title: Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing.
abstract: Disease-specific antibodies can serve as highly effective biomarkers but have been identified for only a relatively small number of autoimmune diseases. A method was developed to identify disease-specific binding motifs through integration of bacterial display peptide library screening, next-generation sequencing (NGS) and computational analysis. Antibody specificity repertoires were determined by identifying bound peptide library members for each specimen using cell sorting and performing NGS. A computational algorithm, termed Identifying Motifs Using Next- generation sequencing Experiments (IMUNE), was developed and applied to discover disease- and healthy control-specific motifs. IMUNE performs comprehensive pattern searches, identifies patterns statistically enriched in the disease or control groups and clusters the patterns to generate motifs. Using celiac disease sera as a discovery set, IMUNE identified a consensus motif (QPEQPF[PS]E) with high diagnostic sensitivity and specificity in a validation sera set, in addition to novel motifs. Peptide display and sequencing (Display-Seq) coupled with IMUNE analysis may thus be useful to characterize antibody repertoires and identify disease-specific antibody epitopes and biomarkers.
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.|Serimmune, Inc, Santa Barbara, CA 93105, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Pantazes
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.|Serimmune, Inc, Santa Barbara, CA 93105, USA.
authors.forename: Jack
authors.initials: J
authors.lastname: Reifert
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Bozekowski
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Kelly N
authors.initials: KN
authors.lastname: Ibsen
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Murray
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.|Serimmune, Inc, Santa Barbara, CA 93105, USA.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Daugherty
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000906:Antibodies / Q000737:chemistry / Q000378:metabolism*; D000918:Antibody Specificity; D015415:Biomarkers / Q000097:blood; D001798:Blood Proteins / Q000032:analysis* / Q000276:immunology; D002446:Celiac Disease / Q000097:blood / Q000175:diagnosis* / Q000276:immunology; D002469:Cell Separation / Q000295:instrumentation / Q000379:methods; D000939:Epitopes / Q000032:analysis* / Q000276:immunology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry / Q000276:immunology / Q000378:metabolism
chemical_list: D000906:Antibodies; D015415:Biomarkers; D001798:Blood Proteins; D000939:Epitopes; D019151:Peptide Library; D010455:Peptides