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Brindl N, Boekhoff H, Bauer AS, Gaida MM, Dang HT, Kaiser J, Hoheisel JD, Felix K. Use of Autoreactive Antibodies in Blood of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasms (IPMN) for Grade Distinction and Detection of Malignancy. Cancers (Basel) 2022; 14:cancers14153562. [PMID: 35892825 PMCID: PMC9332220 DOI: 10.3390/cancers14153562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: A reliable non-invasive distinction between low- and high-risk pancreatic intraductal papillary mucinous neoplasms (IPMN) is needed to effectively detect IPMN with malignant potential. This would improve preventative care and reduce the risk of developing pancreatic cancer and overtreatment. The present study aimed at exploring the presence of autoreactive antibodies in the blood of patients with IPMN of various grades of dysplasia. (2) Methods: A single-center cohort was studied composed of 378 serum samples from patients with low-grade IPMN (n = 91), high-grade IPMN (n = 66), IPMN with associated invasive cancer (n = 30), pancreatic ductal adenocarcinoma (PDAC) stages T1 (n = 24) and T2 (n = 113), and healthy controls (n = 54). A 249 full-length recombinant human protein microarray was used for profiling the serum samples. (3) Results: 14 proteins were identified as potential biomarkers for grade distinction in IPMN, yielding high specificity but mediocre sensitivity. (4) Conclusions: The identified autoantibodies are potential biomarkers that may assist in the detection of malignancy in IPMN patients.
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Affiliation(s)
- Niall Brindl
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
- Correspondence: (N.B.); (K.F.); Tel.: +49-163-638-1860 (N.B.)
| | - Henning Boekhoff
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
| | - Andrea S. Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
| | - Matthias M. Gaida
- Institute of Pathology, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany;
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
- TRON, Translational Oncology at the University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Hien T. Dang
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19144, USA;
| | - Jörg Kaiser
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
| | - Jörg D. Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (H.B.); (A.S.B.); (J.D.H.)
| | - Klaus Felix
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Correspondence: (N.B.); (K.F.); Tel.: +49-163-638-1860 (N.B.)
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2
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Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale. Int J Mol Sci 2022; 23:ijms23073515. [PMID: 35408876 PMCID: PMC8999133 DOI: 10.3390/ijms23073515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
A novel resemblance-ranking peptide library with 160,000 10-meric peptides was designed to search for selective binders to antibodies. The resemblance-ranking principle enabled the selection of sequences that are most similar to the human peptidome. The library was synthesized with ultra-high-density peptide arrays. As proof of principle, screens for selective binders were performed for the therapeutic anti-CD20 antibody rituximab. Several features in the amino acid composition of antibody-binding peptides were identified. The selective affinity of rituximab increased with an increase in the number of hydrophobic amino acids in a peptide, mainly tryptophan and phenylalanine, while a total charge of the peptide remained relatively small. Peptides with a higher affinity exhibited a lower sum helix propensity. For the 30 strongest peptide binders, a substitutional analysis was performed to determine dissociation constants and the invariant amino acids for binding to rituximab. The strongest selective peptides had a dissociation constant in the hundreds of the nano-molar range. The substitutional analysis revealed a specific hydrophobic epitope for rituximab. To show that conformational binders can, in principle, be detected in array format, cyclic peptide substitutions that are similar to the target of rituximab were investigated. Since the specific binders selected via the resemblance-ranking peptide library were based on the hydrophobic interactions that are widespread in the world of biomolecules, the library can be used to screen for potential linear epitopes that may provide information about the cross-reactivity of antibodies.
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3
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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4
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Ghassem-Zadeh S, Hufnagel K, Bauer A, Frossard JL, Yoshida M, Kutsumi H, Acha-Orbea H, Neulinger-Muñoz M, Vey J, Eckert C, Strobel O, Hoheisel JD, Felix K. Novel Autoantibody Signatures in Sera of Patients with Pancreatic Cancer, Chronic Pancreatitis and Autoimmune Pancreatitis: A Protein Microarray Profiling Approach. Int J Mol Sci 2020; 21:E2403. [PMID: 32244327 PMCID: PMC7177860 DOI: 10.3390/ijms21072403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Identification of disease-associated autoantibodies is of high importance. Their assessment could complement current diagnostic modalities and assist the clinical management of patients. We aimed at developing and validating high-throughput protein microarrays able to screen patients' sera to determine disease-specific autoantibody-signatures for pancreatic cancer (PDAC), chronic pancreatitis (CP), autoimmune pancreatitis and their subtypes (AIP-1 and AIP-2). In-house manufactured microarrays were used for autoantibody-profiling of IgG-enriched preoperative sera from PDAC-, CP-, AIP-1-, AIP-2-, other gastrointestinal disease (GID) patients and healthy controls. As a top-down strategy, three different fluorescence detection-based protein-microarrays were used: large with 6400, intermediate with 345, and small with 36 full-length human recombinant proteins. Large-scale analysis revealed 89 PDAC, 98 CP and 104 AIP immunogenic antigens. Narrowing the selection to 29 autoantigens using pooled sera first and individual sera afterwards allowed a discrimination of CP and AIP from PDAC. For validation, predictive models based on the identified antigens were generated which enabled discrimination between PDAC and AIP-1 or AIP-2 yielded high AUC values of 0.940 and 0.925, respectively. A new repertoire of autoantigens was identified and their assembly as a multiplex test will provide a fast and cost-effective tool for differential diagnosis of pancreatic diseases with high clinical relevance.
