Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma [scRNA-seq]

Tumor intrinsic adaptations with emerging resistant clones following T cell targeted immunotherapies pose a major barrier to durable remissions in multiple myeloma (MM). Through integrated genomic, transcriptomic, and epigenomic interrogation of clonal plasma cells, we observed antigenic drift in 68.4% of relapsed cases following anti-GPRC5D T cell engager (TCE) therapy. These escape events were driven by three distinct mutational mechanisms involving i) focal to large biallelic deletions at the GPRC5D gene locus, ii) monoallelic deletion coupled with GPRC5D single nucleotide variants (SNVs) or insertions/deletions (indels) on the remaining allele, as well as iii) epigenetic GPRC5D promoter/enhancer silencing. Beyond biallelic deletions resulting in complete antigenic loss, we demonstrate that GPRC5D SNVs and indels mutate anti-GPRC5D TCE binding epitopes or more commonly affect G-protein couple receptor family conserved motifs critical for protein membrane trafficking resulting in endoplasmic reticulum (ER) GPRC5D trapping. Multiple subclones bearing distinct genomic alterations at GPRC5D locus co-emerged within individual cases, depicting their convergent evolutionary trajectories. Importantly, anti-GPRC5D TCEs with varying epitope specificity, affinity, and valency differentially targeted mutant subclones, underscoring their non-redundant functional roles in overcoming resistance Overall design: Experiments were conducted on primary patient bone marrow samples, after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Unbiased mRNA profiling were conducted by using scRNA-seq from the GemCode system (10x Genomics) accordingly to the manufacturer's protocols. Single cell library preparation of CD138+ were carried out on the Chromium platform (10x Genomics) using the Single Cell 3' reagent kits v3 according to the manufacturer's protocol. Samples were processed with CellRanger suite v7.1.0 against the human reference genome GRCh38 with default parameters