“Untargeting” Autoantibodies Using Genome Editing, a Proof-of-Concept Study

Autoantibodies are useful biomarkers of autoimmune diseases and some have direct pathogenic role. Current standard therapies for elimination of specific B/plasma-cell clones are not fully efficient. In this proof-of-concept study, we used the CRISPR/Cas9 genome-editing system to knockout V(D)J rearrangements that produce pathogenic autoantibodies in vitro . HEK293T cell lines were established with stable expression of two monoclonal antibodies, a humanized anti-dsDNA (clone 3H9) and a human-derived anti-nAChR-α1-subunit (clone B12L). For each clone, five CRISPR/Cas9 guided-RNAs (T-gRNAs) were designed to target the heavy chain CDR2/3 variable regions. After CRISPR/Cas9 editing, levels of secreted immunoglobulins were evaluated, in addition to 3H9 anti-dsDNA reactivity by ELISA and B12L anti-AChR reactivity using cells overexpressing mouse genes of AChR-α1/β1/δ/γ/ε-subunits. The T-gRNAs decreased the expression of the heavy chain to ∼50-60%, compared to >90% in Non-Target-gRNA. Levels of secreted IgG and reactivity to the respective target antigens decreased ∼90% and ∼95% after knockout with the T-gRNAs compared to Non-Target-gRNA for clones 3H9 and B12L, respectively. Sequencing indicated the presence of indels at the Cas9 cut-site, which could lead to codon jam, the likely cause of the knockout. Additionally, remaining secreted 3H9 antibodies presented variable reactivity to dsDNA among the five T-gRNA, suggesting that the exact Cas9 cut-site and indels may further interfere with antibody-antigen interaction. CRISPR/Cas9 genome-editing was very effective to knockout the Heavy-Chain-IgG genes, considerably affecting the secretion and binding capacity of the autoantibodies in vitro , warranting application of this concept to in vivo models as a potential novel therapeutic approach for autoantibody-mediated diseases. Highlights ➢ Autoantibodies can have a direct pathogenic role in some autoimmune diseases. ➢ Elimination of specific B/plasma-cell clones is not attainable with current therapies. ➢ CRISPR/Cas9 allows targeting of specific DNA sites, such as V(D)J rearrangements. ➢ CRISPR/Cas9 genome-editing was very effective in knocking out the heavy chain of autoantibodies. ➢ Indels introduced at Cas9 cut site interfered with autoantibody-antigen interaction.