Determination of B-Cell Epitopes in Patients with Celiac Disease: Peptide Microarrays

Most antibodies recognize conformational or discontinuous epitopes that have a specific 3-dimensional shape; however, determination of discontinuous B-cell epitopes is a major challenge in bioscience. Moreover, the current methods for identifying peptide epitopes often involve laborious, high-cost p...

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Bibliographic Details
Published in:PloS one 2016-01, Vol.11 (1), p.e0147777-e0147777
Main Authors: Choung, Rok Seon, Marietta, Eric V, Van Dyke, Carol T, Brantner, Tricia L, Rajasekaran, John, Pasricha, Pankaj J, Wang, Tianhao, Bei, Kang, Krishna, Karthik, Krishnamurthy, Hari K, Snyder, Melissa R, Jayaraman, Vasanth, Murray, Joseph A
Format: Article
Language:English
Subjects:
Adolescent
Adult
Aged
Amino Acid Sequence
Antibodies
Antigenic determinants
Autoimmune diseases
B cells
B-Lymphocytes - chemistry
B-Lymphocytes - immunology
B-Lymphocytes - pathology
Biochemistry
Biology and Life Sciences
Biomarkers
Biopsy
Care and treatment
Case-Control Studies
Celiac disease
Celiac Disease - diagnosis
Celiac Disease - immunology
Celiac Disease - pathology
Computation
Computer applications
Development and progression
Diagnosis
Diagnostic systems
Disease
Epitopes
Epitopes, B-Lymphocyte - analysis
Epitopes, B-Lymphocyte - immunology
Female
Gastroenterology
Gliadin
Gliadin - chemistry
Gliadin - immunology
Gluten
Hepatology
Humans
Immunoglobulins
Lymphocytes B
Male
Medical diagnosis
Medicine and Health Sciences
Middle Aged
Molecular Sequence Data
Pathogenesis
Patients
Peptide Fragments - chemistry
Peptide Fragments - immunology
Peptides
Physiological aspects
Population
Protein Array Analysis - instrumentation
Protein Array Analysis - methods
Protein Isoforms - chemistry
Protein Isoforms - immunology
Research and Analysis Methods
Sensitivity and Specificity
Silicon
Silicon wafers
Test procedures
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Description
Summary:Most antibodies recognize conformational or discontinuous epitopes that have a specific 3-dimensional shape; however, determination of discontinuous B-cell epitopes is a major challenge in bioscience. Moreover, the current methods for identifying peptide epitopes often involve laborious, high-cost peptide screening programs. Here, we present a novel microarray method for identifying discontinuous B-cell epitopes in celiac disease (CD) by using a silicon-based peptide array and computational methods. Using a novel silicon-based microarray platform with a multi-pillar chip, overlapping 12-mer peptide sequences of all native and deamidated gliadins, which are known to trigger CD, were synthesized in situ and used to identify peptide epitopes. Using a computational algorithm that considered disease specificity of peptide sequences, 2 distinct epitope sets were identified. Further, by combining the most discriminative 3-mer gliadin sequences with randomly interpolated3- or 6-mer peptide sequences, novel discontinuous epitopes were identified and further optimized to maximize disease discrimination. The final discontinuous epitope sets were tested in a confirmatory cohort of CD patients and controls, yielding 99% sensitivity and 100% specificity. These novel sets of epitopes derived from gliadin have a high degree of accuracy in differentiating CD from controls, compared with standard serologic tests. The method of ultra-high-density peptide microarray described here would be broadly useful to develop high-fidelity diagnostic tests and explore pathogenesis.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0147777