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Many cancer therapies induce high response rates, with some resulting in undetectable disease as assessed using standard clinical assays. This is particularly true in leukemia and lymphoma, where patients often achieve deep remission yet ultimately suffer relapse. This highlights a critical need to better understand the ultra-rare persistent cells that survive therapy but remain inaccessible to current techniques. Here we developed Live-cell Pick-Seq (LiP-Seq), an advanced platform leveraging multiplexed live-cell imaging to identify and retrieve individual target cells for downstream analysis. LiP-Seq enables high-resolution transcriptomic profiling of single, viable lymphoma cells present at frequencies as low as 10-6, providing a technological window into the biology of these elusive reservoirs. Applying this method to mantle cell lymphoma (MCL) patients following CD19 CAR-T cell therapy, we identified a recurrent upregulation of the immune modulator IFITM2 in the persistent cell fraction. Functional validation demonstrated that IFITM2 overexpression conferred protection against CAR T-cell cytotoxicity in vitro, implicating it as a potential survival mechanism under therapeutic pressure. Our results provide a first transcriptomic characterization of viable, ultra-rare persistent cells via LiP-Seq, establishing a new paradigm for identifying and targeting features that may enable treatment evasion.