BCR repertoire analysis and cloning of antibody candidates targeting native and Asp7-isomerized β-amyloid

Abstract

Computational approaches are increasingly used to prioritize monoclonal antibody (mAB) candidates from BCR-seq datasets. However, the reliable identification of B cells encoding antibodies against rare antigenic epitopes remains challenging. We employed a repertoire-guided workflow combining antigen-tetramer sorting of B cells from immunized mice, followed by low-input bulk BCR-seq, which yielded informative clonal repertoires. Clustering analysis allowed us to prioritize IGH and IGK clonotypes potentially targeting {beta}-amyloid and the isoAsp7 proteoform (isoD7-A{beta}1-16), implicated in Alzheimer's disease. We observed recurrent IGHV8-12 and IGKV1-117 usage, consistent with canonical mouse anti-A{beta} responses. Focusing on isoD7-A{beta} -associated candidates, we selected fourteen candidate IGH--IGK combinations for recombinant expression including variants containing IGKV8-21, IGKV8-19, IGKV2-112 together with IGHV1-75, IGHV10-1 or IGHV8-12. Several recombinant mABs showed detectable binding activity to isoD7-A{beta}, including a candidate with preferential recognition of isoD7-A{beta}, supporting the feasibility of the approach but underscoring the challenge of accurate chain pairing. These results provide proof of principle that repertoire-guided analysis can prioritize candidate IGH and IGK chains and propose possible heavy-light chain combinations based on their co-representation across samples while experimental testing remains necessary to identify antibodies with preferential recognition of isoD7-A{beta}.