Pharmacological SOS1 inhibitor BI-3406 synergizes with BCR::ABL1 TKIs reducing leukemia stem cells and overcoming imatinib resistance in CML

Disease persistence and resistance remain major challenges in chronic myeloid leukemia (CML). We evaluated pharmacological SOS1 inhibition with BI-3406, alone or in combination with BCR::ABL1 tyrosine-kinase inhibitors (TKI), across complementary preclinical models. In p210 BCR/ABL transgenic mice, BI-3406 plus imatinib was well-tolerated, markedly prolonged survival, improved hematologic indices, reduced splenomegaly, and decreased bone-marrow LSK/hematopoietic stem and progenitor cells compared to either agent alone. In human CML cell lines and primary patient-derived bone-marrow cells, combined therapeutic treatments with BI-3406 and imatinib (standard of care BCR-ABL TKI) or next-generation TKIs showed strong synergistic suppression of cellular proliferation and increased apoptosis relative to single-agent treatment. Remarkably, drug combinations containing BI-3406 also restored TKI sensitivity to primary bone-marrow cell samples derived from a variety of CML patients that had been initially identified as clinically resistant to imatinib. Mechanistically, BI-3406 attenuated RAS/RAC-ERK/AKT signaling, while SOS1 knockdown phenocopied BI-3406-mediated imatinib sensitization, supporting an on-target SOS1-dependent therapeutic effect. Upregulation of the membrane transport protein SLC22A4 following combination treatment may contribute to the rescued TKI sensitivity but is probably not the sole underlying mechanism as BI-3406+imatinib retained strong synergistic activity despite SLC22A4 knockdown. Comparison of the transcriptomic profiles revealed that the combined BI-3406+imatinib drug regimen triggered the strongest repression of oncogenic, metabolic and stemness-associated transcriptional programs in treated CML cells. Consistently, serial replating MethoCult assays functionally confirmed the impairment of clonogenic self-renewal capacity and the depletion of murine LSK and human Lin⁻CD34⁺CD38⁻ stem/progenitor-enriched compartments after dual SOS1 and BCR::ABL1 inhibition. Our data support SOS1 targeting as a rational therapeutic strategy to potentiate TKI efficacy, impair CML stem/progenitor self-renewal, and restore drug responsiveness in clinically relevant TKI-resistant settings.