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Aparna GM, Tetala KKR. Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules 2023; 13:602. [PMID: 37189350 PMCID: PMC10135839 DOI: 10.3390/biom13040602] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018-2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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Affiliation(s)
| | - Kishore K. R. Tetala
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore 632014, Tamilnadu, India;
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Ahn JH, Kang CK, Kim EM, Kim AR, Kim A. Proteomics for Early Detection of Non-Muscle-Invasive Bladder Cancer: Clinically Useful Urine Protein Biomarkers. Life (Basel) 2022; 12:395. [PMID: 35330146 PMCID: PMC8950253 DOI: 10.3390/life12030395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Bladder cancer is the fourth most common cancer in men, and most cases are non-muscle-invasive. A high recurrence rate is a critical problem in non-muscle-invasive bladder cancer. The availability of few urine tests hinders the effective detection of superficial and small bladder tumors. Cystoscopy is the gold standard for diagnosis; however, it is associated with urinary tract infections, hematuria, and pain. Early detection is imperative, as intervention influences recurrence. Therefore, urinary biomarkers need to be developed to detect these bladder cancers. Recently, several protein candidates in the urine have been identified as biomarkers. In the present narrative review, the current status of the development of urinary protein biomarkers, including FDA-approved biomarkers, is summarized. Additionally, contemporary proteomic technologies, such as antibody-based methods, mass-spectrometry-based methods, and machine-learning-based diagnosis, are reported. Furthermore, new strategies for the rapid and correct profiling of potential biomarkers of bladder cancer in urine are introduced, along with their limitations. The advantages of urinary protein biomarkers and the development of several related technologies are highlighted in this review. Moreover, an in-depth understanding of the scientific background and available protocols in research and clinical applications of the surveillance of non-muscle bladder cancer is provided.
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Affiliation(s)
- Jae-Hak Ahn
- Department of Urology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Korea;
| | - Chan-Koo Kang
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Gyeongbuk, Korea;
- School of Life Science, Handong Global University, Pohang 37554, Gyungbuk, Korea
| | - Eun-Mee Kim
- Department of Emergency Medical Technology, Korea Nazarene University, Cheonan 31172, Chungcheongnam-do, Korea;
| | - Ah-Ram Kim
- Department of Advanced Convergence, Handong Global University, Pohang 37554, Gyeongbuk, Korea;
- School of Life Science, Handong Global University, Pohang 37554, Gyungbuk, Korea
| | - Aram Kim
- Department of Urology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul 05030, Korea;
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Gebhardt C, Lehmann M, Reif MM, Zacharias M, Gemmecker G, Cordes T. Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*. Chemphyschem 2021; 22:1566-1583. [PMID: 34185946 PMCID: PMC8457111 DOI: 10.1002/cphc.202000935] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/01/2021] [Indexed: 12/23/2022]
Abstract
The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well-kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation. Minor differences in apparent dye-protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes in smFRET studies or other fluorescence applications.
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Affiliation(s)
- Christian Gebhardt
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Maria M. Reif
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Martin Zacharias
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Gerd Gemmecker
- Bavarian NMR Center (B NMRZ), Department of ChemistryTechnical University of MunichLichtenbergstr. 485748GarchingGermany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
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Antibody Arrays: Barcode Technology. Methods Mol Biol 2020. [PMID: 33237411 DOI: 10.1007/978-1-0716-1064-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Antibody microarray is a fundamental, high-content technology for analyzing biomarkers with a multiplexity even at the proteomic level. Recent advancement in this field has driven the antibody array into a new territory related with single-cell analysis. Here we describe a flow pattern-based method for producing a high-density barcode antibody microarray for the detection of proteins in fluidic samples and in single cells. The antibody microarray is fabricated by a perpendicularly oriented flow patterning of single-stranded barcode DNAs, which are then converted into DNA-antibody conjugates. Compared to conventional microarrays, this barcode antibody microarray features a simple and high-throughput assay while achieving both high sensitivity and specificity. This barcode technology provides new clues for developing next-generation antibody microarrays and can be widely used in protein biomarker discovery, cell signaling network analysis, and disease diagnosis and prognosis.
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Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing. Commun Biol 2020; 3:339. [PMID: 32620783 PMCID: PMC7334203 DOI: 10.1038/s42003-020-1068-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/11/2020] [Indexed: 12/27/2022] Open
Abstract
The composition of serum proteins is reflecting the current health status and can, with the right tools, be used to detect early signs of disease, such as an emerging cancer. An earlier diagnosis of cancer would greatly increase the chance of an improved outcome for the patients. However, there is still an unmet need for proficient tools to decipher the information in the blood proteome, which calls for further technological development. Here, we present a proof-of-concept study that demonstrates an alternative approach for multiplexed protein profiling of serum samples in solution, using DNA barcoded scFv antibody fragments and next generation sequencing. The outcome shows high accuracy when discriminating samples derived from pancreatic cancer patients and healthy controls and represents a scalable alternative for serum analysis. Brofelth, Ekstrand et al use DNA barcoded scFv antibody fragments and next generation sequencing for multiplex profiling of proteins in serum from pancreatic cancer patients with high accuracy. This approach can potentially be used in high throughput precision diagnosis.
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Yang L, Yu Y, Ma C, Wang H, Dai J, Duan H, Fu Z, Wu P, Wang D, Yu X. Development of RBC Membrane Antigen Arrays for Validating Blood Grouping Reagents. J Proteome Res 2018; 17:3237-3245. [PMID: 30114910 DOI: 10.1021/acs.jproteome.8b00370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibody reagents have been remained as a standard approach to characterize blood group (BG) antigens in clinic. The specificity and cross-reactivity of these BG antibodies are routine detected using the gel microcolumn assay (GMA). However, the GMA is neither specific nor sensitive, thus increasing the risk of improperly matched RBC transfusions. In this work, we describe a bead-based RBC membrane antigen array to detect BG antibody-antigen binding with ∼700-fold higher sensitivity and dynamic range than the GMA. RBC membrane antigen arrays were fabricated using fragmented RBC membranes highly enriched in BG panel antigens. The arrays were then used to screen the interactions of 15 BG reagents to three antigen panels. The majority of the antibody reactions (i.e., 86.7%; 39/45) aligned with those obtained with the GMA. The six cross-reactive, nonspecific antibody reactions identified only by our arrays (i.e., 13.3%; 6/45) were confirmed by agglutination inhibition and genotyping assays. These results demonstrate that our RBC membrane antigen array has great potential in screening BG antibodies and improving the safety of RBC transfusions.
