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Epitope binning for multiple antibodies simultaneously using mammalian cell display and DNA sequencing.

Ning Lin1, Kotaro Miyamoto1, Takumi Ogawara1

  • 1School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.

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|May 28, 2024
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Epitope Binning-seq enables simultaneous epitope analysis of multiple antibodies, simplifying antibody drug discovery. This novel platform efficiently groups antibodies by epitope similarity, accelerating the identification of promising drug candidates.

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Area of Science:

  • Biotechnology
  • Immunology
  • Drug Discovery

Background:

  • Epitope binning is crucial for antibody drug discovery but conventional methods are complex.
  • Current techniques require individual antibody production, limiting throughput.

Purpose of the Study:

  • To establish a novel, high-throughput epitope binning platform.
  • To enable simultaneous analysis of multiple antibodies for epitope similarity.

Main Methods:

  • Epitope Binning-seq utilizes flow cytometry and next-generation sequencing.
  • Query antibodies (qAbs) on cells are analyzed against fluorescently labeled reference antibodies (rAbs).
  • Fluorescence-negative cells are sequenced to identify qAbs with similar epitopes to the rAb.

Main Results:

  • The system successfully identified and binned 14 query antibodies simultaneously.
  • Sensitivity and reliability were confirmed using pertuzumab and trastuzumab targeting HER2.
  • The platform demonstrated effectiveness with antibodies at various abundances.

Conclusions:

  • Epitope Binning-seq offers a versatile and efficient platform for antibody epitope evaluation.
  • This method can significantly expedite the identification of clinically relevant antibodies.
  • The platform is applicable to a wide range of antibodies and antigens.