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Affiliation(s)
- Sahar Ghassem-Zadeh
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
- Department of Biochemistry, University of Lausanne, 1066 Epalinges-Lausanne, Switzerland;
| | - Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
| | - Andrea Bauer
- Department of Functional Genomics, DKFZ, 69120 Heidelberg, Germany; (A.B.); (J.D.H.)
| | - Jean-Louis Frossard
- Department of Medical Specialties, Division of Gastroenterology, University Hospital of Geneva, 1205 Geneva, Switzerland;
| | - Masaru Yoshida
- Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Hiromu Kutsumi
- Center for Clinical Research and Advanced Medicine Shiga University of Medical Science Seta Tsukinowa-cho, Otsu 520-2192, Japan;
| | - Hans Acha-Orbea
- Department of Biochemistry, University of Lausanne, 1066 Epalinges-Lausanne, Switzerland;
| | - Matthias Neulinger-Muñoz
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
| | - Johannes Vey
- Institute of Medical Biometry and Informatics, University Medical Center Ruprecht-Karls University Heidelberg, 69120 Heidelberg, Germany;
| | - Christoph Eckert
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
| | - Jörg D. Hoheisel
- Department of Functional Genomics, DKFZ, 69120 Heidelberg, Germany; (A.B.); (J.D.H.)
| | - Klaus Felix
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, 69120 Heidelberg, Germany; (S.G.-Z.); (M.N.-M.); (O.S.)
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5
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Chlamydia trachomatis Whole-Proteome Microarray Analysis of The Netherlands Chlamydia Cohort Study. Microorganisms 2019; 7:microorganisms7120703. [PMID: 31888186 PMCID: PMC6956083 DOI: 10.3390/microorganisms7120703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022] Open
Abstract
Chlamydia trachomatis (Ct) whole-proteome microarrays were utilized to identify antibody patterns associated with infection; pelvic inflammatory disease (PID), tubal factor infertility, chronic pelvic pain (CPP) and ectopic pregnancy in a subsample of the Netherlands Chlamydia cohort study. Serum pools were analyzed on whole-proteome arrays. The 121 most reactive antigens identified during whole-proteome arrays were selected for further analysis with minimized microarrays that allowed for single sera analysis. From the 232 single sera; 145 (62.5%) serum samples were reactive for at least one antigen. To discriminate between positive and negative serum samples; we created a panel of in total 18 antigens which identified 96% of all microarray positive samples. Antigens CT_858; CT_813 and CT_142 were most reactive. Comparison of antibody reactivity's among women with and without Ct related sequelae revealed that the reactivity of CT_813 and CT_142 was less common among women with PID compared to women without (29.0% versus 58.6%, p = 0.005 and 25.8% versus 50.6%, p = 0.017 respectively). CT_858 was less common among CPP cases compared to controls (33.3% versus 58.6; p = 0.028). Using a whole-proteome array to select antigens for minimized arrays allows for the identification of novel informative antigens as general infection markers or disease associated antigens.
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6
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Hufnagel K, Reininger D, Ng SW, Gassert N, Rohland JK, Shahryarhesami S, Bauer AS, Waterboer T, Hoheisel JD. In situ, Cell-free Protein Expression on Microarrays and Their Use for the Detection of Immune Responses. Bio Protoc 2019; 9:e3152. [PMID: 33654961 DOI: 10.21769/bioprotoc.3152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 11/02/2022] Open
Abstract
Until recently, whole-proteome microarrays for comprehensive studies of protein interactions were mostly produced by individual cloning and cellular expression of very many open reading frames, followed by protein isolation and purification as well as array production. To overcome this cumbersome process, we have developed a method to generate microarrays representing entire proteomes by a combination of multiple spotting and on-chip, cell-free protein expression. Here, we describe the protocol for the production of bacterial protein microarrays. With slight adaptations, however, the procedure can be applied to the proteome of any organism. Expression constructs of each gene are generated by PCR on bacterial genomic DNA followed by a common secondary amplification that is adding relevant regulative elements to either end of the constructs. The unpurified PCR-products are spotted onto the microarray surface. Full-length proteins are directly expressed in situ in a cell-free manner and stay attached to the surface without further action. As an example of a typical application, we describe here the proteome-wide analysis of the immune response to a bacterial infectious agent by characterizing the binding profiles of the antibodies in patient sera.
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Affiliation(s)
- Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Dennis Reininger
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siu Wang Ng
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadine Gassert
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane K Rohland
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Soroosh Shahryarhesami
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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7
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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8
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Brambilla D, Chiari M, Gori A, Cretich M. Towards precision medicine: the role and potential of protein and peptide microarrays. Analyst 2019; 144:5353-5367. [DOI: 10.1039/c9an01142k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.
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Affiliation(s)
- Dario Brambilla
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
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9
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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10
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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11
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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12
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Hufnagel K, Lueong S, Willhauck-Fleckenstein M, Hotz-Wagenblatt A, Miao B, Bauer A, Michel A, Butt J, Pawlita M, Hoheisel JD, Waterboer T. Immunoprofiling of Chlamydia trachomatis using whole-proteome microarrays generated by on-chip in situ expression. Sci Rep 2018; 8:7503. [PMID: 29760479 PMCID: PMC5951824 DOI: 10.1038/s41598-018-25918-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 04/25/2018] [Indexed: 11/09/2022] Open
Abstract
Using Chlamydia trachomatis (Ct) as a complex model organism, we describe a method to generate bacterial whole-proteome microarrays using cell-free, on-chip protein expression. Expression constructs were generated by two successive PCRs directly from bacterial genomic DNA. Bacterial proteins expressed on microarrays display antigenic epitopes, thereby providing an efficient method for immunoprofiling of patients and allowing de novo identification of disease-related serum antibodies. Through comparison of antibody reactivity patterns, we newly identified antigens recognized by known Ct-seropositive samples, and antigens reacting only with samples from cervical cancer (CxCa) patients. Large-scale validation experiments using high-throughput suspension bead array serology confirmed their significance as markers for either general Ct infection or CxCa, supporting an association of Ct infection with CxCa. In conclusion, we introduce a method for generation of fast and efficient proteome immunoassays which can be easily adapted for other microorganisms in all areas of infection research.
