DNTTIP1 drives leukaemogenesis through MiDAC-mediated epigenetic silencing of BMF

Abstract

Background: Acute leukaemia is a highly aggressive malignancy with significant unmet therapeutic needs, partly due to epigenetic dysregulation. Here, we uncover deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1) within the mitotic deacetylase complex (MiDAC) as a previously unrecognised epigenetic regulator crucial for leukaemic cell survival and elucidate its mechanistic and translational significance.

Methods: Using cellular, biochemical, and genetic perturbations, coupled with validation in multiple in vivo leukaemia mouse models, we characterised DNTTIP1's role in acute leukaemia. An integrated multi-omics analysis incorporating RNA-seq, cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) revealed that DNTTIP1 recruits histone deacetylase 1/2 (HDAC1/2) to silence BCL2-modifying factor (BMF) and drive leukaemogenesis, validated by chromatin immunoprecipitation quantitative PCR (ChIP-qPCR). Drug synergy assays identify poly(ADP-ribose) polymerase (PARP)/HDAC/BCL2 inhibitor combinatorial efficacy.

Results: DNTTIP1 depletion impaired MiDAC recruitment in acute leukaemia, leading to histone H3 lysine 27 (H3K27) hyperacetylation at the BMF promoter and reactivating this effector. Upregulated BMF disrupted BCL2-mediated survival, triggering coordinated autophagy and apoptosis. Combined HDAC1/2 and BCL2 inhibition exerts synergistic anti-leukaemic effects, a therapeutic strategy currently under clinical evaluation. Further, PARP inhibition profoundly enhanced this synergy by impairing DNA damage repair, unveiling a novel triple-combination strategy.

Conclusions: Our work defines the DNTTIP1‒HDAC1/2‒BMF axis as a pivotal epigenetic vulnerability in acute leukaemia and provides preclinical rationale for targeting this axis. These findings offer a validated biological framework for advancing this targeted combination therapy into clinical trials.

Keywords

acute leukaemia / apoptosis / autophagy / BMF / DNTTIP1 / MiDAC

References

[1] Lhermitte L, Barreau S, Morf D, et al. Automated identification of leukocyte subsets improves standardization of database-guided expert-supervised diagnostic orientation in acute leukemia: a EuroFlow study. Modern Pathol. 2021; 34(1): 59-69.

[2] Zhao A, Zhou H, Yang J, Li M, Niu T. Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther. 2023; 8(1): 71.

[3] Fong CY, Morison J, Dawson MA. Epigenetics in the hematologic malignancies. Haematologica. 2014; 99(12): 1772-1783.

[4] Hu D, Shilatifard A. Epigenetics of hematopoiesis and hematological malignancies. Genes Dev. 2016; 30(18): 2021-2041.

[5] Asmamaw MD, He A, Zhang L-R, Liu H-M, Gao Y. Histone deacetylase complexes: structure, regulation and function. Biochim Biophys Acta Rev Cancer. 2024; 1879(5):189150.

[6] Mustafa AM, Krämer OH. Pharmacological modulation of the crosstalk between aberrant janus kinase signaling and epigenetic modifiers of the histone deacetylase family to treat cancer. Pharmacol Rev. 2023; 75(1): 35-61.

[7] Stomper J, Rotondo JC, Greve G, Lübbert M. Hypomethylating agents (HMA) for the treatment of acute myeloid leukemia and myelodysplastic syndromes: mechanisms of resistance and novel HMA-based therapies. Leukemia. 2021; 35(7): 1873-1889.

[8] Kantarjian H, Borthakur G, Daver N, et al. Current status and research directions in acute myeloid leukemia. Blood Cancer J. 2024; 14(1): 163.

[9] Fischer MA, Mustafa AM, Hausmann K, et al. Novel hydroxamic acid derivative induces apoptosis and constrains autophagy in leukemic cells. J Adv Res. 2024; 60: 201-214.

[10] Mustafa AM, Petrosino G, Fischer MA, et al. The deacetylases HDAC1/HDAC2 control JAK2(V617F)-STAT signaling through the ubiquitin ligase SIAH2. Signal Transduct Target Ther. 2025; 10(1): 275.

[11] Zhou L, Ruvolo VR, McQueen T, et al. HDAC inhibition by SNDX-275 (Entinostat) restores expression of silenced leukemia-associated transcription factors Nur77 and Nor1 and of key pro-apoptotic proteins in AML. Leukemia. 2013; 27(6): 1358-1368.

[12] Zhang MC, Fang Y, Wang L, et al. Clinical efficacy and molecular biomarkers in a phase II study of tucidinostat plus R-CHOP in elderly patients with newly diagnosed diffuse large B-cell lymphoma. Clin Epigenet. 2020; 12(1): 160.

[13] Carlos J, Tavares MT, Lima K, et al. Enhancing venetoclax efficacy in leukemia through association with HDAC inhibitors. Cell Death Discov. 2025; 11(1): 147.