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Affiliation(s)
- Lu Yang
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Yang Yu
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Chunya Ma
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Jiayu Dai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Hu Duan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Zhonglin Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Ping Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
| | - Deqing Wang
- Department of Blood Transfusion , Chinese PLA General Hospital , Beijing , 100853 , China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (PHOENIX Center, Beijing) , Beijing Institute of Lifeomics , Beijing , 102206 , China
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Optomechanical devices for deep plasma cancer proteomics. Semin Cancer Biol 2017; 52:26-38. [PMID: 28867489 DOI: 10.1016/j.semcancer.2017.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/22/2017] [Accepted: 08/30/2017] [Indexed: 12/27/2022]
Abstract
Most of the cancer deaths could be avoided by early detection of the tumor when it is confined to its primary site and it has not metastasized. To this aim, one of the most promising strategies is the discovery and detection of protein biomarkers shed by the young tumor to the bloodstream. Proteomic technologies, mainly mass spectrometry and multiplexed immunoassays, have rapidly developed during last years with improved limits of detection and multiplexing capability. Unfortunately, these developments together major investments and large international efforts have not resulted into new useful protein biomarkers. Here, we analyze the potential and limitations of current proteomic technologies for detecting protein biomarkers released into circulation by the tumor. We find that these technologies can hardly probe the deepest region of the plasma proteome, at concentrations below the pg/mL level, where protein biomarkers for early cancer detection may exist. This clearly indicates the need of incorporating novel ultrasensitive techniques to the proteomic tool-box that can cover the inaccessible regions of the plasma proteome. We here propose biological detectors based on nanomechanical systems for discovery and detection of cancer protein biomarkers in plasma. We review the modes of operation of these devices, putting our focus on recent developments on nanomechanical sandwich immunoassays and nanomechanical spectrometry. The first technique enables reproducible immunodetection of proteins at concentrations well below the pg/mL level, with a limit of detection on the verge of 10 ag/mL. This technology can potentially detect low abundance tumor-associated proteins in plasma at the very early stages of the tumor. The second technique enables the identification of individual intact proteins by two physical coordinates, the mass and stiffness, instead of the mass-to-charge ratio of the protein constituents. This technology enormously simplifies the identification of proteins and it can provide useful information on interactions and posttranslational modifications, that otherwise is lost in mass spectrometry.
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Abstract
Histological grade is one of the most commonly used prognostic factors for patients diagnosed with breast cancer. However, conventional grading has proven technically challenging, and up to 60% of the tumors are classified as histological grade 2, which represents a heterogeneous cohort less informative for clinical decision making. In an attempt to study and extend the molecular puzzle of histologically graded breast cancer, we have in this pilot project searched for additional protein biomarkers in a new space of the proteome. To this end, we have for the first time performed protein expression profiling of breast cancer tumor tissue, using recombinant antibody microarrays, targeting mainly immunoregulatory proteins. Thus, we have explored the immune system as a disease-specific sensor (clinical immunoproteomics). Uniquely, the results showed that several biologically relevant proteins reflecting histological grade could be delineated. In more detail, the tentative biomarker panels could be used to i) build a candidate model classifying grade 1 vs. grade 3 tumors, ii) demonstrate the molecular heterogeneity among grade 2 tumors, and iii) potentially re-classify several of the grade 2 tumors to more like grade 1 or grade 3 tumors. This could, in the long-term run, lead to improved prognosis, by which the patients could benefit from improved tailored care.
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Delfani P, Sturfelt G, Gullstrand B, Carlsson A, Kassandra M, Borrebaeck CAK, Bengtsson AA, Wingren C. Deciphering systemic lupus erythematosus-associated serum biomarkers reflecting apoptosis and disease activity. Lupus 2016; 26:373-387. [PMID: 27694630 DOI: 10.1177/0961203316669240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Systemic lupus erythematosus (SLE) is a severe chronic inflammatory autoimmune connective tissue disease. Despite major efforts, SLE remains a poorly understood disease with unpredictable course, unknown etiology and complex pathogenesis. Apoptosis combined with deficiency in clearing apoptotic cells is an important etiopathogenic event in SLE, which could contribute to the increased load of potential autoantigen(s); however, the lack of disease-specific protein signatures deciphering SLE and the underlying biological processes is striking and represents a key limitation. In this retrospective pilot study, we explored the immune system as a specific sensor for disease, in order to advance our understanding of SLE. To this end, we determined multiplexed serum protein expression profiles of crude SLE serum samples, using antibody microarrays. The aim was to identify differential immunoprofiles, or snapshots of the immune response modulated by the disease, reflecting apoptosis, a key process in the etiology of SLE and disease activity. The results showed that multiplexed panels of SLE-associated serum biomarkers could be decoded, in particular reflecting disease activity, but potentially the apoptosis process as well. While the former biomarkers could display a potential future use for prognosis, the latter biomarkers might help shed further light on the apoptosis process taking place in SLE.
