1
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Nagy K, McBride R, Head SR, Ordoukhanian P, Law M. Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes. Methods Mol Biol 2023; 2578:63-81. [PMID: 36152281 DOI: 10.1007/978-1-0716-2732-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding antibody specificity and defining response profiles to antigens continue to be essential to both vaccine research and therapeutic antibody development. Peptide scanning assays enable mapping of continuous epitopes in order to delineate antibody-antigen interactions beyond traditional immunoassay formats. We have developed a relatively low-cost method to generate peptide microarray slides for antibody binding studies that allow for interrogation of up to 1536 overlapping peptides derived from the target antigens on a single microslide. Using an IntavisAG MultiPep RS peptide synthesizer and a Digilab MicroGrid II 600 microarray printer robot, each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface. Interrogation of the surface can then be performed using polyclonal immune sera or monoclonal antibodies, and sensitive detection using an InnoScan 1100 AL scanner with fluorescent-conjugated secondary reagents maximizes conservation of reagents.
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Affiliation(s)
- Kenna Nagy
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan McBride
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven R Head
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Mansun Law
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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2
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Chen F, Nagy K, Chavez D, Willis S, McBride R, Giang E, Honda A, Bukh J, Ordoukhanian P, Zhu J, Frey S, Lanford R, Law M. Antibody Responses to Immunization With HCV Envelope Glycoproteins as a Baseline for B-Cell-Based Vaccine Development. Gastroenterology 2020; 158:1058-1071.e6. [PMID: 31809725 PMCID: PMC7371413 DOI: 10.1053/j.gastro.2019.11.282] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS We investigated antibody responses to hepatitis C virus (HCV) antigens E1 and E2 and the relevance of animal models for vaccine development. We compared antibody responses to vaccination with recombinant E1E2 complex in healthy volunteers, non-human primates (NHPs), and mice. METHODS We analyzed 519 serum samples from participants in a phase 1 vaccine trial (ClinicalTrials.gov identifier NCT00500747) and compared them with serum or plasma samples from C57BL/6J mice (n = 28) and rhesus macaques (n = 4) immunized with the same HCV E1E2 antigen. Blood samples were collected at different time points and analyzed for antibody binding, neutralizing activity, and epitope specificity. Monoclonal antibodies from the immunized NHPs were isolated from single plasmablasts and memory B cells, and their immunogenetic properties were characterized. RESULTS Antibody responses of the volunteers, NHPs, and mice to the non-neutralizing epitopes on the E1 N-terminus and E2 hypervariable region 1 did not differ significantly. Antibodies from volunteers and NHPs that neutralized heterologous strains of HCV primarily interacted with epitopes in the antigen region 3. However, the neutralizing antibodies were not produced in sufficient levels for broad neutralization of diverse HCV isolates. Broadly neutralizing antibodies similar to the human VH1-69 class antibody specific for antigen region 3 were produced in the immunized NHPs. CONCLUSIONS In an analysis of vaccinated volunteers, NHPs, and mice, we found that recombinant E1E2 vaccine antigen induces high-antibody titers that are insufficient to neutralize diverse HCV isolates. Antibodies from volunteers and NHPs bind to the same neutralizing epitopes for virus neutralization. NHPs can therefore be used as a preclinical model to develop HCV vaccines. These findings also provide useful baseline values for development of vaccines designed to induce production of neutralizing antibodies.
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Affiliation(s)
- Fang Chen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Kenna Nagy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Deborah Chavez
- Southwest National Primate Research Center at Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Shelby Willis
- NGS and Microarray Research Cores, The Scripps Research Institute, La Jolla, California, USA
| | - Ryan McBride
- NGS and Microarray Research Cores, The Scripps Research Institute, La Jolla, California, USA
| | - Erick Giang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew Honda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Phillip Ordoukhanian
- NGS and Microarray Research Cores, The Scripps Research Institute, La Jolla, California, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Sharon Frey
- Saint Louis University Center for Vaccine Development, St. Louis, Missouri, USA
| | - Robert Lanford
- Southwest National Primate Research Center at Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California.
