JMJD1C forms condensate to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells

Abstract

JMJD1C (Jumonji Domain Containing 1C), a member of the lysine demethylase 3 (KDM3) family, is universally required for the survival of several types of acute myeloid leukemia (AML) cells with different genetic mutations, representing a therapeutic opportunity with broad application. Yet how JMJD1C regulates the leukemic programs of various AML cells is largely unexplored. Here we show that JMJD1C interacts with the master hematopoietic transcription factor RUNX1, which thereby recruits JMJD1C to the genome to facilitate a RUNX1-driven transcriptional program that supports leukemic cell survival. The underlying mechanism hinges on the long N-terminal disordered region of JMJD1C, which harbors two inseparable abilities: condensate formation and direct interaction with RUNX1. This dual capability of JMJD1C may influence enhancer-promoter contacts crucial for the expression of key leukemic genes regulated by RUNX1. Our findings demonstrate a previously unappreciated role for the non-catalytic function of JMJD1C in transcriptional regulation, underlying a mechanism shared by different types of leukemias.

Keywords

acute myeloid leukemia / JMJD1C / RUNX1 / phase separation / enhancer-promoter interaction / enzymatic activity independent function

References

[1] Abdel-Wahab O, Levine RL. Mutations in epigenetic modifiers in the pathogenesis and therapy of acute myeloid leukemia. Blood 2013;121:3563–3572.

[2] Ahn JH, Davis ES, Daugird TA et al. Phase separation drives aberrant chromatin looping and cancer development. Nature 2021;595:591–595.

[3] Alberti S, Gladfelter A, Mittag T. Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates. Cell 2019;176:419–434.

[4] Amann JM, Nip J, Strom DK et al. ETO, a target of t(8;21) in acute leukemia, makes distinct contacts with multiple histone deacetylases and binds mSin3A through its oligomerization domain. Mol Cell Biol 2001;21:6470–6483.

[5] Ben-Ami O, Friedman D, Leshkowitz D et al. Addiction of t(8;21) and inv(16) acute myeloid leukemia to native RUNX1. Cell Rep 2013;4:1131–1143.

[6] Benyoucef A, Palii CG, Wang C et al. UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia. Genes Dev 2016;30:508–521.

[7] Bernt KM, Zhu N, Sinha AU et al. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell 2011;20:66–78.

[8] Bolognesi A, Sliwa-Gonzalez A, Prasad R et al. Fluorescence Recovery After Photo-Bleaching (FRAP) and Fluorescence Loss in Photo-Bleaching (FLIP) experiments to study protein dynamics during budding yeast cell division. Methods Mol Biol 2016;1369:25–44.

[9] Brauchle M, Yao Z, Arora R et al. Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation. PLoS One 2013;8:e60549.

[10] Cancer Genome Atlas Research Network, Ley TJ, Miller C et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013;368:2059–2074.

[11] Chandrashekar DS, Bashel B, Balasubramanya SAH et al. UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia 2017;19:649–658.

[12] Chandrashekar DS, Karthikeyan SK, Korla PK et al. UALCAN: an update to the integrated cancer data analysis platform. Neoplasia 2022;25:18–27.

[13] Chen M, Zhu N, Liu X et al. JMJD1C is required for the survival of acute myeloid leukemia by functioning as a coactivator for key transcription factors. Genes Dev 2015;29:2123–2139.

[14] Chen Q, Cevher MA, Jiang Q et al. LYL1 facilitates AETFC assembly and gene activation by recruiting CARM1 in t(8;21) AML. Proc Natl Acad Sci U S A 2022;119:e2213718119.

[15] Chong S, Graham TGW, Dugast-Darzacq C et al. Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. Mol Cell 2022;82:2084–2097.e5.

[16] Daigle SR, Olhava EJ, Therkelsen CA et al. Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor. Cancer Cell 2011;20:53–65.

[17] Deng W, Rupon JW, Krivega I et al. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 2014;158:849–860.