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Affiliation(s)
- P Delfani
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - G Sturfelt
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - B Gullstrand
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - A Carlsson
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - M Kassandra
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - C A K Borrebaeck
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - A A Bengtsson
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - C Wingren
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
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A Multicenter Trial Defining a Serum Protein Signature Associated with Pancreatic Ductal Adenocarcinoma. INTERNATIONAL JOURNAL OF PROTEOMICS 2015; 2015:587250. [PMID: 26587286 PMCID: PMC4637476 DOI: 10.1155/2015/587250] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/28/2015] [Indexed: 01/06/2023]
Abstract
Background. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with rapid tumor progression and poor prognosis. This study was motivated by the lack of sensitive and specific PDAC biomarkers and aimed to identify a diagnostic, serum protein signature for PDAC. Methods. To mimic a real life test situation, a multicenter trial comprising a serum sample cohort, including 338 patients with either PDAC or other pancreatic diseases (OPD) and controls with nonpancreatic conditions (NPC), was analyzed on 293-plex recombinant antibody microarrays targeting immunoregulatory and cancer-associated antigens. Results. Serum samples collected from different hospitals were analyzed and showed that (i) sampling from five different hospitals could not be identified as a preanalytical variable and (ii) a multiplexed biomarker signature could be identified, utilizing up to 10 serum markers that could discriminate PDAC from controls, with sensitivities and specificities in the 91–100% range. The first protein profiles associated with the location of the primary tumor in the pancreas could also be identified. Conclusions. The results demonstrate that robust enough serum signatures could be identified in a multicenter trial, potentially contributing to the development of a multiplexed biomarker immunoassay for improved PDAC diagnosis.
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Abstract
Sensing clinically relevant biomolecules is crucial for the detection and prevention of disease. Currently used detection methods tend to be expensive, time intensive, and specific for only one particular biomolecule of interest. Nanoparticle-based arrays using conjugated polymers have emerged as an analytical and potential clinical tool, allowing detection of a wide range of biomolecules using selective, not specific, sensor components. In this report, we highlight recent progress in nanoparticle - polymer sensor arrays in both the fundamental understanding of how the sensor arrays function as well as the detection of clinically relevant bacteria and cells.
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Affiliation(s)
- Brian Creran
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003 (USA), Phone Number - 413-545-2058, Fax Number - 413-545-4490
| | - Uwe H F Bunz
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany, Phone Number - +49 6221 54-8401
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003 (USA), Phone Number - 413-545-2058, Fax Number - 413-545-4490
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A well-based reverse-phase protein array of formalin-fixed paraffin-embedded tissue. Methods Mol Biol 2015; 1312:129-39. [PMID: 26043998 DOI: 10.1007/978-1-4939-2694-7_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biomarkers from tissue-based proteomic studies directly contribute to defining disease states as well as promise to improve early detection or provide for further targeted therapeutics. In the clinical setting, tissue samples are preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks for histological examination. However, proteomic analysis of FFPE tissue is complicated due to the high level of covalently cross-linked proteins arising from formalin fixation. To address these challenges, we developed well-based reverse-phase protein array (RPPA). This approach is a robust protein isolation methodology (29.44 ± 7.8 μg per 1 mm(3) of FFPE tissue) paired with a novel on electrochemiluminescence detection system. Protein samples derived from FFPE tissue by means of laser capture dissection, with as few as 500 shots, demonstrate measurable signal differences for different proteins. The lysates coated to the array plate, dried up and vacuum-sealed, remain stable up to 2 months at room temperature. This methodology is directly applicable to FFPE tissue and presents the direct opportunity of addressing hypothesis within clinical trials and well-annotated clinical tissue repositories.
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Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 2014; 15:218-31. [PMID: 25266292 DOI: 10.1002/pmic.201400261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/25/2014] [Indexed: 01/17/2023]
Abstract
Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.
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Affiliation(s)
- Nikita Gahoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Petersson L, Dexlin-Mellby L, Bengtsson AA, Sturfelt G, Borrebaeck CAK, Wingren C. Multiplexing of miniaturized planar antibody arrays for serum protein profiling--a biomarker discovery in SLE nephritis. LAB ON A CHIP 2014; 14:1931-1942. [PMID: 24763547 DOI: 10.1039/c3lc51420j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the quest to decipher disease-associated biomarkers, miniaturized and multiplexed antibody arrays may play a central role in generating protein expression profiles, or protein maps, of crude serum samples. In this conceptual study, we explored a novel, 4-times larger pen design, enabling us to, in a unique manner, simultaneously print 48 different reagents (antibodies) as individual 78.5 μm(2) (10 μm in diameter) sized spots at a density of 38,000 spots cm(-2) using dip-pen nanolithography technology. The antibody array set-up was interfaced with a high-resolution fluorescent-based scanner for sensitive sensing. The performance and applicability of this novel 48-plex recombinant antibody array platform design was demonstrated in a first clinical application targeting SLE nephritis, a severe chronic autoimmune connective tissue disorder, as the model disease. To this end, crude, directly biotinylated serum samples were targeted. The results showed that the miniaturized and multiplexed array platform displayed adequate performance, and that SLE-associated serum biomarker panels reflecting the disease process could be deciphered, outlining the use of miniaturized antibody arrays for disease proteomics and biomarker discovery.
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Affiliation(s)
- Linn Petersson
- Dept. of Immunotechnology and CREATE Health, Medicon Village, Lund University, Medicon Village, Building no. 406, SE-22381 Lund, Sweden.
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González-González M, Bartolome R, Jara-Acevedo R, Casado-Vela J, Dasilva N, Matarraz S, García J, Alcazar JA, Sayagues JM, Orfao A, Fuentes M. Evaluation of homo- and hetero-functionally activated glass surfaces for optimized antibody arrays. Anal Biochem 2014; 450:37-45. [PMID: 24440232 DOI: 10.1016/j.ab.2014.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/07/2014] [Indexed: 11/17/2022]
Abstract
Antibody arrays hold great promise for biomedical applications, but they are typically manufactured using chemically functionalized surfaces that still require optimization. Here, we describe novel hetero-functionally activated glass surfaces favoring oriented antibody binding for improved performance in protein microarray applications. Antibody arrays manufactured in our facility using the functionalization chemistries described here proved to be reproducible and stable and also showed good signal intensities. As a proof-of-principle of the glass surface functionalization protocols described in this article, we built antibody-based arrays functionalized with different chemistries that enabled the simultaneous detection of 71 human leukocyte membrane differentiation antigens commonly found in peripheral blood mononuclear cells. Such detection is specific and semi-quantitative and can be performed in a single assay under native conditions. In summary, the protocol described here, based on the use of antibody array technology, enabled the concurrent detection of a set of membrane proteins under native conditions in a specific, selective, and semi-quantitative manner and in a single assay.
