Detection of neoantigen-reactive T cell clones based on the clonal expansion using next-generation sequencing of T cell receptor β complementarity-determining region 3

Area of Science:

• Immunology
• Oncology
• Biotechnology

Background:

• Developing effective biomarkers for cancer immunotherapy, specifically immune checkpoint inhibitors (ICIs), is crucial.
• Identifying tumor antigen (Ag)-specific T cells requires sensitive and efficient assays.

Purpose of the Study:

• To demonstrate a sensitive method for detecting Ag-reactive T cell clones based on clonal expansion rather than cytokine production.
• To establish a novel platform for biomarker development and therapeutic strategies in cancer immunotherapy.

Main Methods:

• Utilized next-generation sequencing (NGS) of T cell receptor beta (TCR β) complementarity-determining region 3 (CDR3) sequences.
• Employed model neoantigens (NeoAgs) to stimulate T cells and detect clonal expansion.
• Compared the sensitivity of the NGS-based method against enzyme-linked immunospot (ELISPOT).

Main Results:

• Demonstrated a 100-fold higher sensitivity in detecting T cell clonal frequencies compared to ELISPOT.
• Showcased the ability to track sequential increases in T cell clonal frequencies following Ag stimulation.
• Confirmed that TCRβ CDR3 sequences can serve as markers for dynamic changes during immunotherapy.

Conclusions:

• The developed TCRβ NGS-based method offers a highly sensitive approach for identifying Ag-reactive T cells.
• This method provides a novel platform for developing mechanism-driven biomarkers for ICIs.
• The findings support the potential for new therapeutic strategies and biomarker discovery in cancer immunotherapy.