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Cheng HP, Yang TH, Wang JC, Chuang HS. Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection. SENSORS (BASEL, SWITZERLAND) 2024; 24:2904. [PMID: 38733011 PMCID: PMC11086254 DOI: 10.3390/s24092904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Demand is strong for sensitive, reliable, and cost-effective diagnostic tools for cancer detection. Accordingly, bead-based biosensors have emerged in recent years as promising diagnostic platforms based on wide-ranging cancer biomarkers owing to the versatility, high sensitivity, and flexibility to perform the multiplexing of beads. This comprehensive review highlights recent trends and innovations in the development of bead-based biosensors for cancer-biomarker detection. We introduce various types of bead-based biosensors such as optical, electrochemical, and magnetic biosensors, along with their respective advantages and limitations. Moreover, the review summarizes the latest advancements, including fabrication techniques, signal-amplification strategies, and integration with microfluidics and nanotechnology. Additionally, the challenges and future perspectives in the field of bead-based biosensors for cancer-biomarker detection are discussed. Understanding these innovations in bead-based biosensors can greatly contribute to improvements in cancer diagnostics, thereby facilitating early detection and personalized treatments.
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Affiliation(s)
- Hui-Pin Cheng
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
| | - Tai-Hua Yang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
- Department of Orthopedic Surgery, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Jhih-Cheng Wang
- Department of Urology, Chimei Medical Center, Tainan 710, Taiwan
- Department of Electrical Engineering, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [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: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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Smolko CM, Janes KA. An ultrasensitive fiveplex activity assay for cellular kinases. Sci Rep 2019; 9:19409. [PMID: 31857650 PMCID: PMC6923413 DOI: 10.1038/s41598-019-55998-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Protein kinases are enzymes whose abundance, protein-protein interactions, and posttranslational modifications together determine net signaling activity in cells. Large-scale data on cellular kinase activity are limited, because existing assays are cumbersome, poorly sensitive, low throughput, and restricted to measuring one kinase at a time. Here, we surmount the conventional hurdles of activity measurement with a multiplexing approach that leverages the selectivity of individual kinase-substrate pairs. We demonstrate proof of concept by designing an assay that jointly measures activity of five pleiotropic signaling kinases: Akt, IκB kinase (IKK), c-jun N-terminal kinase (JNK), mitogen-activated protein kinase (MAPK)-extracellular regulated kinase kinase (MEK), and MAPK-activated protein kinase-2 (MK2). The assay operates in a 96-well format and specifically measures endogenous kinase activation with coefficients of variation less than 20%. Multiplex tracking of kinase-substrate pairs reduces input requirements by 25-fold, with ~75 µg of cellular extract sufficient for fiveplex activity profiling. We applied the assay to monitor kinase signaling during coxsackievirus B3 infection of two different host-cell types and identified multiple differences in pathway dynamics and coordination that warrant future study. Because the Akt–IKK–JNK–MEK–MK2 pathways regulate many important cellular functions, the fiveplex assay should find applications in inflammation, environmental-stress, and cancer research.
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Affiliation(s)
- Christian M Smolko
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA. .,Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
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Technological advances for interrogating the human kinome. Biochem Soc Trans 2017; 45:65-77. [PMID: 28202660 DOI: 10.1042/bst20160163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022]
Abstract
There is increasing appreciation among researchers and clinicians of the value of investigating biology and pathobiology at the level of cellular kinase (kinome) activity. Kinome analysis provides valuable opportunity to gain insights into complex biology (including disease pathology), identify biomarkers of critical phenotypes (including disease prognosis and evaluation of therapeutic efficacy), and identify targets for therapeutic intervention through kinase inhibitors. The growing interest in kinome analysis has fueled efforts to develop and optimize technologies that enable characterization of phosphorylation-mediated signaling events in a cost-effective, high-throughput manner. In this review, we highlight recent advances to the central technologies currently available for kinome profiling and offer our perspectives on the key challenges remaining to be addressed.