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Affiliation(s)
- María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Raquel Bartolome
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | | | - Juan Casado-Vela
- Spanish National Research Council (CSIC)-Spanish National Biotechnology Centre (CNB), 28049 Madrid, Spain
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Jacinto García
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J A Alcazar
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J M Sayagues
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
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Izzotti A, Centofanti M, Saccà SC. Molecular diagnostics of ocular diseases: the application of antibody microarray. Expert Rev Mol Diagn 2014; 12:629-43. [DOI: 10.1586/erm.12.57] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Tribl F, Meyer HE, Marcus K. Analysis of organelles within the nervous system: impact on brain and organelle functions. Expert Rev Proteomics 2014; 5:333-51. [DOI: 10.1586/14789450.5.2.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Wilson R. Sensitivity and specificity: twin goals of proteomics assays. Can they be combined? Expert Rev Proteomics 2014; 10:135-49. [DOI: 10.1586/epr.13.7] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Abstract
Affinity proteomics, represented by antibody arrays, is a multiplex technology for high-throughput protein expression profiling of crude proteomes in a highly specific, sensitive, and miniaturized manner. The antibodies are individually deposited in an ordered pattern, an array, onto a solid support. Next, the sample is added, and any specifically bound proteins are detected and quantified using mainly fluorescence as the mode of detection. The binding pattern is then converted into a relative protein expression map, or protein atlas, delineating the composition of the sample at the molecular level. The technology provides unique opportunities for various applications, such as protein expression profiling, biomarker discovery, disease diagnostics, prognostics, evidence-based therapy selection, and disease monitoring. Here, we describe the generation and use of planar antibody arrays for serum protein profiling.
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Borrebaeck CAK, Sturfelt G, Wingren C. Recombinant antibody microarray for profiling the serum proteome of SLE. Methods Mol Biol 2014; 1134:67-78. [PMID: 24497355 DOI: 10.1007/978-1-4939-0326-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Systemic lupus erythematosus (SLE) is a severe autoimmune connective tissue disease. Our current knowledge about the serum proteome, or serum biomarker panels, reflecting disease and disease status is still very limited. Affinity proteomics, represented by recombinant antibody arrays, is a novel, multiplex technology for high-throughput protein expression profiling of crude serum proteomes in a highly specific, sensitive, and miniaturized manner. The antibodies are deposited one by one in an ordered pattern, an array, onto a solid support. Next, the sample is added, and any specifically bound proteins are detected and quantified. The binding pattern is then converted into a relative protein expression map, or protein map, deciphering the composition of the sample at the molecular level. The methodology provides unique opportunities for delineating serum biomarkers reflecting SLE, thus paving the way for improved diagnosis, classification, and prognosis.
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Affiliation(s)
- Carl A K Borrebaeck
- Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
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23
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Cancer proteomics. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Sandström A, Andersson R, Segersvärd R, Löhr M, Borrebaeck CAK, Wingren C. Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures. Proteomics Clin Appl 2013; 6:486-96. [PMID: 22930578 DOI: 10.1002/prca.201200051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Pancreatitis is an inflammatory state of the pancreas, for which high-performing serological biomarkers are lacking. The aim of the present study was to evaluate the use of affinity proteomics for identifying potential markers of disease and stratifying pancreatitis subtypes. EXPERIMENTAL DESIGN High-content, recombinant antibody microarrays were applied for serum protein expression profiling of 113 serum samples from patients with chronic, acute, and autoimmune pancreatitis, as well as healthy controls. The sample groups were compared using supervised classification based on support vector machine analysis. RESULTS This discovery study showed that pancreatitis subtypes could be discriminated with high accuracy. Using unfiltered data, the individual subtypes, as well as the combined pancreatitis cohort, were distinguished from healthy controls with high AUC values (0.96-1.00). Moreover, characteristic protein patterns and AUC values in the range of 0.69-0.95 were observed for the individual pancreatitis entities when compared to each other, and to all other samples combined. CONCLUSIONS AND CLINICAL RELEVANCE This study demonstrated the potential of the antibody microarray approach for stratification of pancreatitis. Distinct candidate multiplex serum biomarker signatures for chronic, acute, and autoimmune pancreatitis were defined, which could enhance our fundamental knowledge of the underlying molecular mechanisms, and potentially lead to improved diagnosis.
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Affiliation(s)
- Anna Sandström
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
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25
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Functional protein microarray: an ideal platform for investigating protein binding property. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11515-012-1236-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Bosco A, Bano F, Parisse P, Casalis L, DeSimone A, Micheletti C. Hybridization in nanostructured DNA monolayers probed by AFM: theory versus experiment. NANOSCALE 2012; 4:1734-41. [PMID: 22301788 DOI: 10.1039/c2nr11662f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nanografted monolayers (NAMs) of DNA show novel physico-chemical properties that make them ideally suited for advanced biosensing applications. In comparison with alternative solid-phase techniques for diagnostic DNA detection, NAMs have the advantage of combining a small size with a high homogeneity of the DNA surface coverage. These two properties favour the extreme miniaturization and ultrasensitivity in high-throughput biosensing devices. The systematic use of NAMs for quantitative DNA (and protein) detection has so far suffered from the lack of a control on key fabrication parameters, such as the ss- or ds-DNA surface coverage. Here we report on a combined experimental-computational study that allows us to estimate the surface density of the grafted DNA by analyzing the sample mechanical response, that is the DNA patch height vs. applied tip load curves. It is shown that the same analysis scheme can be used to detect the occurrence of hybridization with complementary strands in solution and estimate its efficiency. Thanks to these quantitative relationships it is possible to use a single AFM-based setup to: (i) fabricate a DNA NAM, (ii) control the DNA surface coverage, and (iii) characterize its level of hybridization helping the design of NAMs with pre-determined fabrication parameters.