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3
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Martinez Viedma MDP, Kose N, Parham L, Balmaseda A, Kuan G, Lorenzana I, Harris E, Crowe JE, Pickett BE. Peptide arrays of three collections of human sera from patients infected with mosquito-borne viruses. F1000Res 2019; 8:1875. [PMID: 32201571 PMCID: PMC7065662.2 DOI: 10.12688/f1000research.20981.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 03/29/2024] Open
Abstract
Background: Global outbreaks caused by emerging or re-emerging arthropod-borne viruses (arboviruses) are becoming increasingly more common. These pathogens include the mosquito-borne viruses belonging to the Flavivirus and Alphavirus genera. These viruses often cause non-specific or asymptomatic infection, which can confound viral prevalence studies. In addition, many acute phase diagnostic tests rely on the detection of viral components such as RNA or antigen. Standard serological tests are often not reliable for diagnosis after seroconversion and convalescence due to cross-reactivity among flaviviruses. Methods: In order to contribute to development efforts for mosquito-borne serodiagnostics, we incubated 137 human sera on individual custom peptide arrays that consisted of over 866 unique peptides in quadruplicate. Our bioinformatics workflow to analyze these data incorporated machine learning, statistics, and B-cell epitope prediction. Results: Here we report the results of our peptide array data analysis, which revealed sets of peptides that have diagnostic potential for detecting past exposure to a subset of the tested human pathogens including Zika virus. These peptides were then confirmed using the well-established ELISA method. Conclusions: These array data, and the resulting peptides can be useful in diverse efforts including the development of new pan-flavivirus antibodies, more accurate epitope mapping, and vaccine development against these viral pathogens.
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Affiliation(s)
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Leda Parham
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Ivette Lorenzana
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Brett E Pickett
- J. Craig Venter Institute, La Jolla, CA, 92137, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA
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4
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Martinez Viedma MDP, Kose N, Parham L, Balmaseda A, Kuan G, Lorenzana I, Harris E, Crowe JE, Pickett BE. Peptide arrays of three collections of human sera from patients infected with mosquito-borne viruses. F1000Res 2019; 8:1875. [PMID: 32201571 PMCID: PMC7065662 DOI: 10.12688/f1000research.20981.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 03/29/2024] Open
Abstract
Background: Global outbreaks caused by emerging or re-emerging arthropod-borne viruses (arboviruses) are becoming increasingly more common. These pathogens include the mosquito-borne viruses belonging to the Flavivirus and Alphavirus genera. These viruses often cause non-specific or asymptomatic infection, which can confound viral prevalence studies. In addition, many acute phase diagnostic tests rely on the detection of viral components such as RNA or antigen. Standard serological tests are often not reliable for diagnosis after seroconversion and convalescence due to cross-reactivity among flaviviruses. Methods: In order to contribute to development efforts for mosquito-borne serodiagnostics, we incubated 137 human sera on individual custom peptide arrays that consisted of over 866 unique peptides in quadruplicate. Our bioinformatics workflow to analyze these data incorporated machine learning, statistics, and B-cell epitope prediction. Results: Here we report the results of our peptide array data analysis, which revealed sets of peptides that have diagnostic potential for detecting past exposure to a subset of the tested human pathogens including Zika virus. These peptides were then confirmed using the well-established ELISA method. Conclusions: These array data, and the resulting peptides can be useful in diverse efforts including the development of new pan-flavivirus antibodies, more accurate epitope mapping, and vaccine development against these viral pathogens.
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Affiliation(s)
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Leda Parham
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Ivette Lorenzana
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - James E. Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Brett E. Pickett
- J. Craig Venter Institute, La Jolla, CA, 92137, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA
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5
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Martinez Viedma MDP, Kose N, Parham L, Balmaseda A, Kuan G, Lorenzana I, Harris E, Crowe JE, Pickett BE. Peptide arrays incubated with three collections of human sera from patients infected with mosquito-borne viruses. F1000Res 2019; 8:1875. [PMID: 32201571 PMCID: PMC7065662 DOI: 10.12688/f1000research.20981.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2020] [Indexed: 11/24/2022] Open
Abstract
Background: Global outbreaks caused by emerging or re-emerging arthropod-borne viruses (arboviruses) are becoming increasingly more common. These pathogens include the mosquito-borne viruses belonging to the Flavivirus and Alphavirus genera. These viruses often cause non-specific or asymptomatic infection, which can confound viral prevalence studies. In addition, many acute phase diagnostic tests rely on the detection of viral components such as RNA or antigen. Standard serological tests are often not reliable for diagnosis after seroconversion and convalescence due to cross-reactivity among flaviviruses. Methods: In order to contribute to development efforts for mosquito-borne serodiagnostics, we incubated 137 human sera on individual custom peptide arrays that consisted of over 866 unique peptides in quadruplicate. Our bioinformatics workflow to analyze these data incorporated machine learning, statistics, and B-cell epitope prediction. Results: Here we report the results of our peptide array data analysis, which revealed sets of peptides that have diagnostic potential for detecting past exposure to a subset of the tested human pathogens including Zika virus. These peptides were then confirmed using the well-established ELISA method. Conclusions: These array data, and the resulting peptides can be useful in diverse efforts including the development of new pan-flavivirus antibodies, more accurate epitope mapping, and vaccine development against these viral pathogens.