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Zhang J, Yin L, Wu J, Zhang Y, Xu T, Ma R, Cao H, Tang J. Detection of serum VEGF and MMP-9 levels by Luminex multiplexed assays in patients with breast infiltrative ductal carcinoma. Exp Ther Med 2014; 8:175-180. [PMID: 24944618 PMCID: PMC4061234 DOI: 10.3892/etm.2014.1685] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/27/2014] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to assess the effect of the combined detection of serum vascular endothelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP-9) by Luminex multiplexed assays for the diagnosis, treatment and prognosis of breast cancer. Preoperative levels of serum VEGF and MMP-9 were detected via a lipid chip-based method in 301 breast cancer cases, 83 breast fibroadenoma cases and 40 healthy adults. Postoperative levels of VEGF and MMP-9 were also detected in 118 breast cancer cases. The levels of serum VEGF and MMP-9 in patients with breast infiltrative ductal carcinoma (IDC) were higher than those in the breast fibroadenoma and healthy control groups (P<0.05); there was no statistically significant difference between the breast fibroadenoma and healthy groups (P>0.05). The levels of VEGF and MMP-9 were shown to correlate with the clinical stage, tumor size and the lymph node metastasis status. However, the levels were not associated with age or gender (P>0.05). In addition, the serum level of MMP-9 exhibited a significantly correlation with the VEGF level (r=0.601, P<0.001). Subgroup analysis revealed that in patients with IDC, serum levels of VEGF and MMP-9 prior to surgery were significantly higher than those following surgery (P<0.05). Therefore, the serum levels of VEGF and MMP-9 can be used as markers for the diagnosis of breast IDC and may also be valuable for the prediction of lymph nodes metastasis.
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Affiliation(s)
- Junying Zhang
- Department of Oncology, Xuzhou Medical College, Xuzhou, Jiangsu 221004, P.R. China
| | - Li Yin
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
| | - Jianzhong Wu
- Research Center for Clinical Oncology, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
| | - Ye Zhang
- Research Center for Clinical Oncology, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
| | - Tao Xu
- Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
| | - Rong Ma
- Research Center for Clinical Oncology, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
| | - Haixia Cao
- Research Center for Clinical Oncology, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
| | - Jinhai Tang
- Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210009, P.R. China
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Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
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Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
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Heubach Y, Planatscher H, Sommersdorf C, Maisch D, Maier J, Joos TO, Templin MF, Poetz O. From spots to beads-PTM-peptide bead arrays for the characterization of anti-histone antibodies. Proteomics 2013; 13:1010-5. [PMID: 23401470 DOI: 10.1002/pmic.201200383] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 01/21/2013] [Accepted: 01/31/2013] [Indexed: 12/21/2022]
Abstract
Antibodies that recognize PTMs of histones play a central role in epigenetic proteomic research. Modification-specific antibodies are employed in chromatin immunoprecipitation, for Western blotting and during the immunoprecipitation steps for MS-based global proteomic analyses. Knowledge about the antibodies' off-target binding is essential for the interpretation of experimental data. To address this challenge we developed a fast and cost efficient system for generating peptide bead arrays. We employed this method to establish a bead-based peptide array containing 384 peptides displaying phosphorylated, acetylated, methylated, and citrullinated N-terminal regions of histones H2A, H2B, H3 and H4 and controls. We profiled the binding of 40 PTM-specific antibodies important for epigenetic proteomic research.
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Affiliation(s)
- Yvonne Heubach
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
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8
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A multiple reaction monitoring (MRM) method to detect Bcr-Abl kinase activity in CML using a peptide biosensor. PLoS One 2013; 8:e56627. [PMID: 23437189 PMCID: PMC3577862 DOI: 10.1371/journal.pone.0056627] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
The protein kinase Bcr-Abl plays a major role in the pathogenesis of chronic myelogenous leukemia (CML), and is the target of the breakthrough drug imatinib (Gleevec™). While most patients respond well to imatinib, approximately 30% never achieve remission or develop resistance within 1–5 years of starting imatinib treatment. Evidence from clinical studies suggests that achieving at least 50% inhibition of a patient’s Bcr-Abl kinase activity (relative to their level at diagnosis) is associated with improved patient outcomes, including reduced occurrence of resistance and longer maintenance of remission. Accordingly, sensitive assays for detecting Bcr-Abl kinase activity compatible with small amounts of patient material are desirable as potential companion diagnostics for imatinib. Here we report the detection of Bcr-Abl activity and inhibition by imatinib in the human CML cell line K562 using a cell-penetrating peptide biosensor and multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer. MRM enabled reproducible, selective detection of the peptide biosensor at fmol levels from aliquots of cell lysate equivalent to ∼15,000 cells. This degree of sensitivity will facilitate the miniaturization of the entire assay procedure down to cell numbers approaching 15,000, making it practical for translational applications in patient cells in which the limited amount of available patient material often presents a major challenge.