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Affiliation(s)
- Alessandro Bosco
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136, Trieste, Italy
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Rodenburg W, Reimerink JH, Imholz S, Godeke GJ, Pennings JLA, Schielen PCJI, Koster MPH, de Vries A. Quantitative performance of antibody array technology in a prenatal screening setting. Clin Chem Lab Med 2011; 50:325-32. [PMID: 22035138 DOI: 10.1515/cclm.2011.767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/03/2011] [Indexed: 11/15/2022]
Abstract
BACKGROUND Antibody microarrays (Ab-array) represent a new, innovative proteomics platform for high-throughput protein expression profiling in body fluids. Because they allow for multiplexed measurements in small sample volumes, Ab-arrays are an interesting alternative to conventional indirect sandwich immunoassay (ELISA or DELFIA) tests in clinical or population screening if sets of markers are to be analyzed simultaneously. However, to allow implementation of Ab-arrays in clinical or population screening programs, it is of vital importance to establish that this method is both sensitive and quantitative. METHODS This study developed and optimized a duplex Ab-array for pregnancy-associated plasma protein A (PAPP-A) and human chorion gonadotropin (fβ-hCG), two serum biomarkers currently analyzed by conventional biochemical techniques in prenatal screening. Serum samples from pregnant women, representing the dynamic range of both markers, were analyzed on Ab-arrays, and validated to the, in prenatal screening routinely applied, AutoDelfia system. RESULTS Two different array hybridization conditions were tested, i.e., direct and indirect labeling, of which the indirect method displayed a sensitive and quantitative performance and a low intra- and inter-assay variation. CONCLUSIONS Taken together, these findings indicate that Ab-array technology is a promising alternative for ELISA or DELFIA in population screening programs, allowing future quantitative analysis of multiple biomarkers simultaneously in small volumes of serum.
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Affiliation(s)
- Wendy Rodenburg
- Laboratory for Health Protection Research, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
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Holm A, Wu W, Lund-Johansen F. Antibody array analysis of labelled proteomes: how should we control specificity? N Biotechnol 2011; 29:578-85. [PMID: 21840428 DOI: 10.1016/j.nbt.2011.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/15/2022]
Abstract
Researchers who use protein binders in multiplexed assays can be divided into two camps. One believes that arrays with proteome-wide coverage will become a reality once we have developed binders for all proteins. The sceptics claim that detection with immobilized protein binders and sample labelling will not provide the required specificity. In this article, we review the evidence showing that antibody array analysis of labelled samples can provide meaningful data and discuss the issues raised by the sceptics. We argue that direct the evidence for monospecificity has yet to be published. This will require assays designed to resolve the proteins captured by each binder. One option is to combine array measurement with protein separation. We have developed an assay where labelled sample proteins are separated by size exclusion chromatography (SEC) before contact with microsphere-based arrays (Size-MAP; size exclusion chromatography-resolved microsphere-based affinity proteomics). The effect is an 'antibody array Western blot' where reactivity of immobilized binders is resolved against the size of the proteins in the sample. We show that Size-MAP is useful to discriminate monospecific- and polyreactive antibodies and for automatic detection of reacting with the same target. The possibility to test specificity directly in array-based measurement should be useful to select the best binders and to determine whether the DNA microarray for the proteome is a realistic goal or not.
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Affiliation(s)
- Anders Holm
- Department of Immunology, Clinic of Specialized Medicine and Surgery Oslo University Hospital, Rikshospitalet, N-0027 Oslo, Norway
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Ray S, Reddy PJ, Jain R, Gollapalli K, Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 2011; 11:2139-61. [PMID: 21548090 DOI: 10.1002/pmic.201000460] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 02/28/2011] [Accepted: 03/07/2011] [Indexed: 01/22/2023]
Abstract
Serum is an ideal biological sample that contains an archive of information due to the presence of a variety of proteins released by diseased tissue, and serum proteomics has gained considerable interest for the disease biomarker discovery. Easy accessibility and rapid protein changes in response to disease pathogenesis makes serum an attractive sample for clinical research. Despite these advantages, the analysis of serum proteome is very challenging due to the wide dynamic range of proteins, difficulty in finding low-abundance target analytes due to the presence of high-abundance serum proteins, high levels of salts and other interfering compounds, variations among individuals and paucity of reproducibility. Sample preparation introduces pre-analytical variations and poses major challenges to analyze the serum proteome. The label-free detection techniques such as surface plasmon resonance, microcantilever, few nanotechniques and different resonators are rapidly emerging for the analysis of serum proteome and they have exhibited potential to overcome few limitations of the conventional techniques. In this article, we will discuss the current status of serum proteome analysis for the biomarker discovery and address key technological advancements, with a focus on challenges and amenable solutions.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Differential gene expression analysis of placentas with increased vascular resistance and pre-eclampsia using whole-genome microarrays. J Pregnancy 2011; 2011:472354. [PMID: 21490790 PMCID: PMC3066560 DOI: 10.1155/2011/472354] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/30/2010] [Accepted: 12/30/2010] [Indexed: 01/11/2023] Open
Abstract
Pre-eclampsia is a pregnancy complication characterized by hypertension and proteinuria. There are several factors associated with an increased risk of developing pre-eclampsia, one of which is increased uterine artery resistance, referred to as “notching”. However, some women do not progress into pre-eclampsia whereas others may have a higher risk of doing so. The placenta, central in pre-eclampsia pathology, may express genes associated with either protection or progression into pre-eclampsia. In order to search for genes associated with protection or progression, whole-genome profiling was performed. Placental tissue from 15 controls, 10 pre-eclamptic, 5 pre-eclampsia with notching, and 5 with notching only were analyzed using microarray and antibody microarrays to study some of the same gene product and functionally related ones. The microarray showed 148 genes to be significantly altered between the four groups. In the preeclamptic group compared to notch only, there was increased expression of genes related to chemotaxis and the NF-kappa B pathway and decreased expression of genes related to antigen processing and presentation, such as human leukocyte antigen B. Our results indicate that progression of pre-eclampsia from notching may involve the development of inflammation. Increased expression of antigen-presenting genes, as seen in the notch-only placenta, may prevent this inflammatory response and, thereby, protect the patient from developing pre-eclampsia.
