B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

Area of Science:

• Immunology
• Bioinformatics
• Genomics

Background:

• B-cell receptors (BCRs) are crucial for adaptive immunity, recognizing pathogen antigens.
• V(D)J recombination and somatic hypermutation create a vast BCR repertoire, requiring single-cell analysis.
• Single-cell RNA sequencing enables simultaneous capture of paired BCR chains and transcriptomic data.

Purpose of the Study:

• To develop a novel bioinformatics tool, VDJPuzzle, for reconstructing full-length B-cell receptor sequences.
• To extract somatic mutations within the VDJ regions of reconstructed BCRs.
• To validate the accuracy of VDJPuzzle in reconstructing BCR sequences.

Main Methods:

• Development of the VDJPuzzle bioinformatics tool.
• Application of VDJPuzzle to single-cell RNA sequencing data from human and murine B cells.
• Validation of reconstructed BCR sequences using single-cell Sanger sequencing.

Main Results:

• VDJPuzzle successfully reconstructed productive, full-length BCR heavy and light chains.
• 100% of human and 96.5% of murine B cells had their BCRs reconstructed.
• Reconstructed BCR sequences were validated by single-cell Sanger sequencing.

Conclusions:

• VDJPuzzle is an effective tool for reconstructing paired BCR sequences from single-cell RNA sequencing data.
• The tool accurately identifies somatic mutations in the VDJ regions.
• VDJPuzzle facilitates the study of BCR repertoire and adaptive immune responses.