Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing

Caitlin A. Kowalsky, Matthew S. Faber, Aritro Nath, Hailey E. Dann, Vince W. Kelly, Li Liu, Purva Shanker, Ellen K. Wagner, Jennifer A. Maynard, Christina Chan, Timothy A. Whitehead

Research output: Contribution to journalArticle

  • 14 Citations

Abstract

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Herewe show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. Inall threecases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps canbe prepared at a rate of four per day.

LanguageEnglish (US)
Pages26457-26470
Number of pages14
JournalJournal of Biological Chemistry
Volume290
Issue number44
DOIs
StatePublished - Oct 30 2015

Profile

Epitope Mapping
High-Throughput Nucleotide Sequencing
Mutagenesis
Epitopes
Antibodies
Pertussis Toxin
DNA Sequence Analysis
Libraries
Pathogens
Vaccines
Antigens
Pipelines
Display devices
Throughput
DNA
Neoplasms

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Kowalsky, C. A., Faber, M. S., Nath, A., Dann, H. E., Kelly, V. W., Liu, L., ... Whitehead, T. A. (2015). Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. Journal of Biological Chemistry, 290(44), 26457-26470. DOI: 10.1074/jbc.M115.676635

Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. / Kowalsky, Caitlin A.; Faber, Matthew S.; Nath, Aritro; Dann, Hailey E.; Kelly, Vince W.; Liu, Li; Shanker, Purva; Wagner, Ellen K.; Maynard, Jennifer A.; Chan, Christina; Whitehead, Timothy A.

In: Journal of Biological Chemistry, Vol. 290, No. 44, 30.10.2015, p. 26457-26470.

Research output: Contribution to journalArticle

Kowalsky, CA, Faber, MS, Nath, A, Dann, HE, Kelly, VW, Liu, L, Shanker, P, Wagner, EK, Maynard, JA, Chan, C & Whitehead, TA 2015, 'Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing' Journal of Biological Chemistry, vol 290, no. 44, pp. 26457-26470. DOI: 10.1074/jbc.M115.676635
Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L et al. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. Journal of Biological Chemistry. 2015 Oct 30;290(44):26457-26470. Available from, DOI: 10.1074/jbc.M115.676635
Kowalsky, Caitlin A. ; Faber, Matthew S. ; Nath, Aritro ; Dann, Hailey E. ; Kelly, Vince W. ; Liu, Li ; Shanker, Purva ; Wagner, Ellen K. ; Maynard, Jennifer A. ; Chan, Christina ; Whitehead, Timothy A./ Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. In: Journal of Biological Chemistry. 2015 ; Vol. 290, No. 44. pp. 26457-26470
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