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Series GSE45996 Query DataSets for GSE45996
Status Public on Apr 12, 2013
Title Inferring Epitopes of a Polymorphic Antigen Amidst Broadly Cross-Reactive Antibodies Using Protein Microarrays: a Study of OspC Proteins of Borrelia burgdorferi
Platform organism Borreliella burgdorferi
Sample organisms Homo sapiens; Peromyscus leucopus
Experiment type Protein profiling by protein array
Summary Epitope mapping studies aim to identify the binding sites of antibody-antigen interactions to enhance the development of vaccines, diagnostics and immunotherapeutic compounds. However, mapping is a laborious process employing time- and resource-consuming ‘wet bench’ techniques or epitope prediction software that are still in their infancy. For polymorphic antigens, another challenge is characterizing cross-reactivity between epitopes, teasing out distinctions between broadly cross-reactive responses, limited cross-reactions among variants and the truly type-specific responses. A refined understanding of cross-reactive antibody binding could guide the selection of the most informative subsets of variants for diagnostics and multivalent subunit vaccines. We explored the antibody binding reactivity of sera from human patients and Peromyscus leucopus rodents infected with Borrelia burgdorferi to the polymorphic outer surface protein C (OspC), an attractive candidate antigen for vaccine and improved diagnostics for Lyme disease. We constructed a protein microarray displaying 23 natural variants of OspC and quantified the degree of cross-reactive antibody binding between all pairs of variants, using Pearson correlation calculated on the reactivity values using three independent transforms of the raw data: (1) logarithmic, (2) rank, and (3) binary indicators. We observed that the global amino acid sequence identity between OspC pairs was a poor predictor of cross-reactive antibody binding. Then we asked if specific regions of the protein would better explain the observed cross-reactive binding and performed in silico screening of the linear sequence and 3-dimensional structure of OspC. This analysis pointed to the C-terminal helix of the structure as a major determinant of type-specific cross-reactive antibody binding. We developed bioinformatics methods to systematically analyze the relationship between local sequence/structure variation and cross-reactive antibody binding patterns among variants of a polymorphic antigen, and this method can be applied to other polymorphic antigens for which immune response data is available for multiple variants.
Overall design Antibody profiling was performed on sera from Borrelia burgdorferi infected and non-infected humans and Peromyscus leucopus rodents against 23 variants of the surface protein OspC . For infected human serum samples, the OspC type of the infecting B. burgdorferi strain is unknown; for experimentally-infected P. leucopus serum samples, it is known. Of human serum samples, 55 were from infected individuals and 25 from naive controls. Of P. leucopus serum samples, 23 were from infected individuals and 7 were from naive controls.
Contributor(s) Baum E, Randall AZ, Zeller M, Barbour AG
Citation(s) 23221801, 23826301
Submission date Apr 11, 2013
Last update date Aug 13, 2019
Contact name Elisabeth Baum
Organization name University of California Irvine
Street address Med Surge II
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
Platforms (1)
GPL17008 OspC Protein Microarray
Samples (110)
GSM1121427 902111
GSM1121428 902436
GSM1121429 902622
BioProject PRJNA196868

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45996_raw_data.txt.gz 6.4 Kb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table

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