The novel hypomethylating agent NTX-301 reprograms epigenetic and Hippo signaling pathways and exhibits pre-clinical activity in venetoclax-resistant and TP53-mutant AML.
Jul 2026· Clinical Cancer Research· pp. OF1-OF15· 0 citations
Medicine
TL;DR
Data suggest that NTX-301 exerts potent anti-leukemia activities superior to 5-AZA and synergizes with VEN in VEN-resistant and TP53-mutant AML, in part by suppressing DNMT1 and inducing DNA damage responses and apoptosis, by inducing p53 signaling and demethylating LATS1/2, thus activating Hippo signaling.
Abstract
Background
Hypomethylating agent (HMA) and the BCL-2 inhibitor venetoclax (VEN) combinations have evolved into frontline therapies for patients with acute myeloid leukemia (AML), yielding high response rates. However, most patients ultimately relapse, particularly those with TP53 mutations. We investigated mechanisms of action and therapeutic efficacy of NTX-301, a next-generation HMA. Methods used include flow cytometry-based cell viability assays, Western blot, reverse-phase protein arrays, RNA-sequencing, CyTOF single-cell mass cytometry, and methylation profiling in various therapy-resistant AML models.
Results
We demonstrate that NTX-301 exhibits superior efficacy compared to 5-azacytidine (5-AZA) in 5-AZA or VEN-resistant AML. It synergizes with VEN in VEN- or VEN/HMA-resistant and TP53-mutant AML blasts and stem/progenitor cells (combination index<1). NTX-301 inhibits DNMT1 and increases p73, caspase-8/activated caspase-8 levels in TP53-WT and TP53-mutant AML and activates p53 signaling. It extends survival (≥45%) in both, xenograft and PDX models. Methylation profiling revealed that NTX-301 is a more targeted HMA compared to 5-AZA, enabling suppression of functionally enriched genes/pathways. Pathway analysis of 954 commonly hypomethylated genes showed profoundly greater enrichment of Hippo signaling in NTX-301-treated compared to 5-AZA-treated cells, and enrichment of insulin signaling, VEGF pathway, and cell cycle selectively in NTX-301- but not in 5-AZA-treated cells. NTX-301-mediated Hippo signaling was validated at protein levels.
Conclusion
Data suggest that NTX-301 exerts potent anti-leukemia activities superior to 5-AZA and synergizes with VEN in VEN-resistant and TP53-mutant AML, in part by suppressing DNMT1 and inducing DNA damage responses and apoptosis, by inducing p53 signaling and demethylating LATS1/2, thus activating Hippo signaling.
Hypomethylating agents (HMAs), such as azacitidine and decitabine, are widely used in elderly or medically unfit patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). However, most patients eventually develop primary or acquired resistance and outcomes following HMA failure remain poor, particularly in transplantation-ineligible patients. This study evaluated the efficacy of CDK7 inhibition as a therapeutic strategy for overcoming HMA resistance in vitro. HMA-resistant AML cells (MOLM/AZA-1 and MOLM/DEC-5) were generated to evaluate the therapeutic activity of the CDK7 inhibitor, YPN-005. Cell viability was assessed using a CellTiter-Glo assay. Western blotting was performed to examine the dysregulation of DNA methyltransferases (DNMTs) and apoptotic markers. Cell cycle distribution and apoptosis were evaluated using flow cytometry. Transcriptomic changes were analyzed using quantitative reverse transcription polymerase chain reaction. YPN-005 demonstrated potent growth-inhibitory effects in HMA-resistant AML cells, with an efficacy comparable to that observed in parental MOLM-13 cells. Mechanistically, CDK7 inhibition reduced DNMT expression and decreased the phosphorylation of RNA polymerase II (Ser2/5/7). YPN-005 significantly induced apoptosis, as evidenced by increased Annexin V positivity and the activation of PARP and caspase-3. Notably, CD40 expression was markedly upregulated at both the transcript and protein levels. CDK7 inhibition effectively induces apoptosis in HMA-resistant AML cells by suppressing RNA polymerase II phosphorylation and downregulating aberrant DNMT expression. Furthermore, the induction of CD40 suggests a potential role for CDK7 blockade in modulating immunophenotypic features. These findings support CDK7 inhibition as a promising therapeutic strategy for overcoming resistance to epigenetic therapies in patients with AML/MDS.
