Therapy-induced senescence reprograms non-M3 AML into a drug-exploitable APL-like state

Abstract

Abstract Cellular senescence is a dynamic cancer cell condition with both tumor-suppressive and relapse-promoting features. While terminating cell proliferation, it may sustain disease persistence through its senescence-associated secretory phenotype (SASP), immune alteration, and stem-like reprogramming. Here, we identify therapy-induced senescence (TIS) as a unifying, plastic state across newly diagnosed (nd), genetically diverse non-M3 acute myeloid leukemias (AML) that reprograms blasts towards an acute promyelocytic leukemia (APL)-like phenotype with distinct plasticity-related therapeutic vulnerabilities. We established a short-term ex vivo chemotherapy assay to quantify the patient-individual TIS capacity of primary AML blasts by fluorescent senescence-associated β-galactosidase activity, further characterized by p16INK4a expression, Ki67 loss, and H3K9me3 heterochromatin remodeling. Like daunorubicin or cytarabin, hypomethylating agents, hydroxyurea, and anti-CD33 antibody-drug conjugates also triggered TIS to varying extents, showing that diverse agents converge on senescence and prime AML cells for potential senolytic elimination. Probing baseline transcriptomes of nd AML samples by an AML TIS-high signature of the top-100 differentially expressed genes failed to stratify outcomes across TCGA (n=172), OHSU Beat AML (n=405), and MLL Munich Leukemia Laboratory (n=433) cohorts. Unexpectedly, a 13-gene subclassifier, determined by unsupervised cluster analysis of the top-100 genes and unrelated to the M3-typical t(15;17) PML::RARA translocation, identified 65 of 67 genetically defined APL cases across these nearly 1,000 all-subtype AML transcriptomes, suggesting that TIS rendered non-M3 AML APL-like. Multi-omic analyses including bulk and single-cell RNA sequencing plus PRC2/SUZ12 and H3K27me3 ChIP-seq unveiled TIS-related loss of polycomb repression, epigenetic remodeling, and transcriptional reprogramming, yet independent of PML::RARA, as the underlying molecular mechanism. Functionally, TIS-associated APL-like plasticity conferred sensitivity to differentiation therapies such as all-trans retinoic acid (ATRA) and histone deacetylase inhibitors, and to Bcl2-targeting agents with senolytic activity. Patient-derived xenograft models validated these vulnerabilities as sequential TIS followed by senescence targeting achieved durable control exclusively in models able to mount a senescence response. Given the biologically unifying and ATRA-sensitizing role of TIS-associated M3-like plasticity, we assessed its clinical relevance in three independent cohorts totaling 92 newly diagnosed patients. TIS capacity at diagnosis robustly stratified outcomes, predicted superior disease-free and overall survival, and was associated with favorable ELN classification, normal cytogenetics, and NPM1 or DNMT3A mutations, while being lowest in adverse-risk SRSF2-mutant AML. Our findings uncover TIS-related M3-like plasticity as a novel state exploitable by a two-punch strategy of senesence induction first followed by targeted interventions through pro-differentiation or senolytic approaches, establishing a new therapeutic paradigm with immediate clinical potential and broader relevance to other malignancies where therapy-induced plasticity dictates outcome.