Engineering antibodies in B cells using endogenous AID activity

ongoing

The AutoEngineering project aims to develop an innovative strategy for B cell engineering by exploiting natural DNA breaks to generate antibodies that surpass common reactivity profiles. The project is based on our surprising finding that in B cells endogenous AID (activation-induced cytidine deaminase) activity can lead to the insertion of a pathogen receptor resulting in broadly reactive antibodies. To unravel this new mechanism of diversification, my laboratory established and developed new methodologies to identify insert-containing antibodies in genomic DNA, mRNA, proteins and cells. We found that insertions in antibody transcripts derive from distant genes, occur across individuals and are inducible in vitro, and we have preliminary evidence that in vitro activation of AID enables integration of a nucleofected DNA substrate. Avoiding exogenous nucleases, this project aims at developing efficient and safe engineering of B cells to produce antibodies by design. Aim 1. By screening for genomic insertions in antibody genes of healthy donors, DNA-repair deficient patients, and manipulated in vitro B cell cultures, we will gain insights into the mechanism of insertion and define biomarkers of DNA repair. Aim 2. The knowledge gained will be used to optimize substrate design and insert integration, while minimizing the potential for off-target integration. We will also explore the possibility to guide AID to target sites using RNAs, and design substrates that allow efficient splicing of an inserted exon. Aim 3. To gain breadth on pathogen recognition and to circumvent the limitation of the heterodimeric antibody binding site, we will use the above approach to engineer B cells to produce antibodies containing receptors for HIV (CD4) and HCV (CD81). Insertion of slim receptor-domains with precise targeting of crucial sites may generate B cells with exceptional potency to reduce the risk for escape mutants, thereby paving a way for artificial immunity.