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Ghosh G, Yan X, Kron SJ, Palecek SP. Activity assay of epidermal growth factor receptor tyrosine kinase inhibitors in triple-negative breast cancer cells using peptide-conjugated magnetic beads. Assay Drug Dev Technol 2012; 11:44-51. [PMID: 22994968 DOI: 10.1089/adt.2012.454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer with limited treatment options. Epidermal growth factor receptor I (EGFR) has emerged as a promising target in TNBC. Limited success of the EGFR kinase inhibiting small molecules in clinical trials may be attributed in part to inaccuracy in identifying EGFR signatures in patient tumors. In light of the absence of a simple correlation between EGFR expression and its degree of activation, a simple and reliable tool that can quantify EGFR kinase activity in tumor samples may be of therapeutic value in predicting patient-specific EGFR targeted therapies. This study reports the development of an assay that can quantitatively profile EGFR kinase activities and inhibitor sensitivities in TNBC cell lysates by using peptide reporters covalently tethered to magnetic beads in a controlled orientation. The use of magnetic beads provides rapid sample handling and easy product isolation. The potential of this approach was demonstrated by screening a set of five clinically relevant EGFR tyrosine kinase inhibitors. Formatted for microwell plates, this magnetic bead-based kinase assay may be used as a complementary approach for direct high-throughput screening of small molecule inhibitors.
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Affiliation(s)
- Gargi Ghosh
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, 53706, USA.
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10
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Zhou G, Khan F, Dai Q, Sylvester JE, Kron SJ. Photocleavable peptide-oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS. MOLECULAR BIOSYSTEMS 2012; 8:2395-404. [PMID: 22772337 DOI: 10.1039/c2mb25163a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Robust methods for highly parallel, quantitative analysis of cellular protein tyrosine kinase activities may provide tools critically needed to decipher oncogenic signaling, discover new targeted drugs, diagnose cancer and monitor patients. Here, we describe proof-of-principle for a novel protein kinase assay with the potential to help overcome these challenges. MALDI-TOF mass spectrometry provides an ideal tool for label-free multiplexed analysis of peptide phosphorylation, but is poorly matched to homogeneous assays and complex samples. Thus, we conjugated a common oligonucleotide tag to multiple peptide substrates, offering efficient capture from solution-phase kinase reactions by annealing to the complementary sequence tethered to PEG-passivated superparamagnetic microparticles. To enable reversible conjugation, we developed a novel bifunctional cross-linker allowing simple and efficient preparation of photocleavable peptide-oligonucleotide conjugates. After washing away contaminants and following photorelease, MALDI-TOF analysis yielded relative phosphorylation of each peptide with high sensitivity and specificity. Validating the hybridization-mediated multiplexed kinase assay, when three peptide substrate-oligonucleotide conjugates were mixed with the tyrosine kinase c-Abl and ATP, we readily observed their differential phosphorylation yet measured a common IC(50) for the Abl kinase inhibitor imatinib. This new assay enables analysis of protein kinase activities in a multiplexed format amenable to screening inhibitors against multiple kinases in parallel, an important capability for drug discovery and predictive diagnostics.