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Affiliation(s)
- Katrin Hufnagel
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
| | - Smiths Lueong
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Willhauck-Fleckenstein
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beiping Miao
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Bauer
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Michel
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Butt
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis (B070), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections (F020), German Cancer Research Center (DKFZ), Heidelberg, Germany
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13
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Jara-Acevedo R, Díez P, González-González M, Dégano RM, Ibarrola N, Góngora R, Orfao A, Fuentes M. Screening Phage-Display Antibody Libraries Using Protein Arrays. Methods Mol Biol 2018; 1701:365-380. [PMID: 29116516 DOI: 10.1007/978-1-4939-7447-4_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phage-display technology constitutes a powerful tool for the generation of specific antibodies against a predefined antigen. The main advantages of phage-display technology in comparison to conventional hybridoma-based techniques are: (1) rapid generation time and (2) antibody selection against an unlimited number of molecules (biological or not). However, the main bottleneck with phage-display technology is the validation strategies employed to confirm the greatest number of antibody fragments. The development of new high-throughput (HT) techniques has helped overcome this great limitation. Here, we describe a new method based on an array technology that allows the deposition of hundreds to thousands of phages by micro-contact on a unique nitrocellulose surface. This setup comes in combination with bioinformatic approaches that enables simultaneous affinity screening in a HT format of antibody-displaying phages.
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Affiliation(s)
- Ricardo Jara-Acevedo
- ImmunoStep SL. Edificio Centro de Investigación del Cáncer. Avda. Coimbra s/n, 37007, Salamanca, Spain
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Rosa María Dégano
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Center (CSIC/USAL/IBSAL), Francisco Vitoria 6-16, 37007, Salamanca, Spain.
- Proteomics Unit, Cancer Research Center (CSIC/USAL/IBSAL), 37007, Salamanca, Spain.
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14
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Abstract
INTRODUCTION Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management. Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods that have been studied in the last five years. We also discuss the applications of each microarray method. Expert commentary: Given the growing roles and impact of cell-free protein microarrays in research and medicine, we discuss: 1) the current technical and practical limitations of cell-free protein microarrays; 2) the biomarker discovery and verification pipeline using protein microarrays; and 3) how cell-free protein microarrays will advance over the next five years, both in their technology and applications.
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Affiliation(s)
- Xiaobo Yu
- a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing Institute of Lifeomics , Beijing , China
| | - Brianne Petritis
- b The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Hu Duan
- a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing Institute of Lifeomics , Beijing , China
| | - Danke Xu
- c State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , China
| | - Joshua LaBaer
- b The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
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15
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Adeola HA, Van Wyk JC, Arowolo A, Ngwanya RM, Mkentane K, Khumalo NP. Emerging Diagnostic and Therapeutic Potentials of Human Hair Proteomics. Proteomics Clin Appl 2017; 12. [PMID: 28960873 DOI: 10.1002/prca.201700048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Indexed: 01/22/2023]
Abstract
The use of noninvasive human substrates to interrogate pathophysiological conditions has become essential in the post- Human Genome Project era. Due to its high turnover rate, and its long term capability to incorporate exogenous and endogenous substances from the circulation, hair testing is emerging as a key player in monitoring long term drug compliance, chronic alcohol abuse, forensic toxicology, and biomarker discovery, among other things. Novel high-throughput 'omics based approaches like proteomics have been underutilized globally in comprehending human hair morphology and its evolving use as a diagnostic testing substrate in the era of precision medicine. There is paucity of scientific evidence that evaluates the difference in drug incorporation into hair based on lipid content, and very few studies have addressed hair growth rates, hair forms, and the biological consequences of hair grooming or bleaching. It is apparent that protein-based identification using the human hair proteome would play a major role in understanding these parameters akin to DNA single nucleotide polymorphism profiling, up to single amino acid polymorphism resolution. Hence, this work seeks to identify and discuss the progress made thus far in the field of molecular hair testing using proteomic approaches, and identify ways in which proteomics would improve the field of hair research, considering that the human hair is mostly composed of proteins. Gaps in hair proteomics research are identified and the potential of hair proteomics in establishing a historic medical repository of normal and disease-specific proteome is also discussed.
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Affiliation(s)
- Henry A Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Jennifer C Van Wyk
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Afolake Arowolo
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Reginald M Ngwanya
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Khwezikazi Mkentane
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Nonhlanhla P Khumalo
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
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16
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Personalised proteome analysis by means of protein microarrays made from individual patient samples. Sci Rep 2017; 7:39756. [PMID: 28045055 PMCID: PMC5206632 DOI: 10.1038/srep39756] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/28/2016] [Indexed: 11/21/2022] Open
Abstract
DNA sequencing has advanced to a state that permits studying the genomes of individual patients as nearly a matter of routine. Towards analysing a tissue’s protein content in a similar manner, we established a method for the production of microarrays that represent full-length proteins as they are encoded in individual specimens, exhibiting the particular variations, such as mutations or splice variations, present in these samples. From total RNA isolates, each transcript is copied to a specific location on the array by an on-chip polymerase elongation reaction, followed by in situ cell-free transcription and translation. These microarrays permit parallel analyses of variations in protein structure and interaction that are specific to particular samples.
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17
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Lee KH, Kwon JH, Kim DM. Direct translational analysis of electrophoretically separated DNA using a cell-free protein synthesis system. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2016.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Abstract
Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.
