Chromatin remodeler SATB2 thorough Bmi1/PRC1 activity controls transformation and reprogramming of ph+ B-cell progenitors

Abstract B-cell progenitor acute lymphoblastic leukemia (B-ALL) remains a high-mortality malignancy (~40%), despite the advent of allogeneic hematopoietic stem cell transplantation, tyrosine kinase inhibitors (TKIs) and chimeric antigen receptor T cell therapies. Particularly, Ph⁺ and Ph-like B-ALL subtypes, with IKZF1 alterations and overexpression/activation of Polycomb Repressive Complex 1 (PRC1) associated genes exhibit the highest risk of refractoriness and relapse. These phenotypes are driven by epigenetic reprogramming that confers B-cell progenitors with stem-like properties, enhanced self-renewal, and differentiation arrest. We have previously shown that the chromatin organizer SATB2, a downstream target of BCR-ABL/aPKCι/Rac GTPase/MEK/ERK signaling, is upregulated during blastic transformation and contributes to progression to B-ALL (Nayak et al., Nat Commun 2019). Separately, we identified BMI1/PRC1 activation as a key driver of leukemogenesis and therapy resistance in B-ALL (Sengupta et al., Blood 2012; Nayak et al., Nat Commun 2022). However, the upstream regulatory networks governing BMI1/PRC1 activation, chromatin remodeling, and lineage reprogramming in leukemic initiating cells (LICs) remain poorly understood. We hypothesize that SATB2 orchestrates the epigenetic and transcriptional programs that govern transformation of Ph⁺ B-cell progenitors into LICs, in part through regulation of BMI1/PRC1. To test this hypothesis, we utilized a conditional Satb2 knockout mice (Mx1-Cre; Satb2fl/fl) combined with retroviral p190 BCR-ABL transduction/transplantation to generate a murine Ph⁺ B-ALL model. Additionally, we performed SATB2 knockdown in human Ph⁺ B-ALL cell lines and leukemic cells from patient-derived xenografts (PDX) to assess its role in human disease. Integration of SATB2 chromatin immunoprecipitation (ChIP) sequencing with RNA sequencing revealed that SATB2 expression is elevated in both murine and human Ph⁺ and Ph-like B-ALL. We found that SATB2 deletion significantly impaired B-ALL development (median survival: 92 vs. 40 days; P<0.01), reduced colony formation, and promoted B-cell differentiation (Immature B-cells: 45% ± 4.8% vs. 10% ± 3.1% in WT). In the absence of BCR-ABL, normal B-cell development was preserved, indicating SATB2 is dispensable for homeostatic lymphopoiesis. Mechanistically, SATB2 chromatin binding revealed occupancy at both promoter and enhancer regions of hematopoietic and lymphoid regulators including Sox4, Lef1, and Bmi1, functioning as a transcriptional activator, while repressing non-hematopoietic lineage programs. The reintroduction of SATB2 or its target genes (Sox4, Lef1) in SATB2-deficient B-ALL progenitors restored clonogenic potential. SATB2 directly binds the Bmi1 locus, and its deficiency resulted in ~75% decrease in Bmi1 expression and ~60% reduction in PRC1 activity (measured via H2AK119ub1 levels). Ectopic Bmi1 expression rescued leukemogenesis, differentiation arrest, and serial replating in Satb2-deficient cells and SATB2-deficient Ph⁺ B-cell leukemic progenitors showed enhanced sensitivity to both TKIs and Bmi1 inhibitors, highlighting potential for therapeutic synergy. In summary, our results define SATB2 as a central chromatin regulator in Ph⁺ B-ALL that enables leukemic reprogramming by activating self-renewal and lymphoid transcriptional programs while repressing lineage-inappropriate genes. SATB2-driven activation of BMI1/PRC1 establishes a key epigenetic axis sustaining LIC identity and therapy resistance. These findings position the SATB2-BMI1/PRC1 pathway as a novel, targetable epigenetic vulnerability that could be exploited in combinatorial therapies with TKIs for high-risk Ph⁺ B-ALL.