Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information.

Area of Science:

• Immunology
• Bioinformatics
• Molecular Biology

Background:

• T cell receptors (TCRs) are crucial for immunology research.
• Current methods often lack full-length coding sequences, hindering applications.
• Existing TCR data is limited to V/J gene symbols and CDR3 amino acid sequences.

Purpose of the Study:

• To introduce Stitchr, a software tool for generating complete TCR coding sequences.
• To address the limitation of incomplete TCR sequence information in research.
• To facilitate TCR engineering and manipulation.

Main Methods:

• Stitchr software tool development.
• Input: V/J gene symbols and CDR3 amino acid sequence.
• Output: Full-length coding nucleotide sequences for TCR cDNA.
• Validation through synthesis, transduction into Jurkat cells, and antigen specificity testing.
• Companion script Thimble for high-throughput processing.

Main Results:

• Stitchr successfully generates complete TCR coding sequences from minimal input.
• Synthesized TCR sequences recapitulated parental antigen specificity in Jurkat cells.
• The Thimble script processed one million TCRs in under ten minutes on a standard PC.

Conclusions:

• Stitchr systematizes TCR sequence production and modification.
• The tool is expected to increase the speed, repeatability, and reproducibility of TCR research.
• Stitchr is available on GitHub for broader accessibility.