Insights from single-cell omics: cellular heterogeneity as a foundation of clinical outcome in chronic myeloid leukemia

The BCR::ABL1 tyrosine kinase inhibitors (TKI) in chronic myeloid leukemia (CML) represent a paradigm for molecularly targeted therapy. However, clinical outcomes (rate/depth of response, treatment-free remission [TFR], progression to blast crisis [BC]) and adverse events vary among patients. While additional somatic mutations have been invoked to explain varying clinical outcomes, we here propose a complementary perspective based on single-cell omics (sc-omics) approaches that have enabled unprecedented resolution of the cellular ecosystems, including their composition, interactions, and activity. In patients who were treatment-naïve and in chronic phase (CP), this has revealed differences in the growth-rate of BCR::ABL1+ clones, ratio of TKI-insensitive leukemic stem cells (LSC) to residual hematopoietic stem cells (HSC), and immune cell composition, factors that collectively contribute to variability in therapy efficacy. Together these findings suggest that cellular heterogeneity serves as a foundation of clinical outcome in CML. Patients who remain in CP exhibit an erythroid signature in LSC, while those progressing to BC manifest an inflammatory profile, additional mutations, and expansion of early progenitors. Deep responders with active natural killer, and regulatory T cells are more likely to sustain TFR. Similarly, the outcomes of donor lymphocyte infusion after allogeneic stem cell transplant are heterogeneous, and reflect differences in preexisting T-cell clonotypes, their expansion, and interaction with leukemic cells in responders vs nonresponders. Here, we summarize key insights from sc-omics in CML, and propose an actionable road map to further leverage these technologies. This includes mechanistically explaining heterogeneity, predicting therapy response and BC, tracking leukemogenic clones longitudinally, targeting TKI-insensitive LSC, and restoring hematopoiesis from residual HSCs.