Recombination junctions from antibody isotype switching classify immune and DNA repair dysfunction.

Area of Science:

• Immunology
• Genetics
• Molecular Biology

Background:

• Assessing immunocompetence and DNA repair necessitates methods sensitive to complex genetic and molecular factors beyond monogenic disorders.
• B cells have been instrumental in studying DNA repair mechanisms for decades.

Purpose of the Study:

• To introduce SWIBRID (SWItch junction Breakpoint Repertoire IDentification), a tool for systematic profiling of genomic junctions formed during B cell antibody class switch recombination (CSR).
• To demonstrate SWIBRID's capability in detecting DNA repair deficiencies and identifying genetic defects through analysis of CSR junctions.

Main Methods:

• SWIBRID utilizes a blood-based PCR followed by long-read sequencing and bioinformatic analysis to profile genomic junctions generated during CSR in B cells.
• The method analyzes specific DNA double-strand break (DSB) repair defects and their distinct CSR junction patterns.

Main Results:

• SWIBRID accurately detects immunodeficiencies (AUC 0.99) and DNA repair defects (AUC 0.84) in 68 patients.
• Distinct CSR junction patterns were observed for specific DNA repair defects, including cancer-associated mutations.
• The tool successfully distinguished different types of DSB repair knockouts and identified genetic defects in cell lines, uncovering novel patient groups.

Conclusions:

• SWIBRID offers a scalable, blood-based approach to assess immunocompetence and DNA repair proficiency by analyzing CSR junctions.
• The tool aids in the identification of pathogenic defects, supports early diagnosis, and addresses molecular heterogeneity in patient outcomes.