Bon-Kwan Koo, Eun-Ji Choi, J. Moon et al.· Blood Research· 0 citations
TP53-mutated acute myeloid leukemia (AML) has dismal outcomes with current treatments and represents a critical unmet need. TP53-mutated AML is proposed to be susceptible to immunotherapeutic approaches but, to date, there is no established immunotherapy for this sub-group. Expression of stimulator of interferon genes (STING), a key innate immune driver that activates interferon (IFN) signaling, is decreased by epigenetic silencing or mutation in many cancers, including those with TP53 mutations. Here, we report that response to the next-generation synthetic STING agonist C92 is potentiated in AML cell lines and primary cells with TP53-mutated versus wild-type (WT) cells, representing a previously undescribed vulnerability of these leukemia cells to STING small molecule therapies. Moreover, combining treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC), significantly increases STING activation, with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes. Cell death in TP53 KO versus WT AML is specifically dependent on innate immune zinc finger NFX1-type containing 1 (ZNFX1) and Z-DNA-binding protein 1 (ZBP1) driving increased cleavage and activation of Receptor-Interacting-Serine/Threonine-Protein Kinase 3 (RIPK3) and mixed lineage kinase domain-like protein (MLKL), suggesting mechanisms of necroptosis. Finally, C92 and DAC combination significantly reduces leukemia burden in humanized AML mouse models, accompanied by increased immune responses, including cytokines and cytotoxic T lymphocytes in the leukemia microenvironment. These results support development of clinical trial strategies combining STING agonists with DNMTis for patients with TP53-mutated AML. Summary TP53-mutated AML potentiates effects of novel next-generation STING agonist C92, with unique allosteric and non-cyclic dinucleotide (non-CD) mechanism of action, inducing increased STING activation and cytokine release STING agonists and DNMTis, synergistically increase STING activation with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes in TP53-mutated AML STING agonists induce necroptosis via a STING-ZNFX1-ZBP1-necroptosis axis in TP53-mutated AML. This drug combination reduces leukemia burden, activates immune responses in AML models and supports translation for high-risk AML patients. Statement of Translational Relevance This pre-clinical study identifies a novel therapeutic vulnerability in (TP53)-mutated acute myeloid leukemia (AML), a poor prognosis subtype with a critical unmet need. Novel next-generation STING agonist C92, with unique allosteric and non-cyclic dinucleotide (non-CD) mechanism of action, induces increased STING activation and cytokine release, compared with WT TP53 in AML cell lines and primary cells, and has superior STING activity with respect to several STING agonists currently in clinical studies. Combining C92 treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC) synergistically increases STING activation, with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes, driving ZNFX1-driven inflammatory necroptotic cell death. Utilizing humanized mouse models, C92 in combination with DAC significantly reduces leukemia burden and enhances cytotoxic T-cell responses in the tumor microenvironment, supporting clinical translation for high-risk AML patients.
K. Tripathi, Lora Stojanovic, Zahra Gohari et al.· bioRxiv· 0 citations
PURPOSE
To investigate novel combination strategies for TP53-mutated acute myeloid leukemia (AML), focusing on the potential synergy between PI3Kγ inhibition and Azacitidine, and to elucidate the underlying molecular mechanisms.
MATERIALS AND METHODS
We detected the expression of PI3Kγ (PIK3CG/PIK3R5) in TP53 mutant and wildtype AML cell lines using the CCLE database, RT-qPCR, and western blot. We evaluated the influence of Azacitidine (AZA) and PI3Kγ inhibitor (Eganelisib) in AML cells, conducted in vivo combination therapy experiments, and identified synergistic targets through RNA sequencing and siRNA technology.
RESULTS
TP53-mutated AML showed hypermethylation of PI3Kγ promoters and reduced PI3Kγ expression. AZA treatment selectively activated the PI3Kγ signaling in TP53-mutated cells. Eganelisib combined with AZA demonstrated potent synergy, suppressing proliferation and inducing apoptosis in TP53-mutated AML (ZIP synergy score > 10). This combination extended survival in xenograft models (33.0 vs. 18.0 days, p < 0.01). RNA-seq identified serglycin (SRGN) as a candidate mediator potentially linking AZA-induced transcriptional reprogramming to ROS-mediated cell death. SRGN knockdown elevated ROS levels and sensitized cells to AZA. The combinatorial treatment significantly increased ROS levels compared to monotherapy.
CONCLUSION
We provide the first preclinical evidence that PI3Kγ inhibition sensitizes TP53-mutated AML to AZA through a mechanism potentially involving the SRGN-ROS axis, offering a translatable combinatorial strategy for patients with this aggressive leukemia subtype.
