ScSeq of human antigen-escaping tumor variants reveals their plasma-cell-like phenotype 3687

Description Antigen escape remains a major problem of targeted immunotherapies. Following bsAb (BiTE) therapy, CD19 Ag escape occurs in > 30% of relapsing B-ALL patients. Early data from trials of CD3xCD20 bsAb revealed > 60% of relapsing patients with tumoral CD20 loss. We hypothesized that Ag- (CD19- or CD20-) tumor cells which cause relapse, might be present at low levels prior to therapy. We used an exceptional resource- single-cell suspension patient biopsies. Our screen of 20 biopsy samples revealed the presence of rare (0.1% - 2.5%) CD19- and/or CD20- negative cells in all B-NHL samples prior to any therapy. When tested in a killing assay with autologous T cells and anti-CD19 or CD20 bsAbs, only Ag- cells selectively evaded killing by the respective therapy. We characterized rare Ag- cells using scRNAseq and confirmed the existence of unique transcriptomic signatures of CD20- lymphoma cells. Unexpectedly, the CD20- cells exhibited a plasma-cell-like transcriptome. We confirmed the presence of the mRNA candidates on the protein level and have identified several targetable molecules with the most promising candidates currently being functionally validated. Lastly, we provide a comprehensive overview of pre-therapy hallmarks of Ag- tumor cells. Transcriptomic data from Ag- cells may reveal the utility or futility of current combination-targeting strategies. Therefore, characterization of the ‘escaping’ tumor cells is critical for predicting optimal partner therapies.