SR-1, a monoclonal antibody targeting KIT, blocks binding of its ligand SCF and is being explored clinically as briquilimab, a humanized aglycosylated form. Unlike Fab-79D, another KIT-targeting antibody, SR-1 inhibits hematopoietic progenitor cell expansion at more than a tenfold lower concentration, underscoring its potent antagonistic activity. However, SR-1 does not recognize mouse KIT, necessitating precise epitope mapping to engineer resistance mutations.

Through a series of human-mouse KIT chimeras replacing each extracellular domain (ECD), the SR-1 epitope was localized to ECD2. Subsequent fine mapping confined binding to a nine-amino acid segment between positions 118 and 127. A degenerate codon library targeting this region enabled screening for point mutations abolishing SR-1 binding but preserving receptor functionality.

Deep sequencing of sorted cell populations identified key substitutions at residues 121 and 123. Experimental validation revealed two mutants, D121L and S123P, which effectively disrupt SR-1 recognition without compromising SCF affinity or receptor-mediated signaling. Notably, S123P corresponds to a naturally occurring mouse orthologue residue.

Affinity assays confirmed near-total loss of SR-1 binding in D121L variants, while S123P mutants retained partial interaction only at high antibody concentrations. Crucially, these alterations maintained SCF binding kinetics comparable to wild-type KIT and supported normal SCF-driven proliferation in Ba/F3 murine cells engineered to express the human variants.

The team introduced the S123P mutation into human hematopoietic stem and progenitor cells via base editing. When co-cultured with wild-type controls under SR-1 treatment, S123P-edited cells exhibited a competitive growth advantage, highlighting the mutation’s protective effect. Encouragingly, in vivo experiments demonstrated selective enrichment of S123P-modified cells within human grafts in mouse models after SR-1 administration.

Furthermore, the enhanced conditioning regimen facilitated improved engraftment levels and lineage output in bone marrow without detectable detriment to hematopoietic subsets. These findings position targeted KIT epitope editing as a viable strategy for achieving higher chimerism and safer transplantation by circumventing genotoxic approaches.

This work exemplifies precision editing of immune epitopes to fine-tune therapeutic antibody interactions, potentially transforming hematopoietic stem cell transplantation protocols. By preventing antibody-mediated depletion while retaining physiological receptor functions, such innovations could minimize conditioning toxicity and improve clinical outcomes.

Subject of Research: Hematopoietic stem cell transplantation, antibody resistance, KIT receptor, epitope editing, SCF-KIT interaction

Article Title: Non-genotoxic transplantation and in vivo selection through epitope editing

Article References:
Casirati, G., Cosentino, A., Freschi, M. et al. Non-genotoxic transplantation and in vivo selection through epitope editing. Nature (2026). https://doi.org/10.1038/s41586-026-10737-8

DOI: https://doi.org/10.1038/s41586-026-10737-8