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19
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Schinn SM, Broadbent A, Bradley WT, Bundy BC. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA. N Biotechnol 2016; 33:480-7. [PMID: 27085957 DOI: 10.1016/j.nbt.2016.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022]
Abstract
A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - William T Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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20
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Kibat J, Schirrmann T, Knape MJ, Helmsing S, Meier D, Hust M, Schröder C, Bertinetti D, Winter G, Pardes K, Funk M, Vala A, Giese N, Herberg FW, Dübel S, Hoheisel JD. Utilisation of antibody microarrays for the selection of specific and informative antibodies from recombinant library binders of unknown quality. N Biotechnol 2015; 33:574-81. [PMID: 26709003 DOI: 10.1016/j.nbt.2015.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 12/22/2022]
Abstract
Many diagnostic and therapeutic concepts require antibodies of high specificity. Recombinant binder libraries and related selection approaches allow the efficient isolation of antibodies against almost every target of interest. Nevertheless, it cannot be guaranteed that selected antibodies perform well and interact specifically enough with analytes unless an elaborate characterisation is performed. Here, we present an approach to shorten this process by combining the selection of suitable antibodies with the identification of informative target molecules by means of antibody microarrays, thereby reducing the effort of antibody characterisation by concentrating on relevant molecules. In a pilot scheme, a library of 456 single-chain variable fragment (scFv) binders to 134 antigens was used. They were arranged in a microarray format and incubated with the protein content of clinical tissue samples isolated from pancreatic ductal adenocarcinoma and healthy pancreas, as well as recurrent and non-recurrent bladder tumours. We observed significant variation in the expression of the E3 ubiquitin-protein ligase (CHFR) as well as the glutamate receptor interacting protein 2 (GRIP2), for example, always with more than one of the scFvs binding to these targets. Only the relevant antibodies were then characterised further on antigen microarrays and by surface plasmon resonance experiments so as to select the most specific and highest affinity antibodies. These binders were in turn used to confirm a microarray result by immunohistochemistry analysis.
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Affiliation(s)
- Janek Kibat
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ) , Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Department of Pharmacy, Pharmaceutical Technology & Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Thomas Schirrmann
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; YUMAB GmbH, Rebenring 33, 38106 Braunschweig, Germany
| | - Matthias J Knape
- Department of Biochemistry, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Saskia Helmsing
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Doris Meier
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Christoph Schröder
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ) , Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Sciomics GmbH, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany
| | - Daniela Bertinetti
- Department of Biochemistry, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Gerhard Winter
- Department of Pharmacy, Pharmaceutical Technology & Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Khalid Pardes
- The Novo Nordisk Foundation Centre for Protein Research, Protein Structure and Function Program, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mia Funk
- The Novo Nordisk Foundation Centre for Protein Research, Protein Structure and Function Program, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Andrea Vala
- The Novo Nordisk Foundation Centre for Protein Research, Protein Structure and Function Program, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nathalia Giese
- Department of Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Stefan Dübel
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ) , Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
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21
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Catherine C, Lee SW, Ju JW, Kim HC, Shin HI, Kim YJ, Kim DM. Cell-Free Expression and In Situ Immobilization of Parasite Proteins from Clonorchis sinensis for Rapid Identification of Antigenic Candidates. PLoS One 2015; 10:e0143597. [PMID: 26599101 PMCID: PMC4657965 DOI: 10.1371/journal.pone.0143597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 11/06/2015] [Indexed: 01/05/2023] Open
Abstract
Progress towards genetic sequencing of human parasites has provided the groundwork for a post-genomic approach to develop novel antigens for the diagnosis and treatment of parasite infections. To fully utilize the genomic data, however, high-throughput methodologies are required for functional analysis of the proteins encoded in the genomic sequences. In this study, we investigated cell-free expression and in situ immobilization of parasite proteins as a novel platform for the discovery of antigenic proteins. PCR-amplified parasite DNA was immobilized on microbeads that were also functionalized to capture synthesized proteins. When the microbeads were incubated in a reaction mixture for cell-free synthesis, proteins expressed from the microbead-immobilized DNA were instantly immobilized on the same microbeads, providing a physical linkage between the genetic information and encoded proteins. This approach of in situ expression and isolation enables streamlined recovery and analysis of cell-free synthesized proteins and also allows facile identification of the genes coding antigenic proteins through direct PCR of the microbead-bound DNA.
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Affiliation(s)
- Christy Catherine
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305–764, Korea
| | - Seung-Won Lee
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305–764, Korea
| | - Jung Won Ju
- Division of Malaria and Parasitic Diseases, National Institute of Health, Osong 361–951, Korea
| | - Ho-Cheol Kim
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305–764, Korea
| | - Hyun-Il Shin
- Division of Malaria and Parasitic Diseases, National Institute of Health, Osong 361–951, Korea
| | - Yu Jung Kim
- Division of Malaria and Parasitic Diseases, National Institute of Health, Osong 361–951, Korea
| | - Dong-Myung Kim
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305–764, Korea
- * E-mail:
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22
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Díez P, González-González M, Lourido L, Dégano RM, Ibarrola N, Casado-Vela J, LaBaer J, Fuentes M. NAPPA as a Real New Method for Protein Microarray Generation. MICROARRAYS 2015; 4:214-27. [PMID: 27600221 PMCID: PMC4996395 DOI: 10.3390/microarrays4020214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 03/30/2015] [Accepted: 04/14/2015] [Indexed: 11/16/2022]
Abstract
Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover, compared to conventional protein microarrays, NAPPA technology avoids the necessity of protein purification, which is expensive and time-consuming, by substituting expression in situ with an in vitro transcription/translation kit. In summary, NAPPA arrays have been broadly employed in different studies improving knowledge about diseases and responses to treatments. Here, we review the principal advances and applications performed using this platform during the last years.
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - Lucía Lourido
- Rheumatology Division, ProteoRed/ISCIII Proteomics Group, INIBIC, Hospital Universitario de A Coruña, A Coruña 15006, Spain.
| | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - Juan Casado-Vela
- Biotechnology National Centre, Spanish National Research Council (CSIC), Madrid 28049, Spain.
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA.
