ATLAS-seq: a microfluidic single-cell TCR screen for antigen-reactive TCRs

Area of Science:

• Immunology
• Molecular Biology
• Biotechnology

Background:

• Discovering antigen-reactive T cell receptors (TCRs) is crucial for developing effective engineered T cell immunotherapies.
• Conventional methods like MHC multimer staining prioritize high-affinity TCRs, potentially missing those with superior T cell activation efficacy.

Purpose of the Study:

• To develop and validate ATLAS-seq, a microfluidic single-cell screening technology for identifying antigen-reactive T cells based on functional activity.
• To compare the efficacy of TCRs identified by ATLAS-seq against those found using MHC multimer staining.

Main Methods:

• Developed ATLAS-seq, a microfluidic method using aptamer-based sensors to detect IFNγ secretion from single T cells upon antigen stimulation.
• Integrated single-cell RNA and TCR sequencing with the ATLAS-seq platform.
• Screened TCRs reactive to cytomegalovirus (CMV) and prostate-specific antigen (PSA) from peripheral blood mononuclear cells (PBMCs).

Main Results:

• ATLAS-seq successfully isolated and characterized activated T cells.
• Identified distinct TCR clonotypes with significantly higher T cell activation levels compared to those obtained via MHC multimer staining.
• TCRs identified by ATLAS-seq demonstrated enhanced efficacy in target cell killing.

Conclusions:

• ATLAS-seq offers an efficient and versatile platform for screening antigen-reactive TCRs.
• This technology can identify TCRs with superior functional activity for advancing engineered T cell immunotherapy.
• ATLAS-seq overcomes limitations of affinity-based methods for TCR discovery.