CD19-negative relapse after CAR-T cell therapy: mechanisms of antigen escape and lineage switch

CD19 chimeric antigen receptor (CAR)-T cell therapy has transformed the treatment of relapsed/refractory B-cell malignancies, achieving high remission rates. Nonetheless, 20%-40% of patients eventually relapse, classified as either CD19⁺ or CD19^- relapse. Most relapses are CD19⁺, largely due to reduced potency and poor persistence of CAR-T cells after infusion. In contrast, a substantial fraction of patients develops CD19^- relapse driven by selective pressure from CAR-T cell therapy. Post-CAR-T cell CD19^- relapse primarily arises through three mechanisms. First, pre-existing CD19^- subclones, particularly those with progenitor-like features, expand because of their survival advantages. Second, CD19 expression is downregulated through pre-existing or newly acquired genetic alterations (mutations and abnormal splicing), epigenetic silencing, and post-transcriptional dysregulation. Third, lineage switching to a myeloid phenotype increases notably after CAR-T cell treatment. This myeloid conversion is frequently associated with KMT2A rearrangements and is driven by epigenetic reprogramming, impaired expression of B-cell regulators, and the presence of bipotent progenitors within leukemia or lymphoma. CD19^- relapse constitutes a major clinical barrier to the durable efficacy of CD19-CAR T-cell therapy. Understanding these diverse escape mechanisms is crucial for developing preventive strategies and effective salvage therapies to maintain long-term remission. To mitigate CD19^- relapse, a coordinated dual strategy is needed. First, novel therapeutic approaches should be developed, including CAR products targeting alternative antigens, optimized salvage regimens, and CD19 re-induction strategies. Second, high-resolution molecular profiling should be used to identify high-risk patients and guide pre-emptive or combinatorial interventions based on the molecular underpinnings of CD19^- relapse. Together, these approaches will deepen mechanistic insight into CD19^- relapse and enable targeted prevention and management of this key limitation of CAR T-cell therapy.