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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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Carlsson A, Wuttge DM, Ingvarsson J, Bengtsson AA, Sturfelt G, Borrebaeck CAK, Wingren C. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol Cell Proteomics 2011; 10:M110.005033. [PMID: 21350050 PMCID: PMC3098590 DOI: 10.1074/mcp.m110.005033] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are two severe autoimmune connective tissue diseases. The fundamental knowledge about their etiology is limited and the conditions display complex pathogenesis, multifaceted presentations, and unpredictable courses. Despite significant efforts, the lack of fully validated biomarkers enabling diagnosis, classification, and monitoring of disease activity represents significant unmet clinical needs. In this discovery study, we have for the first time used recombinant antibody microarrays for miniaturized, multiplexed serum protein profiling of SLE and SSc, targeting mainly immunoregulatory proteins. The data showed that several candidate SLE-associated multiplexed serum biomarker signatures were delineated, reflecting disease (diagnosis), disease severity (phenotypic subsets), and disease activity. Selected differentially expressed markers were validated using orthogonal assays and a second, independent patient cohort. Further, biomarker signatures differentiating SLE versus SSc were demonstrated, and the observed differences increased with severity of SLE. In contrast, the data showed that the serum profiles of SSc versus healthy controls were more similar. Hence, we have shown that affinity proteomics could be used to de-convolute crude, nonfractionated serum proteomes, extracting molecular portraits of SLE and SSc, further enhancing our fundamental understanding of these complex autoimmune conditions.
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Affiliation(s)
- Anders Carlsson
- Department of Immunotechnology, BMC D13, Lund University, SE-221 84 Lund, Sweden
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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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Assessment and optimisation of normalisation methods for dual-colour antibody microarrays. BMC Bioinformatics 2010; 11:556. [PMID: 21073702 PMCID: PMC3098099 DOI: 10.1186/1471-2105-11-556] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 11/12/2010] [Indexed: 11/29/2022] Open
Abstract
Background Recent advances in antibody microarray technology have made it possible to measure the expression of hundreds of proteins simultaneously in a competitive dual-colour approach similar to dual-colour gene expression microarrays. Thus, the established normalisation methods for gene expression microarrays, e.g. loess regression, can in principle be applied to protein microarrays. However, the typical assumptions of such normalisation methods might be violated due to a bias in the selection of the proteins to be measured. Due to high costs and limited availability of high quality antibodies, the current arrays usually focus on a high proportion of regulated targets. Housekeeping features could be used to circumvent this problem, but they are typically underrepresented on protein arrays. Therefore, it might be beneficial to select invariant features among the features already represented on available arrays for normalisation by a dedicated selection algorithm. Results We compare the performance of several normalisation methods that have been established for dual-colour gene expression microarrays. The focus is on an invariant selection algorithm, for which effective improvements are proposed. In a simulation study the performances of the different normalisation methods are compared with respect to their impact on the ability to correctly detect differentially expressed features. Furthermore, we apply the different normalisation methods to a pancreatic cancer data set to assess the impact on the classification power. Conclusions The simulation study and the data application demonstrate the superior performance of the improved invariant selection algorithms in comparison to other normalisation methods, especially in situations where the assumptions of the usual global loess normalisation are violated.
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Tissue proteome profiling of preeclamptic placenta using recombinant antibody microarrays. Proteomics Clin Appl 2010; 4:794-807. [DOI: 10.1002/prca.201000001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 05/27/2010] [Accepted: 07/16/2010] [Indexed: 12/14/2022]
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µFBI: a microfluidic bead-based immunoassay for multiplexed detection of proteins from a µL sample volume. PLoS One 2010; 5. [PMID: 20957050 PMCID: PMC2948516 DOI: 10.1371/journal.pone.0013125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 08/23/2010] [Indexed: 12/13/2022] Open
Abstract
Background Over the last ten years, miniaturized multiplexed immunoassays have become robust, reliable research tools that enable researchers to simultaneously determine a multitude of parameters. Among the numerous analytical protein arrays available, bead-based assay systems have evolved into a key technology that enables the quantitative protein profiling of biological samples whilst requiring only a minimal amount of sample material. Methodology/Principal Findings A microfluidic bead-based immunoassay, µFBI, was developed to perform bead-based multiplexed sandwich immunoassays in a capillary. This setup allows the simultaneous detection of several parameters and only requires 200 ng of tissue lysate in a 1 µL assay volume. In addition, only 1 µL of detection antibodies and 1 µL of the reporter molecule Streptavidin-Phycoerythrin were required. The µFBI was used to compare the expression of seven receptor tyrosine kinases and their degree of tyrosine phosphorylation in breast cancer tissue and in normal tissue lysates. The total amount of HER-2, as well the degree of tyrosine phosphorylation was much higher in breast cancer tissue than in normal tissue. µFBI and a standard bead-based assay led to identical protein expression data. Moreover, it was possible to reduce the quantity of sample material required by a factor of 100 and the quantity of reagents by a factor of 30. Conclusions/Significance The µFBI, microfluidic bead-based immunoassay, allows the analysis of multiple parameters from a very small amount of sample material, such as tumor biopsies or tissue sections.
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Brennan DJ, O'Connor DP, Rexhepaj E, Ponten F, Gallagher WM. Antibody-based proteomics: fast-tracking molecular diagnostics in oncology. Nat Rev Cancer 2010; 10:605-17. [PMID: 20720569 DOI: 10.1038/nrc2902] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The effective implementation of personalized cancer therapeutic regimens depends on the successful identification and translation of informative biomarkers to aid clinical decision making. Antibody-based proteomics occupies a pivotal space in the cancer biomarker discovery and validation pipeline, facilitating the high-throughput evaluation of candidate markers. Although the clinical utility of these emerging technologies remains to be established, the traditional use of antibodies as affinity reagents in clinical diagnostic and predictive assays suggests that the rapid translation of such approaches is an achievable goal. Furthermore, in combination with, or as alternatives to, genomic and transcriptomic methods for patient stratification, antibody-based proteomics approaches offer the promise of additional insight into cancer disease states. In this Review, we discuss the current status of antibody-based proteomics and its contribution to the development of new assays that are crucial for the realization of individualized cancer therapy.