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Affiliation(s)
- Guangchang Zhou
- Department of Molecular Genetics and Cell Biology, Gordon Center for Integrative Sciences, W522A, The University of Chicago, Chicago, IL 60637, USA
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11
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Arsenault R, Griebel P, Napper S. Peptide arrays for kinome analysis: New opportunities and remaining challenges. Proteomics 2011; 11:4595-609. [DOI: 10.1002/pmic.201100296] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/28/2011] [Accepted: 10/04/2011] [Indexed: 01/08/2023]
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12
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Bourgey M, Lariviere M, Richer C, Sinnett D. ALG: automated genotype calling of Luminex assays. PLoS One 2011; 6:e19368. [PMID: 21573116 PMCID: PMC3089621 DOI: 10.1371/journal.pone.0019368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 04/03/2011] [Indexed: 12/20/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients, 200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific informatics knowledge, or through command line with access to the open source code. The ALG software has been implemented in R and is freely available for non-commercial use either at http://alg.sourceforge.net or by request to mathieu.bourgey@umontreal.ca
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Affiliation(s)
- Mathieu Bourgey
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Quebec, Canada.
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13
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Zhou G, Yan X, Wu D, Kron SJ. Photocleavable peptide-conjugated magnetic beads for protein kinase assays by MALDI-TOF MS. Bioconjug Chem 2011; 21:1917-24. [PMID: 20860375 DOI: 10.1021/bc1003058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides were immobilized onto superparamagnetic beads via photocleavable linkers. This enabled simple, rapid, and label-free protein kinase assays via MALDI-TOF MS detection of substrate peptide phosphorylation. Abltide, a model substrate for the Abl protein tyrosine kinase model, was coupled onto amine-terminated beads, incubated with ATP and recombinant c-Abl kinase, and released and further detected to determine phosphorylation. Abltide phosphorylation was found to depend significantly on the length and composition of linkers to the bead surface. Inserting a diblock spacer of poly(glycine) and poly(ethylene glycol) segments markedly enhanced phosphorylation. To validate the assay, the activity of two small-molecule kinase inhibitors, imatinib and dasatinib, which target the oncogenic mutant tyrosine kinase Bcr-Abl to treat chronic myeloid leukemia (CML), was tested. Examining inhibition of the purified c-Abl or Bcr-Abl in K562 CML cell extracts, IC(50) values were determined to be consistent with the literature. This simple, label-free, MALDI-based protein kinase assay can be readily adapted to allow multiplexed assays of multiple peptide substrates and/or analysis of alternative post-translational modifications as a tool for drug discovery and clinical testing.
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Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
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14
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Schenone S, Brullo C, Musumeci F, Botta M. Novel dual Src/Abl inhibitors for hematologic and solid malignancies. Expert Opin Investig Drugs 2010; 19:931-45. [PMID: 20557276 DOI: 10.1517/13543784.2010.499898] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD c-Src and Bcr-Abl are two non-receptor or cytoplasmic tyrosine kinases (TKs) that play important roles in the development of solid and hematological malignancies. Indeed, Src is overexpressed or hyperactivated in a variety of solid tumors, while Bcr-Abl is the causative agent of chronic myeloid leukemia (CML), where Src is also involved. The two enzymes share significant sequence homology and remarkable structural resemblance. AREAS COVERED IN THIS REVIEW ATP-competitive compounds originally developed as Src inhibitors, showed to be also potent Abl inhibitors. Dasatinib, the first dual Src/Abl inhibitor approved by the US FDA in 2006 for the treatment of imatinib-resistant CML, is currently being tested in several clinical trials for the treatment of different solid tumors. SKI-606 and AZD0530 are two other important dual Src/Abl inhibitors extensively tested in animal models and in clinical trials, but not entered into therapy yet. WHAT THE READER WILL GAIN In this review we will report the latest results regarding dasatinib, SKI-606 and AZD0530, but also the knowledge on new compounds that have appeared in the literature in the last few years, including AP24163, AP24534, XL228, DC2036. We will focus on the most recent clinical trials or on preclinical studies that are in progress on these small-molecule TK inhibitors that represent a targeted therapy with high potential against cancer. TAKE HOME MESSAGE Molecularly targeted therapies, including the inhibition of specific TKs hyperactivated or overexpressed in many human cancers, could be less toxic than the classical non-specific cytotoxic chemotherapeutic agents; they could offer important therapeutic effects, especially if used in association with other agents such as monoclonal antibodies.
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Affiliation(s)
- Silvia Schenone
- University of Genoa, Dipartimento di Scienze Farmaceutiche, Viale Benedetto VX, Genoa, Italy.
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