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
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Romanov V, Davidoff SN, Miles AR, Grainger DW, Gale BK, Brooks BD. A critical comparison of protein microarray fabrication technologies. Analyst 2015; 139:1303-26. [PMID: 24479125 DOI: 10.1039/c3an01577g] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
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Affiliation(s)
- Valentin Romanov
- Wasatch Microfluidics, LLC, 825 N. 300 W., Suite C325, Salt Lake City, UT, USA.
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24
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Wiktor P, Brunner A, Kahn P, Qiu J, Magee M, Bian X, Karthikeyan K, LaBaer J. Microreactor array device. Sci Rep 2015; 5:8736. [PMID: 25736721 PMCID: PMC4348619 DOI: 10.1038/srep08736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/28/2015] [Indexed: 11/22/2022] Open
Abstract
We report a device to fill an array of small chemical reaction chambers (microreactors) with reagent and then seal them using pressurized viscous liquid acting through a flexible membrane. The device enables multiple, independent chemical reactions involving free floating intermediate molecules without interference from neighboring reactions or external environments. The device is validated by protein expressed in situ directly from DNA in a microarray of ~10,000 spots with no diffusion during three hours incubation. Using the device to probe for an autoantibody cancer biomarker in blood serum sample gave five times higher signal to background ratio compared to standard protein microarray expressed on a flat microscope slide. Physical design principles to effectively fill the array of microreactors with reagent and experimental results of alternate methods for sealing the microreactors are presented.
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Affiliation(s)
- Peter Wiktor
- 1] Engineering Arts LLC, Tempe, Arizona, U.S.A [2] The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Al Brunner
- Engineering Arts LLC, Tempe, Arizona, U.S.A
| | - Peter Kahn
- Engineering Arts LLC, Tempe, Arizona, U.S.A
| | - Ji Qiu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Mitch Magee
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Xiaofang Bian
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Kailash Karthikeyan
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
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25
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Betzen C, Alhamdani MSS, Lueong S, Schröder C, Stang A, Hoheisel JD. Clinical proteomics: promises, challenges and limitations of affinity arrays. Proteomics Clin Appl 2015; 9:342-7. [PMID: 25594918 PMCID: PMC5024047 DOI: 10.1002/prca.201400156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/16/2014] [Accepted: 01/13/2015] [Indexed: 12/14/2022]
Abstract
After the establishment of DNA/RNA sequencing as a means of clinical diagnosis, the analysis of the proteome is next in line. As a matter of fact, proteome‐based diagnostics is bound to be even more informative, since proteins are directly involved in the actual cellular processes that are responsible for disease. However, the structural variation and the biochemical differences between proteins, the much wider range in concentration and their spatial distribution as well as the fact that protein activity frequently relies on interaction increase the methodological complexity enormously, particularly if an accuracy and robustness is required that is sufficient for clinical utility. Here, we discuss the contribution that protein microarray formats could play towards proteome‐based diagnostics.
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Affiliation(s)
- Christian Betzen
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany; Department of Pediatric Medicine I, University Children's Hospital Heidelberg, Heidelberg, Germany
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26
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Ding YD, Chang JW, Guo J, Chen D, Li S, Xu Q, Deng XX, Cheng YJ, Chen LL. Prediction and functional analysis of the sweet orange protein-protein interaction network. BMC PLANT BIOLOGY 2014; 14:213. [PMID: 25091279 PMCID: PMC4236729 DOI: 10.1186/s12870-014-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/24/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species. RESULTS In this analysis, we employed ortholog identification and domain combination methods to predict the protein-protein interaction (PPI) network for sweet orange. The K-nearest neighbors (KNN) classification method was used to verify and filter the network. The final predicted PPI network, CitrusNet, contained 8,195 proteins with 124,491 interactions. The quality of CitrusNet was evaluated using gene ontology (GO) and Mapman annotations, which confirmed the reliability of the network. In addition, we calculated the expression difference of interacting genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and also analyzed the EDI distribution and variation in different sub-networks. CONCLUSIONS Gene expression in CitrusNet has significant modular features. Target of rapamycin (TOR) protein served as the central node of the hormone-signaling sub-network. All evidence supported the idea that TOR can integrate various hormone signals and affect plant growth. CitrusNet provides valuable resources for the study of biological functions in sweet orange.
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Affiliation(s)
- Yu-Duan Ding
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Ji-Wei Chang
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Jing Guo
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - DiJun Chen
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Sen Li
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Yun-Jiang Cheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Ling-Ling Chen
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
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Kilb N, Burger J, Roth G. Protein microarray generation by in situ protein expression from template DNA. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Normann Kilb
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
| | - Jürgen Burger
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- Laboratory for MEMS Applications, Department of Microsystems Engineering—IMTEK University of Freiburg Freiburg Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- BIOSS—Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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Erben ED, Fadda A, Lueong S, Hoheisel JD, Clayton C. A genome-wide tethering screen reveals novel potential post-transcriptional regulators in Trypanosoma brucei. PLoS Pathog 2014; 10:e1004178. [PMID: 24945722 PMCID: PMC4055773 DOI: 10.1371/journal.ppat.1004178] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/28/2014] [Indexed: 12/23/2022] Open
Abstract
In trypanosomatids, gene expression is regulated mainly by post-transcriptional mechanisms, which affect mRNA processing, translation and degradation. Currently, our understanding of factors that regulate either mRNA stability or translation is rather limited. We know that often, the regulators are proteins that bind to the 3′-untranslated region; they presumably interact with ribonucleases and translation factors. However, very few such proteins have been characterized in any detail. Here we describe a genome-wide screen to find proteins implicated in post-transcriptional regulation in Trypanosoma brucei. We made a library of random genomic fragments in a plasmid that was designed for expression of proteins fused to an RNA-binding domain, the lambda-N peptide. This was transfected into cells expressing mRNAs encoding a positive or negative selectable marker, and bearing the “boxB” lambda-N recognition element in the 3′-untranslated region. The screen identified about 300 proteins that could be implicated in post-transcriptional mRNA regulation. These included known regulators, degradative enzymes and translation factors, many canonical RNA-binding proteins, and proteins that act via multi-protein complexes. However there were also nearly 150 potential regulators with no previously annotated function, or functions unrelated to mRNA metabolism. Almost 50 novel regulators were shown to bind RNA using a targeted proteome array. The screen also provided fine structure mapping of the hit candidates' functional domains. Our findings not only confirm the key role that RNA-binding proteins play in the regulation of gene expression in trypanosomatids, but also suggest new roles for previously uncharacterized proteins. Survival and adaptation of trypanosomatids to new surroundings requires activation of specific gene networks. This is mainly achieved by post-transcriptional mechanisms, and proteins that bind to specific mRNAs, and influence degradation or translation, are known to be important. However, only few such proteins have been characterized to date. The trypanosome genome encodes over 150 proteins with conserved RNA-binding domains, and it is very likely that additional proteins that do not have such domains could also modulate mRNA fate. Here, we report the results of a genome-wide screen to identify mRNA-fate regulators in Trypanosoma brucei. We used a method called “tethering” to artificially attach protein fragments to an mRNA. Our findings confirmed the role of RNA-binding proteins in the regulation of mRNA fate, and also suggested such roles for many other proteins, including some metabolic enzymes. Our results should serve as a useful resource. Moreover, the tethering screen approach could readily be adapted for use in other organisms.