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Affiliation(s)
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Leda Parham
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Ivette Lorenzana
- Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Brett E Pickett
- J. Craig Venter Institute, La Jolla, CA, 92137, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA
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6
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Saini G, Trenchevska O, Howell LJ, Boyd JG, Smith DP, Jain V, Linford MR. Performance Comparison of Three Chemical Vapor Deposited Aminosilanes in Peptide Synthesis: Effects of Silane on Peptide Stability and Purity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11925-11932. [PMID: 30208711 DOI: 10.1021/acs.langmuir.8b01298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Silicon oxide substrates underwent gas-phase functionalization with various aminosilanes, and the resulting surfaces were evaluated for their suitability as a solid support for solid phase peptide synthesis (SPPS). APTES (3-aminopropyltriethoxysilane), APDEMS (3-aminopropyldiethoxymethylsilane), and APDIPES (3-aminopropyldiisopropylethoxysilane) were individually applied to thermal oxide-terminated silicon substrates via gas-phase deposition. Coated surfaces were characterized by spectroscopic ellipsometry (SE), contact angle goniometry, X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and spectrophotometry. Model oligopeptides with 16 residues were synthesized on the amino surfaces, and the chemical stabilities of the resulting surfaces were evaluated against a stringent side chain deprotection (SCD) step, which contained trifluoroacetic acid (TFA) and trifluoromethanesulfonic acid (TFMSA). Functionalized surface thickness loss during SCD was most acute for APDIPES and the observed relative stability order was APTES > APDEMS > APDIPES. Amino surfaces were evaluated for compatibility with stepwise peptide synthesis where complete deprotection and coupling cycles are paramount. Model trimer syntheses indicated that routine capping of unreacted amines with acetic anhydride significantly increased purity as measured by MALDI-MS. An inverse correlation between the amine loading density and peptide purity was observed. In general, peptide purity was highest for the lowest amine density APDIPES surface.
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Affiliation(s)
- Gaurav Saini
- HealthTell Inc. , Chandler , Arizona 85226 , United States
| | | | - Loren J Howell
- HealthTell Inc. , Chandler , Arizona 85226 , United States
| | - James G Boyd
- HealthTell Inc. , Chandler , Arizona 85226 , United States
| | - David P Smith
- HealthTell Inc. , Chandler , Arizona 85226 , United States
| | - Varun Jain
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Matthew R Linford
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
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7
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Kalaiselvan S, Sankar S, Ramamurthy M, Ghosh AR, Nandagopal B, Sridharan G. Prediction of B Cell Epitopes Among Hantavirus Strains Causing Hemorragic Fever With Renal Syndrome. J Cell Biochem 2016; 118:1182-1188. [PMID: 27748540 DOI: 10.1002/jcb.25765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]
Abstract
Hantavirus infections are now recognized to be a global problem. The hantaviruses include several genotypic variants of the virus with different distributions in varying geographical regions. The virus genotypes seem to segregate in association with certain manifestations specific for each syndrome. They primarily include HFRS, HCPS, febrile illness with or without mild involvement of renal diseases. In the course of our study on hantavirus etiology of febrile illnesses, we recovered a hantavirus strain identified by nPCR. This has been sequenced to be Hantaan-like virus (partial S segment). The current manuscript is focused on understanding the N protein coded by S segment in terms of variation of amino acid sequences of the virus genotypes associated with HFRS. The diagnosis of this infection is achieved by PCR testing of serum/plasma or demonstration of IgM/IgG in serum. The limitations of PCR are temporal often not positive after 7 days of onset of infection. IgM detection is possible around this period and up to 21 days. IgG detection is less definitive in acute infections. Here, we report characterization of the sequence diversity of HFRS strains, 3D structure of Hantaan N protein, and B-cell epitopes on this molecule. We predicted a 20 amino acid sequence length peptide by using BepiPred online server in IEDB analysis resource program. We suggest this peptide may be used for development of geographic region-specific immunoassays like EIAs for antibody detection, monoclonal antibody development, and immunoblots (line immunoassay). J. Cell. Biochem. 118: 1182-1188, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sagadevan Kalaiselvan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Mageshbabu Ramamurthy
