Deep Panning: steps towards probing the IgOme

PLoS One. 2012;7(8):e41469. doi: 10.1371/journal.pone.0041469. Epub 2012 Aug 1.

Abstract

Background: Polyclonal serum consists of vast collections of antibodies, products of differentiated B-cells. The spectrum of antibody specificities is dynamic and varies with age, physiology, and exposure to pathological insults. The complete repertoire of antibody specificities in blood, the IgOme, is therefore an extraordinarily rich source of information-a molecular record of previous encounters as well as a status report of current immune activity. The ability to profile antibody specificities of polyclonal serum at exceptionally high resolution has been an important and serious challenge which can now be overcome.

Methodology/principal findings: Here we illustrate the application of Deep Panning, a method that combines the flexibility of combinatorial phage display of random peptides with the power of high-throughput deep sequencing. Deep Panning is first applied to evaluate the quality and diversity of naïve random peptide libraries. The production of very large data sets, hundreds of thousands of peptides, has revealed unexpected properties of combinatorial random peptide libraries and indicates correctives to ensure the quality of the libraries generated. Next, Deep Panning is used to analyze a model monoclonal antibody in addition to allowing one to follow the dynamics of biopanning and peptide selection. Finally Deep Panning is applied to profile polyclonal sera derived from HIV infected individuals.

Conclusions/significance: The ability to generate and characterize hundreds of thousands of affinity-selected peptides creates an effective means towards the interrogation of the IgOme and understanding of the humoral response to disease. Deep Panning should open the door to new possibilities for serological diagnostics, vaccine design and the discovery of the correlates of immunity to emerging infectious agents.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antibodies, Monoclonal / chemistry*
  • Antibodies, Monoclonal / genetics
  • Antibodies, Monoclonal / immunology
  • Antibody Specificity*
  • B-Lymphocytes / chemistry
  • B-Lymphocytes / immunology
  • Humans
  • Peptide Library*

Substances

  • Antibodies, Monoclonal
  • Peptide Library

Grant support

This research was supported by the The United States – Israel Binational Agricultural Research and Development Fund (BARD) [Research Grant No. IS-4287-10 to TP and JMG]. AR is the recipient of the Marian Gertner Institute for Nanomedical Systems Fellowship. This study was supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University to HA and OP. GK is the recipient of the Jakov, Miriana, and Jorge Saia Doctoral Fellowship. We thank the Frankel Foundation for generous support of this research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.