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Affiliation(s)
- Donal J Brennan
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Ray S, Mehta G, Srivastava S. Label-free detection techniques for protein microarrays: prospects, merits and challenges. Proteomics 2010; 10:731-48. [PMID: 19953541 PMCID: PMC7167936 DOI: 10.1002/pmic.200900458] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein microarrays, on which thousands of discrete proteins are printed, provide a valuable platform for functional analysis of the proteome. They have been widely used for biomarker discovery and to study protein–protein interactions. The accomplishments of DNA microarray technology, which had enabled massive parallel studies of gene expression, sparked great interest for the development of protein microarrays to achieve similar success at the protein level. Protein microarray detection techniques are often classified as being label‐based and label‐free. Most of the microarray applications have employed labelled detection such as fluorescent, chemiluminescent and radioactive labelling. These labelling strategies have synthetic challenges, multiple label issues and may exhibit interference with the binding site. Therefore, development of sensitive, reliable, high‐throughput, label‐free detection techniques are now attracting significant attention. Label‐free detection techniques monitor biomolecular interactions and simplify the bioassays by eliminating the need for secondary reactants. Moreover, they provide quantitative information for the binding kinetics. In this article, we will review several label‐free techniques, which offer promising applications for the protein microarrays, and discuss their prospects, merits and challenges.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Carlsson A, Persson O, Ingvarsson J, Widegren B, Salford L, Borrebaeck CAK, Wingren C. Plasma proteome profiling reveals biomarker patterns associated with prognosis and therapy selection in glioblastoma multiforme patients. Proteomics Clin Appl 2010; 4:591-602. [PMID: 21137077 DOI: 10.1002/prca.200900173] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 01/20/2010] [Accepted: 01/24/2010] [Indexed: 01/29/2023]
Affiliation(s)
- Anders Carlsson
- Department of Immunotechnology, Lund University, Lund, Sweden
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Lung cancer proteomics, clinical and technological considerations. J Proteomics 2010; 73:1851-63. [PMID: 20685322 DOI: 10.1016/j.jprot.2010.05.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 05/21/2010] [Accepted: 05/25/2010] [Indexed: 11/23/2022]
Abstract
The overall survival of lung cancer patients is disappointingly low. This is due to several factors, including the lack of an effective screening strategy to detect tumors at a potentially curable early stage, a marked resistance of lung cancer cells to drug treatment and a still superficial knowledge about the multifactorial cellular networks that are activated or suppressed during cancer progression. Furthermore, the armamentarium of clinicians and researchers in the field does not yet include reliable biomarkers to predict tumor response to treatment and foresee the natural history of the disease. In the present situation, a potential breakthrough is presented by proteomics technologies with the potential to discover relevant biomarkers which can be accurately quantified in multiplexed assays. Proteomics field can also contribute greatly in the understanding of mechanisms in tumor progression and treatment response. In this review we will describe the work that is being done in the field of lung cancer proteomics, focusing on clinically relevant questions that need to be addressed and on the possible applications of novel technologies.
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Matsuda KM, Chung JY, Hewitt SM. Histo-proteomic profiling of formalin-fixed, paraffin-embedded tissue. Expert Rev Proteomics 2010; 7:227-37. [PMID: 20377389 PMCID: PMC7556735 DOI: 10.1586/epr.09.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the functional proteome era, the proteomic profiling of clinicopathologic-annotated tissues is an essential step for mining and evaluating candidate biomarkers for disease. For many diseases, but especially cancer, the development of predictive biomarkers requires performing assays directly on the diseased tissue. The last decade has seen the explosion of both prognostic and predictive biomarkers in the research setting but few of these biomarkers have entered widespread clinical use. Previously, application of routine proteomic methodologies to clinical formalin-fixed and paraffin-embedded tissue specimens has provided unsatisfactory results. In this paper, we will discuss recent advancements in proteomic profiling technology for clinical applications. These approaches focus on the retention of histomorphologic information as an element of the proteomic analysis.
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Affiliation(s)
- Kant M Matsuda
- Tissue Array Research Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
| | - Joon-Yong Chung
- Applied Molecular Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
| | - Stephen M Hewitt
- Tissue Array Research Program and Applied Molecular Pathology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, MSC 4605 Advanced Technology Center, Bethesda, MD 20892-4605, USA
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Bajaj A, Miranda OR, Phillips R, Kim IB, Jerry DJ, Bunz UHF, Rotello VM. Array-based sensing of normal, cancerous, and metastatic cells using conjugated fluorescent polymers. J Am Chem Soc 2010; 132:1018-22. [PMID: 20039629 PMCID: PMC2810251 DOI: 10.1021/ja9061272] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A family of conjugated fluorescent polymers was used to create an array for cell sensing. Fluorescent conjugated polymers with pendant charged residues provided multivalent interactions with cell membranes, allowing the detection of subtle differences between different cell types on the basis of cell surface features. Highly reproducible characteristic patterns were obtained from different cell types as well as from isogenic cell lines, enabling the identification of the cell type as well differentiating between normal, cancerous, and metastatic isogenic cell types with high accuracy.
