, miniaturized, and capable of parallel analysis, protein microarrays have already become an important technology platform for systems biology. In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays, and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.
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Affiliation(s)
- Lina Yang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shujuan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shumin Zhou
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence address. Room 126, 800 Dongchuan Rd. Shanghai 200240, China. Tel: +86-21-34207069; Fax: +86-21-34207069; E-mail:
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Urinary peptide profiling identifies a panel of putative biomarkers for diagnosing and staging endometriosis. Fertil Steril 2011; 95:1261-6.e1-6. [PMID: 21255776 DOI: 10.1016/j.fertnstert.2010.11.066] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 10/14/2010] [Accepted: 11/04/2010] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify a potential diagnostic endometriosis marker using matrix-enhanced laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based urinary proteomics. DESIGN Prospective randomized pilot study. SETTING University hospital, tertiary referral center for endometriosis. PATIENT(S) 53 women undergoing laparoscopic surgery for pain and/or infertility comprising 30 women without endometriosis and 23 with endometriosis. INTERVENTION(S) Laparoscopy and urine specimens. MAIN OUTCOME MEASURE(S) Urinary peptide profiles. RESULT(S) We observed distinct patterns of peptide profiles in the urine samples of women presenting with typical clinical symptoms of endometriosis. Six statistically significant putative peptide markers were identified (four during the periovulatory phase and two during the luteal phase) by comparing controls with moderate/severe endometriosis patients. The periovulatory peptide mass of 1,767.1 Da and the luteal peptide mass of 1,824.3 Da both showed a sensitivity of 75% and a specificity of 85% and 71%, respectively. Also detected were seven peptide markers (two during the periovulatory phase and five during the luteal phase) by comparing the urinary peptide profiles of patients with minimal/mild to moderate/severe endometriosis. The periovulatory peptide mass of 3,280.9 Da and the luteal peptide mass of 1,933.8 Da showed a sensitivity of 82% and 75% and a specificity of 88% and 75%, respectively. CONCLUSION(S) Urinary proteomic analysis may provide a novel method of diagnosing and staging endometriosis.
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Abstract
Affinity proteomics, mainly represented by antibody microarrays, has in recent years been established as a powerful tool for high-throughput (disease) proteomics. The technology can be used to generate detailed protein expression profiles, or protein maps, of focused set of proteins in crude proteomes and potentially even high-resolution portraits of entire proteomes. The technology provides unique opportunities, for example biomarker discovery, disease diagnostics, patient stratification and monitoring of disease, and taking the next steps toward personalized medicine. However, the process of designing high-performing, high-density antibody micro- and nanoarrays has proven to be challenging, requiring truly cross-disciplinary efforts to be adopted. In this mini-review, we address one of these key technological issues, namely, the choice of probe format, and focus on the use of recombinant antibodies vs. polyclonal and monoclonal antibodies for the generation of antibody arrays.
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Detection of oesophageal cancer biomarkers by plasma proteomic profiling of human cell line xenografts in response to chemotherapy. Br J Cancer 2010; 103:232-8. [PMID: 20551956 PMCID: PMC2906736 DOI: 10.1038/sj.bjc.6605741] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background: The incidence of oesophageal adenocarcinoma is increasing worldwide but survival remains poor. Neoadjuvant chemotherapy may improve survival, but targeting treatment to patients who respond to chemotherapy could be improved by the availability of markers of response. This study sought proteomic markers of therapeutic response using an adenocarcinoma xenograft model. Methods: Epirubicin, cisplatin or 5-fluorouracil was administered to severe combined immune-deficient mice bearing OE19 oesophageal adenocarcinoma xenografts. Murine plasma samples from treated and untreated xenografts were analysed by surface-enhanced laser desorption/ionisation time-of-flight mass spectroscopy, and panels of peaks were found using class prediction models that distinguished treatment groups. Proteins in these peaks were identified by mass spectroscopy in tryptic digests of purified fractions. Five paired samples from oesophageal cancer patients before and after chemotherapy were analysed using the same methodology. Results: Plasma protein peaks were identified that differed significantly (P<0.05, ANOVA) between the treated xenograft and control groups. Marker panels predicted treated vs untreated xenografts with sensitivities of 100%, specificities of 86–100% and test efficiencies of 89–100%. Three of the proteins identified in these panels, apolipoprotein A-I, serum amyloid A and transthyretin were confirmed in the clinical samples. Conclusion: Plasma protein markers can be detected in response to chemotherapy in oesophageal adenocarcinoma xenografts and in clinical samples, and have the potential to monitor response and guide chemotherapy in oesophageal adenocarcinoma.
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