Transcriptome Analysis Identifies a Myeloid-Like Signature in Relapsed or Refractory B-Cell Acute Lymphoblastic Leukemia Patients With Poor Response to CD19 Chimeric Antigen Receptor T Cell Therapy

Background: Relapsed or refractory B-cell acute lymphoblastic leukemia (R/R B-ALL) patients exhibit heterogeneous responses to CD19 chimeric antigen receptor T-cell (CAR-T) therapy. However, current studies primarily focus on the CAR-T cells or the leukemia blasts, and the patient's intrinsic molecular characteristics before treatment remain poorly understood. Methods: Fifteen R/R B-ALL patients enrolled in a phase II, single-arm clinical trial (NCT04684147) were stratified at a three-month landmark into 8 good responders and 7 poor responders. Clinical characteristics, genetic alterations and pre-treatment bone marrow transcriptomics were compared between groups, and an exploratory gene-expression score was derived. Results: Differential expression and enrichment analyses identified a myeloid-like signature and upregulation of myeloid-related genes in poor responders. Seven myeloid-related genes were examined in independent patient cohorts, in B-ALL cell lines and at single-cell resolution in one patient; three were expressed by the leukemic cells themselves and four predominantly by monocytes and macrophages. A separate, variance-derived seven-gene least absolute shrinkage and selection operator (LASSO) score separated response groups in the discovery cohort (apparent area under the curve, AUC 1.00), with bias-corrected and external estimates of approximately 0.57–0.59 (external cohort AUC 0.592, 95% confidence interval 0.356–0.828). Conclusions: Pre-treatment transcriptomic profiling revealed a myeloid-like signature in R/R B-ALL patients with poor CD19 CAR-T response, warranting further investigation as a candidate correlate of treatment outcome.