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Affiliation(s)
- Avinash Bajaj
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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Bajaj A, Rana S, Miranda OR, Yawe JC, Jerry DJ, Bunz UHF, Rotello VM. Cell surface-based differentiation of cell types and cancer states using a gold nanoparticle-GFP based sensing array. Chem Sci 2010. [DOI: 10.1039/c0sc00165a] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Avens HJ, Bowman CN. Development of fluorescent polymerization-based signal amplification for sensitive and non-enzymatic biodetection in antibody microarrays. Acta Biomater 2010; 6:83-9. [PMID: 19508906 DOI: 10.1016/j.actbio.2009.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/01/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Antibody microarrays are a critical tool for proteomics, requiring broad, highly sensitive detection of numerous low abundance biomarkers. Fluorescent polymerization-based amplification (FPBA) is presented as a novel, non-enzymatic signal amplification method that takes advantage of the chain-reaction nature of radical polymerization to achieve a highly amplified fluorescent response. A streptavidin-eosin conjugate localizes eosin photoinitiators for polymerization on the chip where biotinylated target protein is bound. The chip is contacted with acrylamide as a monomer, N-methyldiethanolamine as a coinitiator and yellow/green fluorescent nanoparticles (NPs) which, upon initiation, combine to form a macroscopically visible and highly fluorescent film. The rapid polymerization kinetics and the presence of cross-linker favor entrapment of the fluorescent NPs in the polymer, enabling highly sensitive fluorescent biodetection. This method is demonstrated as being appropriate for antibody microarrays and is compared to detection approaches which utilize streptavidin-fluorescein isothiocyanate (SA-FITC) and streptavidin-labeled yellow/green NPs (SA-NPs). It is found that FPBA is able to detect 0.16 + or - 0.01 biotin-antibody microm(-2) (or 40 zmol surface-bound target molecules), while SA-FITC has a limit of detection of 31 + or - 1 biotin-antibody microm(-2) and SA-NPs fail to achieve any significant signal under the conditions evaluated here. Further, FPBA in conjunction with fluorescent stereomicroscopy yields equal or better sensitivity compared to fluorescent detection of SA-eosin using a much more costly microarray scanner. By facilitating highly sensitive detection, FPBA is expected to enable detection of low abundance antigens and also make possible a transition towards less expensive fluorescence detection instrumentation.
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Yang D, Liu X, Jin Y, Zhu Y, Zeng D, Jiang X, Ma H. Electrospinning of Poly(dimethylsiloxane)/Poly(methyl methacrylate) Nanofibrous Membrane: Fabrication and Application in Protein Microarrays. Biomacromolecules 2009; 10:3335-40. [DOI: 10.1021/bm900955p] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dayong Yang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
| | - Xing Liu
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
| | - Yu Jin
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
| | - Ying Zhu
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
| | - Dongdong Zeng
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
| | - Xingyu Jiang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
| | - Hongwei Ma
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, China, and CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, China
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Multiplexed antibody arrays for the discovery and validation of glycosylated protein biomarkers. Bioanalysis 2009; 1:1431-44. [DOI: 10.4155/bio.09.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein glycosylation, the enzymatic linkage of mono- and poly-saccharides to proteins, is a critical determinant of protein function; however, there is a lack of tools for studying the glycosylation of specific proteins in complex samples. A new type of antibody–lectin sandwich assay enables the measurement of the glycosylation of specific proteins that have been captured from complex samples using antibody arrays combined with lectin-based detection probes. Antibody–lectin sandwich arrays have the potential to expand our understanding of the role of glycans and protein glycosylation in disease and to identify and investigate new biomarkers for early detection, disease prognosis and therapeutic response prediction. While antibody–lectin sandwich arrays yield less-detailed structural information regarding protein glycosylation than other available methods, they do provide a simple and reproducible method for investigating changes in protein abundance and glycosylation of multiple proteins and can be easily applied to large or small sample sets. By profiling protein and glycan variations, new disease-associated glycan alterations can be identified and validated for use as biomarkers.
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Detection and differentiation of normal, cancerous, and metastatic cells using nanoparticle-polymer sensor arrays. Proc Natl Acad Sci U S A 2009; 106:10912-6. [PMID: 19549846 DOI: 10.1073/pnas.0900975106] [Citation(s) in RCA: 226] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rapid and effective differentiation between normal and cancer cells is an important challenge for the diagnosis and treatment of tumors. Here, we describe an array-based system for identification of normal and cancer cells based on a "chemical nose/tongue" approach that exploits subtle changes in the physicochemical nature of different cell surfaces. Their differential interactions with functionalized nanoparticles are transduced through displacement of a multivalent polymer fluorophore that is quenched when bound to the particle and fluorescent after release. Using this sensing strategy we can rapidly (minutes/seconds) and effectively distinguish (i) different cell types; (ii) normal, cancerous and metastatic human breast cells; and (iii) isogenic normal, cancerous and metastatic murine epithelial cell lines.
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Wingren C, James P, Borrebaeck CAK. Strategy for surveying the proteome using affinity proteomics and mass spectrometry. Proteomics 2009; 9:1511-7. [PMID: 19235165 DOI: 10.1002/pmic.200800802] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Antibody-based microarrays is a rapidly evolving technology that has gone from the first proof-of-concept studies to more demanding proteome profiling applications, during the last years. Miniaturized microarrays can be printed with large number of antibodies harbouring predetermined specificities, capable of targeting high- as well as low-abundant analytes in complex, nonfractionated proteomes. Consequently, the resolution of such proteome profiling efforts correlate directly to the number of antibodies included, which today is a key limiting factor. To overcome this bottleneck and to be able to perform in-depth global proteome surveys, we propose to interface affinity proteomics with MS-based read-out, as outlined in this technical perspective. Briefly, we have defined a range of peptide motifs, each motif being present in 5-100 different proteins. In this manner, 100 antibodies, binding 100 different motifs commonly distributed among different proteins, would potentially target a protein cluster of 10(4) individual molecules, i.e. around 50% of the nonredundant human proteome. Notably, these motif-specific antibodies would be directly applicable to any proteome in a specie independent manner and not biased towards abundant proteins or certain protein classes. The biological sample is digested, exposed to these immobilized antibodies, whereby motif-containing peptides are specifically captured, enriched and subsequently detected and identified using MS.
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Design of high-density antibody microarrays for disease proteomics: key technological issues. J Proteomics 2009; 72:928-35. [PMID: 19457338 DOI: 10.1016/j.jprot.2009.01.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 01/26/2009] [Accepted: 01/27/2009] [Indexed: 01/01/2023]
Abstract
Antibody-based microarray is a novel proteomic technology setting a new standard for molecular profiling of non-fractionated complex proteomes. The first generation of antibody microarrays has already demonstrated its potential for generating detailed protein expression profiles, or protein atlases, of human body fluids in health and disease, paving the way for new discoveries within the field of disease proteomics. The process of designing highly miniaturized, high-density and high-performing antibody microarray set-ups have, however, proven to be challenging. In this mini-review we discuss key technological issues that must be addressed in a cross-disciplinary manner before true global proteome analysis can be performed using antibody microarrays.
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