[14] Verbeek T, Vrenken KS, Arentsen-Peters S, et al. Selective inhibition of HDAC class IIA as therapeutic intervention for KMT2A-rearranged acute lymphoblastic leukemia. Commun Biol. 2024; 7(1): 1257.

[15] Yang L, Qiu Q, Wang J, et al. Preclinical and first-in-human of purinostat mesylate, a novel selective HDAC I/IIb inhibitor, in relapsed/refractory multiple myeloma and lymphoma. Signal Transduct Target Ther. 2025; 10(1): 201.

[16] Gallinari P, S DiMarco, Jones P, Pallaoro M, Steinkuhler C. HDACs, histone deacetylation and gene transcription: from molecular biology to cancer therapeutics. Cell Res. 2007; 17(3): 195-211.

[17] Barrett AK, Shingare MR, Rechtsteiner A, et al. HDAC activity is dispensable for repression of cell-cycle genes by DREAM and E2F:rB complexes. Nat Commun. 2024; 15(1): 4450.

[18] Lee K, Whedon SD, Wang ZA, Cole PA. Distinct biochemical properties of the class I histone deacetylase complexes. Curr Opin Chem Biol. 2022; 70:102179.

[19] Bantscheff M, Hopf C, Savitski MM, et al. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat Biotechnol. 2011; 29(3): 255-265.

[20] Yamashita N, Shimazaki N, Ibe S, et al. Terminal deoxynucleotidyltransferase directly interacts with a novel nuclear protein that is homologous to p65. Genes Cells. 2001; 6(7): 641-652.

[21] Turnbull RE, Fairall L, Saleh A, et al. The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat Commun. 2020; 11(1): 3252.

[22] Li Y, Meng R, Li S, et al. The ZFP541‒KCTD19 complex is essential for pachytene progression by activating meiotic genes during mouse spermatogenesis. J Genet Genomics. 2022; 49(11): 1029-1041.

[23] Zhang Y, Wang Z, Huang Y, et al. TdIF1: a putative oncogene in NSCLC tumor progression. Signal Transduct Target Ther. 2018; 3: 28.

[24] Ding S, Gao Y, Lv D, et al. DNTTIP1 promotes nasopharyngeal carcinoma metastasis via recruiting HDAC1 to DUSP2 promoter and activating ERK signaling pathway. EBioMedicine. 2022; 81:104100.

[25] Huang DC, Strasser A. BH3-only proteins—essential initiators of apoptotic cell death. Cell. 2000; 103(6): 839-842.

[26] Puthalakath H, Villunger A, O'Reilly LA, et al. Bmf: a proapoptotic BH3-only protein regulated by interaction with the myosin V actin motor complex, activated by anoikis. Science. 2001; 293(5536): 1829-1832.

[27] Moldoveanu T, Follis AV, Kriwacki RW, Green DR. Many players in BCL-2 family affairs. Trends Biochem Sci. 2014; 39(3): 101-111.

[28] Pattingre S, Tassa A, Qu X, et al. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell. 2005; 122(6): 927-939.

[29] Mariño G, Niso-Santano M, Baehrecke EH, Kroemer G. Self-consumption: the interplay of autophagy and apoptosis. Nat Rev Mol Cell Biol. 2014; 15(2): 81-94.

[30] Jung YY, Ahn KS, Shen M. Unveiling autophagy complexity in leukemia: the molecular landscape and possible interactions with apoptosis and ferroptosis. Cancer Lett. 2024; 582:216518.

[31] Zhou Y, Tao L, Qiu J, et al. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther. 2024; 9(1): 132.

[32] Tang L, Zhang H, Zhou F, et al. Targeting autophagy overcomes cancer-intrinsic resistance to CAR-T immunotherapy in B-cell malignancies. Cancer Commun. 2024; 44(3): 408-432.

[33] Fan H, Lu J, Guo Y, et al. BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis. Nat Genet. 2020; 52(12): 1384-1396.

[34] Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013; 14: 7.

[35] Mondal B, Jin H, Kallappagoudar S, et al. The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth. Elife. 2020; 9:e57519.

[36] Wachholz V, Mustafa A-HM, Zeyn Y, et al. Inhibitors of class I HDACs and of FLT3 combine synergistically against leukemia cells with mutant FLT3. Arch Toxicol. 2021; 96(1): 177-193.

[37] Pons M, Zeyn Y, Zahn S, et al. Oncogenic kinase cascades induce molecular mechanisms that protect leukemic cell models from lethal effects of de novo dNTP synthesis inhibition. Cancers. 2021; 13(14): 3464.

[38] Itoh T, Fairall L, Muskett FW, et al. Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting. Nucleic Acids Res. 2015; 43(4): 2033-2044.

[39] Kantarjian HM, DiNardo CD, Kadia TM, et al. Acute myeloid leukemia management and research in 2025. CA Cancer J Clin. 2025; 75(1): 46-67.

[40] Kantarjian H, Aldoss I, Jabbour E. Management of adult acute lymphoblastic leukemia: a review. JAMA Oncol. 2025; 11(7): 771-778.

