Live-cell Pick-Seq (LiP-Seq):Interrogating extremely rare mantle cell lymphoma MRD after CD19-targeted CAR T-cell therapy

Most patients with leukemia or lymphoma achieve remission after treatment but many will relapse due to minimal residual disease (MRD). The limited sensitivity of current techniques for characterizing ultra-rare cells has largely prevented the development of informed strategies to eradicate MRD. Here we developed Live-cell Pick-Seq (LiP-Seq), an advanced platform leveraging multiplexed live-cell imaging to identify and retrieve single tumor cells, enabling the isolation of viable lymphoma MRD cells present at <10-6 for single-cell RNA-sequencing. We next applied LiP-Seq in a clinical MRD setting. We collected 44 paired peripheral blood samples from 11 MCL patients collected at multiple timepoints before and after treatment with CD19-directed CAR T-cell therapy (brexucabtagene autoleucel). All achieved complete remission by PET-CT. Our results provide a first characterization of ultra-rare MRD cells using LiP-Seq, paving the way for precision approaches to prevent relapse.