[18] Di Giammartino DC, Kloetgen A, Polyzos A et al. KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat Cell Biol 2019;21:1179–1190.

[19] Dignam JD, Lebovitz RM, Roeder RG. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 1983;11:1475–1489.

[20] Dohner H, Wei AH, Lowenberg B. Towards precision medicine for AML. Nat Rev Clin Oncol 2021;18:577–590.

[21] Feld C, Sahu P, Frech M et al. Combined cistrome and transcriptome analysis of SKI in AML cells identifies SKI as a co-repressor for RUNX1. Nucleic Acids Res 2018;46:3412–3428.

[22] Ferrara F, Schiffer CA. Acute myeloid leukaemia in adults. Lancet 2013;381:484–495.

[23] Fong CY, Morison J, Dawson MA. Epigenetics in the hematologic malignancies. Haematologica 2014;99:1772–1783.

[24] Fridy PC, Li Y, Keegan S et al. A robust pipeline for rapid production of versatile nanobody repertoires. Nat Methods 2014;11:1253–1260.

[25] Goyama S, Schibler J, Cunningham L et al. Transcription factor RUNX1 promotes survival of acute myeloid leukemia cells. J Clin Invest 2013;123:3876–3888.

[26] Greenblatt SM, Nimer SD. Chromatin modifiers and the promise of epigenetic therapy in acute leukemia. Leukemia 2014;28:1396–1406.

[27] Hnisz D, Abraham BJ, Lee TI et al. Super-enhancers in the control of cell identity and disease. Cell 2013;155:934–947.

[28] Hoogenkamp M, Krysinska H, Ingram R et al. The Pu.1 locus is differentially regulated at the level of chromatin structure and noncoding transcription by alternate mechanisms at distinct developmental stages of hematopoiesis. Mol Cell Biol 2007;27:7425–7438.

[29] Hu X, Wu X, Berry K et al. Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumourigenesis. Nat Cell Biol 2023;25:323–336.

[30] Huang G, Zhang P, Hirai H et al. PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis. Nat Genet 2008;40:51–60.

[31] Iida K, Tsuchiya A, Tamura M et al. RUNX1 inhibition using lipid nanoparticle-mediated silencing RNA delivery as an effective treatment for acute leukemias. Exp Hematol 2022;112-113:1–8.

[32] Izaguirre-Carbonell J, Christiansen L, Burns R et al. Critical role of Jumonji domain of JMJD1C in MLL-rearranged leukemia. Blood Adv 2019;3:1499–1511.

[33] Jiang S, Fagman JB, Chen C et al. Protein phase separation and its role in tumorigenesis. Elife 2020;9:e60264.

[34] Klose RJ, Kallin EM, Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 2006;7:715–727.

[35] Li M, Liu M, Han W et al. LSD1 inhibition disrupts super-enhancer-driven oncogenic transcriptional programs in castration-resistant prostate cancer. Cancer Res 2023;83:1684–1698.

[36] Lin J, Wu Y, Tian G et al. Menin “reads” H3K79me2 mark in a nucleosomal context. Science 2023;379:717–723.

[37] Liu Y, Cheney MD, Gaudet JJ et al. The tetramer structure of the Nervy homology two domain, NHR2, is critical for AML1/ETO’s activity. Cancer Cell 2006;9:249–260.

[38] Liu Y, Chen W, Gaudet J et al. Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO’s activity. Cancer Cell 2007;11:483–497.

[39] Look AT. Oncogenic transcription factors in the human acute leukemias. Science 1997;278:1059–1064.

[40] Loven J, Hoke HA, Lin CY et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 2013;153:320–334.

[41] Ma H, Tu L-C, Naseri A et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 2016;34:528–530.

[42] Magli A, Baik J, Pota P et al. Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. Nat Commun 2019;10:2316.

[43] Mandoli A, Singh AA, Prange KHM et al. The hematopoietic transcription factors RUNX1 and ERG prevent AML1-ETO oncogene overexpression and onset of the Apoptosis Program in t(8;21) AMLs. Cell Rep 2016;17:2087–2100.