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Affiliation(s)
- Esteban D. Erben
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Smiths Lueong
- Division of Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jörg D. Hoheisel
- Division of Functional Genome Analysis, Deutsche Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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Chepelev N, Chepelev L, Alamgir M, Golshani A. Large-Scale Protein-Protein Interaction Detection Approaches: Past, Present and Future. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Syafrizayanti, Betzen C, Hoheisel JD, Kastelic D. Methods for analyzing and quantifying protein–protein interaction. Expert Rev Proteomics 2014; 11:107-20. [DOI: 10.1586/14789450.2014.875857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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31
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Abstract
Protein microarrays are a miniaturized format for assaying functional protein interactions and proteomics using a high-throughput, multiplexed approach. The primary limitations of this technology include the time and cost involved in the production of highly purified individual proteins for arraying and also the limited stability of functional proteins once arrayed. In light of these difficulties, cell-free protein expression systems are being increasingly used to generate protein arrays in situ from coding DNA sequences. This chapter describes the method DNA array to protein array (DAPA) allowing the repeated "printing" of protein arrays directly from a DNA array template using cell-free protein expression. Once the DNA templates have been spotted, the generation of the protein array involves only simple handling procedures and is relatively time and cost-efficient, and protein arrays can easily be produced "on demand" as and when required. The resultant protein array may be used for any downstream applications as for conventionally spotted protein arrays.
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Affiliation(s)
- Elizabeth A Cook
- Protein Technology Group, Babraham Bioscience Technologies Ltd, Babraham Research Campus, Cambridge, UK
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Casado-Vela J, Fuentes M, Franco-Zorrilla JM. Screening of Protein–Protein and Protein–DNA Interactions Using Microarrays. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:231-81. [DOI: 10.1016/b978-0-12-800453-1.00008-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Lee KH, Kim DM. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments. Biotechnol J 2013; 8:1292-300. [DOI: 10.1002/biot.201200385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/16/2013] [Accepted: 09/12/2013] [Indexed: 11/08/2022]
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Festa F, Rollins SM, Vattem K, Hathaway M, Lorenz P, Mendoza EA, Yu X, Qiu J, Kilmer G, Jensen P, Webb B, Ryan ET, LaBaer J. Robust microarray production of freshly expressed proteins in a human milieu. Proteomics Clin Appl 2013; 7:372-7. [PMID: 23027544 DOI: 10.1002/prca.201200063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/07/2012] [Accepted: 08/14/2012] [Indexed: 12/14/2022]
Abstract
PURPOSE In vitro transcription/translation (IVTT) systems are widely used in proteomics. For clinical applications, mammalian systems are preferred for protein folding and activity; however, the level of protein obtained is low. A new system extracted from human cells (1-Step Human Coupled IVT (HCIVT)) has the potential to overcome this problem and deliver high yields of protein expressed in a human milieu. EXPERIMENTAL DESIGN Western blots and self-assembled protein microarrays were used to test the efficiency of protein synthesis by HCIVT compared to rabbit reticulocyte lysate (RRL). The arrays were also used to measure the immune response obtained from serum of patients exposed to pathogens or vaccine. RESULTS HCIVT performed better than RRL in all experiments. The yield of protein synthesized in HCIVT is more than ten times higher than RRL, in both Western blot and protein microarrays. Moreover, HCIVT showed a robust lot-to-lot reproducibility. In immune assays, the signals of many antigens were detected only in HCIVT-expressed arrays, mainly due to the reduction in the background signal and the increased levels of protein on the array. CONCLUSION AND CLINICAL RELEVANCE HCIVT is a robust in vitro transcription and translation system that yields high levels of protein produced in a human milieu. It can be used in applications where protein expression in a mammalian system and high yields are needed. The increased immunogenic response of HCIVT-expressed proteins will be critical for biomarker discovery in many diseases, including cancer.
