Single-Cell proteomics discerns patient-specific subpopulations in pediatric B-cell acute lymphoblastic leukemia

B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer, representing ∼30% of pediatric cancers and ∼80-85% of pediatric ALL cases. Despite high remission rates, relapse remains a major challenge, often driven by therapy-resistant subpopulations, which are masked in bulk analysis, thus limiting our understanding of disease progression and optimal therapeutic intervention. Precision oncology enables proteome-level characterization of patient specific cancer samples and their subpopulations, essential for improving prognostic accuracy and individualized therapies. Single-cell proteomics by mass spectrometry (SCP-MS) enables quantification of hundreds to thousands of proteins at single cell level, uncovering cellular programs that may contribute to minimal residual disease (MRD) and relapse. Here, employing single-cell sorting of leukemic cells coupled with high-sensitivity SCP-MS, we profile individual leukemic blasts and normal immature B-cells from pediatric B-ALL bone marrow aspirates alongside age-matched controls. SCP-MS deconvoluted cellular heterogeneity and revealed subpopulations with variable leukemia-marker expression, highlighting its potential for early detection of relapse-prone phenotypes and personalized pediatric therapy.