[44] Matelot M, Noordermeer D. Determination of high-resolution 3D chromatin organization using circular chromosome conformation capture (4C-seq). Methods Mol Biol 2016;1480:223–241.

[45] McLeod C, Gout AM, Zhou X et al. St. Jude Cloud: a pediatric cancer genomic data-sharing ecosystem. Cancer Discov 2021;11:1082–1099.

[46] Mill CP, Fiskus W, DiNardo CD et al. RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1. Blood 2019;134:59–73.

[47] Mishra BP, Zaffuto KM, Artinger EL et al. The histone methyltransferase activity of MLL1 is dispensable for hematopoiesis and leukemogenesis. Cell Rep 2014;7:1239–1247.

[48] Monahan K, Horta A, Lomvardas S. LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. Nature 2019;565:448–453.

[49] Morgan MAJ, Shilatifard A. Epigenetic moonlighting: catalytic-independent functions of histone modifiers in regulating transcription. Sci Adv 2023;9:eadg6593.

[50] Morita K, Suzuki K, Maeda S et al. Genetic regulation of the RUNX transcription factor family has antitumor effects. J Clin Invest 2017;127:2815–2828.

[51] Ochi Y, Kon A, Sakata T et al. Combined cohesin-RUNX1 deficiency synergistically perturbs chromatin looping and causes myelodysplastic syndromes. Cancer Discov 2020;10:836–853.

[52] Ohguchi H, Hideshima T, Anderson KC. The biological significance of histone modifiers in multiple myeloma: clinical applications. Blood Cancer J 2018;8:83.

[53] Papaemmanuil E, Gerstung M, Bullinger L et al. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med 2016;374:2209–2221.

[54] Patel JP, Gönen M, Figueroa ME et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med 2012;366:1079–1089.

[55] Pencovich N, Jaschek R, Tanay A et al. Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models. Blood 2011;117:e1–14.

[56] Phanstiel DH, Van Bortle K, Spacek D et al. Static and dynamic DNA loops form AP-1-bound activation hubs during macrophage development. Mol Cell 2017;67:1037–1048.e6.

[57] Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009;137:1194–1211.

[58] Piccolo S, Panciera T, Contessotto P et al. YAP/TAZ as master regulators in cancer: modulation, function and therapeutic approaches. Nat Cancer 2023;4:9–26.

[59] Pikman Y, Puissant A, Alexe G et al. Targeting MTHFD2 in acute myeloid leukemia. J Exp Med 2016;213:1285–1306.

[60] Plys AJ, Davis CP, Kim J et al. Phase separation of polycomb-repressive complex 1 is governed by a charged disordered region of CBX2. Genes Dev 2019;33:799–813.

[61] Prange KHM, Mandoli A, Kuznetsova T et al. MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in 11q23 acute myeloid leukemia. Oncogene 2017;36:3346–3356.

[62] Ptasinska A, Pickin A, Assi SA et al. RUNX1-ETO depletion in t(8;21) AML leads to C/EBPalpha-and AP-1-mediated alterations in enhancer-promoter interaction. Cell Rep 2019;28:3022–3031.e7.

[63] Pulikkottil AJ, Bamezai S, Ammer T et al. TET3 promotes AML growth and epigenetically regulates glucose metabolism and leukemic stem cell associated pathways. Leukemia 2022;36:416–425.

[64] Reiter F, Wienerroither S, Stark A. Combinatorial function of transcription factors and cofactors. Curr Opin Genet Dev 2017;43:73–81.

[65] Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019;26:783–791.

[66] Rubin AJ, Barajas BC, Furlan-Magaril M et al. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nat Genet 2017;49:1522–1528.

[67] Sabari BR, Dall’Agnese A, Boija A et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 2018;361:eaar3958.

[68] Schnittger S, Dicker F, Kern W et al. RUNX1 mutations are frequent in de novo AML with noncomplex karyotype and confer an unfavorable prognosis. Blood 2011;117:2348–2357.