Acute myeloid leukemia/myelodysplastic syndromes (AML/MDSs) carrying p53 mutations are refractory to various standard therapies. Arsenic trioxide (ATO) may be effective in restoring function to p53 structural mutants. Here, we report that mutant p53 rescued by ATO treatment strengthened interferon responses triggered by the DNA hypomethylating agent decitabine by transactivating interferon regulatory factor 7 (IRF7) directly. Decitabine also increased the transactivation activity of ATO-rescued mutant p53 by inducing p53-serine-20 phosphorylation and blocking p53-inhibitory mouse double minute 2 homolog (MDM2). ATO and decitabine together killed p53-mutant AML cells and suppressed tumor growth in cell line-derived xenografts. In a first-in-human pilot clinical trial for testing the combination of ATO and decitabine (PANDA-T0 trial, NCT03855371), which enrolled five patients with AML/MDS harboring p53 structural mutations, the ATO and decitabine regimen produced manageable adverse events, and four of the five treated patients achieved complete remission at the level of the bone marrow, associated with p53 activation and interferon response. In 103 p53-mutant patients whose samples were deposited in Ruijin AML/MDS sample repository, 48 distinct p53 missense mutants were identified, 21 of which were classified as ATO and decitabine regimen applicable because of their competencies in activating p53 and interferon responses upon cotreatment. This study establishes an alternative treatment regimen for patients with p53-mutant AML/MDS and provides a proof-of-concept framework for p53-targeted therapy that differentiates between p53 mutations.
TP53-mutated acute myeloid leukemia (AML) is associated with an extremely poor prognosis and is refractory to conventional chemotherapy and allogeneic hematopoietic stem cell transplantation (allo-HSCT). We identified high expression of lysine demethylase 4C (KDM4C) in AML, particularly in TP53-mutated AML. Pharmacological inhibition of KDM4C with QC6352 predominantly induced apoptosis in TP53-wild-type AML cells, whereas it caused limited apoptosis but pronounced senescence and growth arrest in TP53-mutated AML cells. In TP53-mutated AML cells, QC6352 induced senescence-associated cytosolic DNA accumulation and activated the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, leading to the upregulation of NK cell-activating ligands and enhancing NK cell-mediated cytotoxicity. In vivo, QC6352 effectively attenuated AML progression, and its combination with NK cell therapy further reduced leukemic burden and prolonged survival in mice. Collectively, these findings demonstrate that pharmacological KDM4C inhibition with QC6352 induces cellular senescence and enhances the intrinsic immunogenicity of TP53-mutated AML cells through activation of the cGAS-STING pathway. The study supports KDM4C inhibition as a potential therapeutic strategy for TP53-mutated AML, particularly in patients receiving NK cell-based immunotherapy or undergoing allo-HSCT.
Xinyi Zhang, Huilan Liu, L. Geng et al.· Aging and Disease· 0 citations
Highlights What are the main findings? CDK8 inhibition reduced STAT5 S726/731 phosphorylation and promoted differentiation-associated changes in an LSC-enriched TEX cell line AML model. CDK8–BET co-inhibition showed context-dependent synergy in AML cell lines and PDX-derived models. What are the implications of the main findings? CDK8 supports transcriptional and metabolic programs associated with immature AML states. CDK8–BET co-inhibition merits biomarker-guided preclinical evaluation. Abstract Acute myeloid leukaemia (AML) is a therapeutically challenging malignancy driven by the self-renewal, quiescence, and therapy resistance of leukaemic stem cells (LSCs). CDK8, a kinase component of the Mediator complex, regulates oncogenic transcription, and the selective CDK8/CDK19 inhibitor RVU120 (Romaciclib) targets AML cells with CD34+/pSTAT5-high LSC-like characteristics; however, the epigenetic and transcriptional consequences of CDK8 blockade and actionable combinatorial strategies remain incompletely defined. Using the TEX cell line, an LSC-enriched surrogate model, we performed time-resolved RNA-seq, whole-proteome and phosphoproteomics mass spectrometry (MS), and CUT&Tag chromatin profiling following treatment with RVU120 and CCT251921. CDK8 protein–protein interactions were mapped by co-immunoprecipitation MS across five AML models, and synergy with Pelabresib (BET inhibitor) or CB6644 (RUVBL1/2 inhibitor) was assessed by high-content screening in three cell lines and three patient-derived xenograft (PDX) models. Both inhibitors suppressed STAT5 phosphorylation, induced loss of the CD34+/CD38− LSC-enriched phenotype, and drove erythromegakaryocytic differentiation. Transcriptomic and proteomic responses were concordant, and CDK8 inhibition triggered widespread enhancer activation with redistribution of RNAP2, BRD3, and NFRKB. CDK8 combined with Pelabresib acted synergistically in MOLM-16 cells and two of three PDX models. These findings identify CDK8 as a transcriptional node of LSC-associated programs and provide a mechanistic rationale for combined CDK8-BET inhibition in molecularly defined AML subsets, which will require validation in functional LSC assays and primary specimens.
M. Statkiewicz, I. Rumieńczyk, U. Pakulska et al.· Cells· 0 citations
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