title: Determination of B-Cell Epitopes in Patients with Celiac Disease: Peptide Microarrays.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America.
authors.forename: Rok Seon
authors.initials: RS
authors.lastname: Choung
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America.
authors.forename: Eric V
authors.initials: EV
authors.lastname: Marietta
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America.
authors.forename: Carol T
authors.initials: CT
authors.lastname: Van Dyke
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America.
authors.forename: Tricia L
authors.initials: TL
authors.lastname: Brantner
authors.affiliation: Vibrant Sciences LLC, San Carlos, CA, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Rajasekaran
authors.affiliation: Center for Neurogastroenterology, Johns Hopkins University, Baltimore, MD, United States of America.
authors.forename: Pankaj J
authors.initials: PJ
authors.lastname: Pasricha
authors.affiliation: Vibrant Sciences LLC, San Carlos, CA, United States of America.
authors.forename: Tianhao
authors.initials: T
authors.lastname: Wang
authors.affiliation: Vibrant Sciences LLC, San Carlos, CA, United States of America.
authors.forename: Kang
authors.initials: K
authors.lastname: Bei
authors.affiliation: Vibrant Sciences LLC, San Carlos, CA, United States of America.
authors.forename: Karthik
authors.initials: K
authors.lastname: Krishna
authors.affiliation: Vibrant Sciences LLC, San Carlos, CA, United States of America.
authors.forename: Hari K
authors.initials: HK
authors.lastname: Krishnamurthy
authors.affiliation: Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, United States of America.
authors.forename: Melissa R
authors.initials: MR
authors.lastname: Snyder
authors.affiliation: Vibrant Sciences LLC, San Carlos, CA, United States of America.
authors.forename: Vasanth
authors.initials: V
authors.lastname: Jayaraman
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Murray
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000595:Amino Acid Sequence; D001402:B-Lymphocytes / Q000737:chemistry* / Q000276:immunology / Q000473:pathology; D016022:Case-Control Studies; D002446:Celiac Disease / Q000175:diagnosis* / Q000276:immunology / Q000473:pathology; D018985:Epitopes, B-Lymphocyte / Q000032:analysis* / Q000276:immunology; D005260:Female; D005903:Gliadin / Q000737:chemistry* / Q000276:immunology; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000276:immunology; D040081:Protein Array Analysis / Q000295:instrumentation / Q000379:methods*; D020033:Protein Isoforms / Q000737:chemistry / Q000276:immunology; D012680:Sensitivity and Specificity
chemical_list: D018985:Epitopes, B-Lymphocyte; D010446:Peptide Fragments; D020033:Protein Isoforms; D005903:Gliadin
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