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Affiliation(s)
- Fernanda Festa
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6401, USA
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Chandrasekhar S, Iyer LK, Panchal JP, Topp EM, Cannon JB, Ranade VV. Microarrays and microneedle arrays for delivery of peptides, proteins, vaccines and other applications. Expert Opin Drug Deliv 2013; 10:1155-70. [PMID: 23662940 DOI: 10.1517/17425247.2013.797405] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Peptide and protein microarray and microneedle array technology provides direct information on protein function and potential drug targets in drug discovery and delivery. Because of this unique ability, these arrays are well suited for protein profiling, drug target identification/validation and studies of protein interaction, biochemical activity, immune responses, clinical prognosis and diagnosis and for gene, protein and drug delivery. AREAS COVERED The aim of this review is to describe and summarize past and recent developments of microarrays in their construction, characterization and production and applications of microneedles in drug delivery. The scope and limitations of various technologies in this respect are discussed. EXPERT OPINION This article offers a review of microarray/microneedle technologies and possible future directions in targeting and in the delivery of pharmacologically active compounds for unmet needs in biopharmaceutical research. A better understanding of the production and use of microarrays and microneedles for delivery of peptides, proteins and vaccines is needed.
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Affiliation(s)
- Saradha Chandrasekhar
- Purdue University, Department of Industrial and Physical Pharmacy, West Lafayette, IN 47907, USA
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Abstract
Protein microarray technology is an emerging field that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. Protein microarrays are composed of two major classes: analytical and functional. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. Applications of protein microarrays, especially functional protein microarrays, have flourished over the past decade as the fabrication technology has matured. In this unit, advances in protein microarray technologies are reviewed, and then a series of examples are presented to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. Relevant areas of research include the detection of various binding properties of proteins, the study of protein post-translational modifications, the analysis of host-microbe interactions, profiling antibody specificity, and the identification of biomarkers in autoimmune diseases.
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Affiliation(s)
- F X Reymond Sutandy
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
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37
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Timm C, Niemeyer CM. On-Chip Protein Biosynthesis. Angew Chem Int Ed Engl 2013; 52:2652-4. [DOI: 10.1002/anie.201208880] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Indexed: 01/18/2023]
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38
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39
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Kim SH, Yoshizawa S, Takeuchi S, Fujii T, Fourmy D. Ultra-high density protein spots achieved by on chip digitalized protein synthesis. Analyst 2013; 138:4663-9. [DOI: 10.1039/c3an00976a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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40
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Sobieściak TD, Zielenkiewicz P. Non-specific clustering of histidine tagged green fluorescent protein mediated by surface interactions: the collective effect in the protein-adsorption behaviour. RSC Adv 2013. [DOI: 10.1039/c3ra42154f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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41
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Seefeld TH, Halpern AR, Corn RM. On-chip synthesis of protein microarrays from DNA microarrays via coupled in vitro transcription and translation for surface plasmon resonance imaging biosensor applications. J Am Chem Soc 2012; 134:12358-61. [PMID: 22793370 DOI: 10.1021/ja304187r] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein microarrays are fabricated from double-stranded DNA (dsDNA) microarrays by a one-step, multiplexed enzymatic synthesis in an on-chip microfluidic format and then employed for antibody biosensing measurements with surface plasmon resonance imaging (SPRI). A microarray of dsDNA elements (denoted as generator elements) that encode either a His-tagged green fluorescent protein (GFP) or a His-tagged luciferase protein is utilized to create multiple copies of mRNA (mRNA) in a surface RNA polymerase reaction; the mRNA transcripts are then translated into proteins by cell-free protein synthesis in a microfluidic format. The His-tagged proteins diffuse to adjacent Cu(II)-NTA microarray elements (denoted as detector elements) and are specifically adsorbed. The net result is the on-chip, cell-free synthesis of a protein microarray that can be used immediately for SPRI protein biosensing. The dual element format greatly reduces any interference from the nonspecific adsorption of enzyme or proteins. SPRI measurements for the detection of the antibodies anti-GFP and antiluciferase were used to verify the formation of the protein microarray. This convenient on-chip protein microarray fabrication method can be implemented for multiplexed SPRI biosensing measurements in both clinical and research applications.
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Affiliation(s)
- Ting H Seefeld
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, United States
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42
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Ahn JH, Kim JH, Reuel NF, Barone PW, Boghossian AA, Zhang J, Yoon H, Chang AC, Hilmer AJ, Strano MS. Label-free, single protein detection on a near-infrared fluorescent single-walled carbon nanotube/protein microarray fabricated by cell-free synthesis. NANO LETTERS 2011; 11:2743-52. [PMID: 21627102 DOI: 10.1021/nl201033d] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Excessive sample volumes continue to be a major limitation in the analysis of protein-protein interactions, motivating the search for label-free detection methods of greater sensitivity. Herein, we report the first chemical approach for selective protein recognition using fluorescent single-walled carbon nanotubes (SWNTs) enabling label-free microarrays capable of single protein detection. Hexahistidine-tagged capture proteins directly expressed by cell-free synthesis on SWNT/chitosan microarray are bound to a Ni(2+) chelated by Nα,Nα-bis(carboxymethyl)-L-lysine grafted to chitosan surrounding the SWNT. The Ni(2+) acts as a proximity quencher with the Ni(2+)/SWNT distance altered upon docking of analyte proteins. This ability to discern single protein binding events decreases the apparent detection limit from 100 nM, for the ensemble average, to 10 pM for an observation time of 600 s. This first use of cell-free synthesis to functionalize a nanosensor extends this method to a virtually infinite number of capture proteins. To demonstrate this, the SWNT microarrays are used to analyze a network of 1156 protein-protein interactions in the staurosporine-induced apoptosis of SH-SY5Y cells, confirming literature predictions.
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Affiliation(s)
- Jin-Ho Ahn
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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43
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Maerkl SJ. Next generation microfluidic platforms for high-throughput protein biochemistry. Curr Opin Biotechnol 2011; 22:59-65. [PMID: 20832278 DOI: 10.1016/j.copbio.2010.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 08/18/2010] [Accepted: 08/18/2010] [Indexed: 10/19/2022]
Abstract
DNA technologies such as cloning, DNA microarrays, and next generation sequencing have transformed the life sciences. Protein technologies on the other hand have not seen such explosive progress. This is mainly due to the inherent difficulty of working with proteins because of their manifold physical characteristics as opposed to the well behaved and well understood DNA polymer. Recent technological advancements have increased the throughput of protein biochemistry to levels where it is becoming of interest to systems biology. Here I review methods for high-throughput in situ synthesis and characterization of proteins and their integration with microfluidic devices. In the near future, the use of gene synthesis, microfluidic based protein synthesis and characterization will give rise to a resurgence of protein biochemistry in the current world of high-throughput genomics.