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Centre for Infectious Diseases & Control, School of Biosciences and Technology, VIT University, Vellore, 632 014, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India
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8
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Gori A, Sola L, Gagni P, Bruni G, Liprino M, Peri C, Colombo G, Cretich M, Chiari M. Screening Complex Biological Samples with Peptide Microarrays: The Favorable Impact of Probe Orientation via Chemoselective Immobilization Strategies on Clickable Polymeric Coatings. Bioconjug Chem 2016; 27:2669-2677. [DOI: 10.1021/acs.bioconjchem.6b00426] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alessandro Gori
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Laura Sola
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Paola Gagni
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Giulia Bruni
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Marta Liprino
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Claudio Peri
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Marina Cretich
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
| | - Marcella Chiari
- Consiglio
Nazionale delle
Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM) Via
Mario Bianco, 9, 20131 Milano, Italy
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9
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Abstract
With the increasing need for understanding antibody specificity in antibody and vaccine research, pepscan assays provide a rapid method for mapping and profiling antibody responses to continuous epitopes. We have developed a relatively low-cost method to generate peptide microarray slides for studying antibody binding. Using a setup of an IntavisAG MultiPep RS peptide synthesizer, a Digilab MicroGrid II 600 microarray printer robot, and an InnoScan 1100 AL scanner, the method allows the interrogation of up to 1536 overlapping, alanine-scanning, and mutant peptides derived from the target antigens. Each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface.
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10
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Bergeron S, Laforte V, Lo PS, Li H, Juncker D. Evaluating mixtures of 14 hygroscopic additives to improve antibody microarray performance. Anal Bioanal Chem 2015; 407:8451-62. [PMID: 26345442 DOI: 10.1007/s00216-015-8992-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 11/27/2022]
Abstract
Microarrays allow the miniaturization and multiplexing of biological assays while only requiring minute amounts of samples. As a consequence of the small volumes used for spotting and the assays, evaporation often deteriorates the quality, reproducibility of spots, and the overall assay performance. Glycerol is commonly added to antibody microarray printing buffers to decrease evaporation; however, it often decreases the binding of antibodies to the surface, thereby negatively affecting assay sensitivity. Here, combinations of 14 hygroscopic chemicals were used as additives to printing buffers for contact-printed antibody microarrays on four different surface chemistries. The ability of the additives to suppress evaporation was quantified by measuring the residual buffer volume in open quill pins over time. The seven best additives were then printed either individually or as a 1:1 mixture of two additives, and the homogeneity, intensity, and reproducibility of both the spotted protein and of a fluorescently labeled analyte in an assay were quantified. Among the 28 combinations on the four slides, many were found to outperform glycerol, and the best additive mixtures were further evaluated by changing the ratio of the two additives. We observed that the optimal additive mixture was dependent on the slide chemistry, and that it was possible to increase the binding of antibodies to the surface threefold compared to 50 % glycerol, while decreasing whole-slide coefficient of variation to 5.9 %. For the two best slides, improvements were made for both the limit of detection (1.6× and 5.9×, respectively) and the quantification range (1.2× and 2.1×, respectively). The additive mixtures identified here thus help improve assay reproducibility and performance, and might be beneficial to all types of microarrays that suffer from evaporation of the printing buffers.
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Affiliation(s)
- Sébastien Bergeron
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - Veronique Laforte
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
- Neurology and Neurosurgery Department, McGill University, 3801 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - Pik-Shan Lo
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - Huiyan Li
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - David Juncker
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1.
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4.
- Neurology and Neurosurgery Department, McGill University, 3801 University Street, Montreal, Quebec, Canada, H3A 2B4.
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