[69] Shi J, Wang E, Milazzo JP et al. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat Biotechnol 2015;33:661–667.

[70] Shi B, Li W, Song Y et al. UTX condensation underlies its tumour-suppressive activity. Nature 2021;597:726–731.

[71] Shia WJ, Okumura AJ, Yan M et al. PRMT1 interacts with AML1-ETO to promote its transcriptional activation and progenitor cell proliferative potential. Blood 2012;119:4953–4962.

[72] Shin Y, Brangwynne CP. Liquid phase condensation in cell physiology and disease. Science 2017;357:eaaf4382.

[73] Shpargel KB, Sengoku T, Yokoyama S et al. UTX and UTY demonstrate histone demethylase-independent function in mouse embryonic development. PLoS Genet 2012;8:e1002964.

[74] Singh AA, Mandoli A, Prange KHM et al. AML associated oncofusion proteins PML-RARA, AML1-ETO and CBFBMYH11 target RUNX/ETS-factor binding sites to modulate H3ac levels and drive leukemogenesis. Oncotarget 2017;8:12855–12865.

[75] Song L, Yao X, Li H et al. Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. Mol Cell 2022;82:4080–4098.e12.

[76] Sroczynska P, Cruickshank VA, Bukowski J-P et al. shRNA screening identifies JMJD1C as being required for leukemia maintenance. Blood 2014;123:1870–1882.

[77] Sun XJ, Wang Z, Wang L et al. A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature 2013;500:93–97.

[78] Tang JL, Hou H-A, Chen C-Y et al. AML1/RUNX1 mutations in 470 adult patients with de novo acute myeloid leukemia: prognostic implication and interaction with other gene alterations. Blood 2009;114:5352–5361.

[79] Tatavosian R, Kent S, Brown K et al. Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation. J Biol Chem 2019;294:1451–1463.

[80] Thoms JAI, Truong P, Subramanian S et al. Disruption of a GATA2-TAL1-ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells. Blood 2021;138:1441–1455.

[81] Wan L, Wen H, Li Y et al. ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia. Nature 2017;543:265–269.

[82] Wang H, Xu X, Nguyen CM et al. CRISPR-mediated programmable 3D genome positioning and nuclear organization. Cell 2018;175:1405–1417.e14.

[83] Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2019;47:11481–11496.

[84] Wang Z, Wang P, Li Y et al. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduct Target Ther 2021;6:24.

[85] Whyte WA, Orlando DA, Hnisz D et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 2013;153:307–319.

[86] Wilkinson AC, Ballabio E, Geng H et al. RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction. Cell Rep 2013;3:116–127.

[87] Wilson NK, Foster SD, Wang X et al. Combinatorial transcriptional control in blood stem/progenitor cells: genomewide analysis of ten major transcriptional regulators. Cell Stem Cell 2010;7:532–544.

[88] Xue B, Dunbrack RL, Williams RW et al. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta 2010;1804:996–1010.

[89] Yamane K, Toumazou C, Tsukada Y-ichi et al. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 2006;125:483–495.

[90] Zhao LJ, Wang Y-Y, Li G et al. Functional features of RUNX1 mutants in acute transformation of chronic myeloid leukemia and their contribution to inducing murine full-blown leukemia. Blood 2012;119:2873–2882.

[91] Zhu N, Chen M, Eng R et al. MLL-AF9-and HOXA9-mediated acute myeloid leukemia stem cell self-renewal requires JMJD1C. J Clin Invest 2016;126:997–1011.

[92] Zhu K, Celwyn IJ, Guan D et al. An intrinsically disordered region controlling condensation of a circadian clock component and rhythmic transcription in the liver. Mol Cell 2023a;83:3457–3469.e7.

[93] Zhu XN, Wei Y-S, Yang Q et al. FBXO22 promotes leukemogenesis by targeting BACH1 in MLL-rearranged acute myeloid leukemia. J Hematol Oncol 2023b;16:9.

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