[41] Péterffy B, Krizsán S, Egyed B, et al. Molecular profiling reveals novel gene fusions and genetic markers for refined patient stratification in pediatric acute lymphoblastic leukemia. Mod Pathol. 2025; 38(6):100741.

[42] Chow RD, Velu P, Deihimi S, et al. Persistent postremission clonal hematopoiesis shapes the relapse trajectories of acute myeloid leukemia. Blood Adv. 2025; 9(8): 1888-1899.

[43] Ibrahim HS, Guo M, Hilscher S, et al. Probing class I histone deacetylases (HDAC) with proteolysis targeting chimera (PROTAC) for the development of highly potent and selective degraders. Bioorg Chem. 2024; 153:107887.

[44] Wang ZA, Millard CJ, Lin CL, et al. Diverse nucleosome site-selectivity among histone deacetylase complexes. Elife. 2020; 9:e57663.

[45] Saorin A, Dehler A, Galvan B, et al. Transcriptional remodeling shapes therapeutic vulnerability to necroptosis in acute lymphoblastic leukemia. Blood. 2025; 146(7): 861-873.

[46] Pervushin NV, Nilov DK, Zhivotovsky B, Kopeina GS. Bcl-2 modifying factor (Bmf): “a mysterious stranger” in the Bcl-2 family proteins. Cell Death Differ. 2026; 33: 3-14.

[47] Fernandez AF, Sebti S, Wei Y, et al. Disruption of the beclin 1-BCL2 autophagy regulatory complex promotes longevity in mice. Nature. 2018; 558(7708): 136-140.

[48] Czabotar PE, Garcia-Saez AJ. Mechanisms of BCL-2 family proteins in mitochondrial apoptosis. Nat Rev Mol Cell Biol. 2023; 24(10): 732-748.

[49] Delgado M, Tesfaigzi Y. BH3-only proteins, Bmf and Bim, in autophagy. Cell Cycle. 2013; 12(22): 3453-3454.

[50] Delgado M, Tesfaigzi Y. Is BMF central for anoikis and autophagy? Autophagy. 2014; 10(1): 168-169.

[51] Kuster L, Grausenburger R, Fuka G, et al. ETV6/RUNX1-positive relapses evolve from an ancestral clone and frequently acquire deletions of genes implicated in glucocorticoid signaling. Blood. 2011; 117(9): 2658-2667.

[52] Zhao Q, Liu H, Peng J, et al. HDAC8 as a target in drug discovery: function, structure and design. Eur J Med Chem. 2024; 280:116972.

[53] Wang JD, Xu JQ, Long ZJ, Weng JY. Disruption of mitochondrial oxidative phosphorylation by chidamide eradicates leukemic cells in AML. Clin Transl Oncol. 2023; 25(6): 1805-1820.

[54] Duque-Afonso J, Yalcin A, Berg T, Abdelkarim M, Heidenreich O, Lübbert M. The HDAC class I-specific inhibitor entinostat (MS-275) effectively relieves epigenetic silencing of the LAT2 gene mediated by AML1/ETO. Oncogene. 2011; 30(27): 3062-3072.

[55] Long G, Wang X, Chen X, et al. Discovery of WDR5-MLL1 and HDAC dual-target inhibitors for the treatment of acute myeloid leukemia. J Med Chem. 2025; 68(2): 1260-1279.

[56] Mieland AO, Petrosino G, Dejung M, et al. The protein deacetylase HDAC10 controls DNA replication in malignant lymphoid cells. Leukemia. 2025; 39(7): 1756-1768.

[57] Zhao X, Yuan L, Gong Z, Li M, Yuan Y, Geng J. New drugs approved by the NMPA in 2024: synthesis and clinical applications. Eur J Med Chem. 2025; 291:117643.

[58] DiNardo CD, Pratz KW, Letai A, et al. Safety and preliminary efficacy of venetoclax with decitabine or azacitidine in elderly patients with previously untreated acute myeloid leukaemia: a non-randomised, open-label, phase 1b study. Lancet Oncol. 2018; 19(2): 216-228.

[59] Zeisig B, Tsai CT, Virely C, et al. Transposable elements as novel therapeutic targets for PARPi-induced synthetic lethality in PcG-mutated blood cancer. Blood. 2025; 146(11): 1314-1330.

[60] Maru B, Messikommer A, Huang L, et al. PARP-1 improves leukemia outcomes by inducing parthanatos during chemotherapy. Cell Rep Med. 2023; 4(9):101191.

[61] Kruglov O, Wu X, Hwang ST, Akilov OE. The synergistic proapoptotic effect of PARP-1 and HDAC inhibition in cutaneous T-cell lymphoma is mediated via Blimp-1. Blood Adv. 2020; 4(19): 4788-4797.

[62] Boila LD, Ghosh S, Bandyopadhyay SK, et al. KDM6 demethylases integrate DNA repair gene regulation and loss of KDM6A sensitizes human acute myeloid leukemia to PARP and BCL2 inhibition. Leukemia. 2023; 37(4): 751-764.

RIGHTS & PERMISSIONS

2026 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.