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Affiliation(s)
- Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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44
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Kimzey MJ, Zarate X, Galbraith DW, Lau SS. Optimizing microarray-based in situ transcription-translation of proteins for matrix-assisted laser desorption ionization mass spectrometry. Anal Biochem 2011; 414:282-6. [PMID: 21477576 DOI: 10.1016/j.ab.2011.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/18/2011] [Accepted: 03/24/2011] [Indexed: 11/18/2022]
Abstract
The analysis of self-assembled protein microarrays, using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, combines two high-throughput platforms for investigation of the proteome. In this article, we describe the fabrication in situ of protein arrays optimized for MALDI characterization. Using the green fluorescent protein (GFP) both as an epitope for immobilization and as a gauge for relative protein expression, we were able to generate amounts of protein on the array slides sufficient for MALDI identification. In addition, expression of N-terminal protein constructs fused to GFP demonstrated mass shifts consistent with that of the full-length protein. We envision this technology to be important for the functional screening of protein interactions.
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Affiliation(s)
- Michael J Kimzey
- Southwest Environmental Health Sciences Center, Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
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46
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Abstract
Protein arrays are miniaturised and highly parallelised formats of interaction-based functional protein assays. Major bottlenecks in protein microarraying are the limited availability and high cost of purified, functional proteins for immobilisation and the limited stability of immobilised proteins in their functional state. In contrast, protein-coding DNA is readily available by PCR, and DNA arrays can be stored over prolonged times without deterioration. This chapter presents a method for the rapid and economical "printing" of replicate protein microarrays directly from a single DNA array template using cell-free protein synthesis, termed "DNA array to protein array," DAPA. The procedure is a truly enabling technology, making customised protein microarrays affordable for laboratories with no access to routine microarray spotting. The experimental effort involved for the printing of a protein array from the template DNA array is comparable to the assembly of a Western blot.
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47
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Abstract
The development of protein microarrays makes possible interaction-based protein assays in miniaturised, multiplexed formats. A major requirement determining their uptake and use is the availability and stability of purified, functional proteins for immobilisation. With conventional methods, involving individual expression and purification of recombinant proteins, the cost of commercial high-content protein arrays is often found to be prohibitively high. Moreover, due to the need for specialised microarray production equipment, custom-made protein arrays containing more focussed sets of proteins of interest are also in little use. In the DNA array to protein array technology described herein, repeated economical printing of protein microarrays from a reusable template DNA microarray is performed on demand by cell-free -protein synthesis. Once the template DNA microarray has been obtained, protein microarrays are made using purely macro-handling procedures, making protein arraying accessible without sophisticated microarraying apparatus.
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Affiliation(s)
- Oda Stoevesandt
- Protein Technology Group, Babraham Bioscience Technologies Ltd, Cambridge, UK.
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48
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Berrade L, Garcia AE, Camarero JA. Protein microarrays: novel developments and applications. Pharm Res 2010; 28:1480-99. [PMID: 21116694 PMCID: PMC3137928 DOI: 10.1007/s11095-010-0325-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/08/2010] [Indexed: 02/05/2023]
Abstract
Protein microarray technology possesses some of the greatest potential for providing direct information on protein function and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical pathways and have been used for the analysis of simultaneous multiple biomolecular interactions involving protein-protein, protein-lipid, protein-DNA and protein-small molecule interactions. Because of this unique ability to analyze many kinds of molecular interactions en masse, the requirement of very small sample amount and the potential to be miniaturized and automated, protein microarrays are extremely well suited for protein profiling, drug discovery, drug target identification and clinical prognosis and diagnosis. The aim of this review is to summarize the most recent developments in the production, applications and analysis of protein microarrays.
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Affiliation(s)
- Luis Berrade
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, California 90033, USA
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49
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Jacak J, Hesch C, Hesse J, Schütz GJ. Identification of immobile single molecules using polarization-modulated asynchronous time delay and integration-mode scanning. Anal Chem 2010; 82:4288-92. [PMID: 20380382 DOI: 10.1021/ac100302s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report the development of a data acquisition method for identifying single molecules on large surfaces with simultaneous characterization of their absorption dipole. The method is based on a previously described device for microarray readout at single molecule sensitivity (Hesse, J.; Sonnleitner, M.; Sonnleitner, A.; Freudenthaler, G.; Jacak, J.; Höglinger, O.; Schindler, H.; Schütz, G. J. Anal. Chem. 2004, 76, 5960-5964). Here, we introduced asynchronous time delay and integration- (TDI-) mode imaging to record also the time course of fluorescence signals: the images thus contain both spatial and temporal information. We demonstrate the principle by modulating the signals via rotating excitation polarization, which allows for discriminating static absorption dipoles against multiple or freely rotating single absorption dipoles. Experiments on BSA carrying different numbers of fluorophores demonstrate the feasibility of the method. Protein species with an average labeling degree of 0.55 and 2.89 fluorophores per protein can be readily distinguished.
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Affiliation(s)
- Jaroslaw Jacak
- Biophysics Institute, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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50
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Helwa R, Hoheisel JD. Analysis of DNA–protein interactions: from nitrocellulose filter binding assays to microarray studies. Anal Bioanal Chem 2010; 398:2551-61. [DOI: 10.1007/s00216-010-4096-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 08/03/2010] [Indexed: 10/19/2022]
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