1
|
Wang J, Zheng P, Yu J, Yang X, Zhang J. Rational design of small-sized peptidomimetic inhibitors disrupting protein-protein interaction. RSC Med Chem 2024; 15:2212-2225. [PMID: 39026653 PMCID: PMC11253864 DOI: 10.1039/d4md00202d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/04/2024] [Indexed: 07/20/2024] Open
Abstract
Protein-protein interactions are fundamental to nearly all biological processes. Due to their structural flexibility, peptides have emerged as promising candidates for developing inhibitors targeting large and planar PPI interfaces. However, their limited drug-like properties pose challenges. Hence, rational modifications based on peptide structures are anticipated to expedite the innovation of peptide-based therapeutics. This review comprehensively examines the design strategies for developing small-sized peptidomimetic inhibitors targeting PPI interfaces, which predominantly encompass two primary categories: peptidomimetics with abbreviated sequences and low molecular weights and peptidomimetics mimicking secondary structural conformations. We have also meticulously detailed several instances of designing and optimizing small-sized peptidomimetics targeting PPIs, including MLL1-WDR5, PD-1/PD-L1, and Bak/Bcl-xL, among others, to elucidate the potential application prospects of these design strategies. Hopefully, this review will provide valuable insights and inspiration for the future development of PPI small-sized peptidomimetic inhibitors in pharmaceutical research endeavors.
Collapse
Affiliation(s)
- Junyuan Wang
- School of Pharmacy, Ningxia Medical University Yinchuan 750004 China
| | - Ping Zheng
- School of Pharmacy, Ningxia Medical University Yinchuan 750004 China
| | - Jianqiang Yu
- School of Pharmacy, Ningxia Medical University Yinchuan 750004 China
| | - Xiuyan Yang
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University Shanghai 200025 China
| | - Jian Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University Yinchuan 750004 China
| |
Collapse
|
2
|
Yang Y, Ahmad E, Premkumar V, Liu A, Ashikur Rahman SM, Nikolovska‐Coleska Z. Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors. Protein Sci 2024; 33:e5019. [PMID: 38747396 PMCID: PMC11094776 DOI: 10.1002/pro.5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.
Collapse
Affiliation(s)
- Yuting Yang
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Ejaz Ahmad
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Vidhya Premkumar
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Alicen Liu
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - S. M. Ashikur Rahman
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Zaneta Nikolovska‐Coleska
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| |
Collapse
|
3
|
Hu H, Muntean AG. The YEATS domain epigenetic reader proteins ENL and AF9 and their therapeutic value in leukemia. Exp Hematol 2023; 124:15-21. [PMID: 37295550 PMCID: PMC10527611 DOI: 10.1016/j.exphem.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Recent studies have uncovered similarities and differences between 2 highly homologous epigenetic reading proteins, namely, ENL (MLLT1) and AF9 (MLLT3) with therapeutic implications. The importance of these proteins has traditionally been exemplified by their involvement in chromosomal translocations with the mixed-lineage leukemia gene (MLL; aka KMT2a). MLL rearrangements occur in a subset of acute leukemias and generate potent oncogenic MLL-fusion proteins that impact epigenetic and transcriptional regulation. Leukemic patients with MLL rearrangements display intermediate-to-poor prognoses, necessitating further mechanistic research. Several protein complexes involved in regulating RNA polymerase II transcription and the epigenetic landscape are hijacked in MLL-r leukemia, which include ENL and AF9. Recent biochemical studies have defined a highly homologous YEATS domain in ENL and AF9 that binds acylated histones, which aids in the localization and retention of these proteins to transcriptional targets. In addition, detailed characterization of the homologous ANC-1 homology domain (AHD) on ENL and AF9 revealed differential association with transcriptional activating and repressing complexes. Importantly, CRISPR knockout screens have demonstrated a unique role for wild-type ENL in leukemic stem cell function, whereas AF9 appears important for normal hematopoietic stem cells. In this perspective, we examine the ENL and AF9 proteins with attention to recent work characterizing the epigenetic reading YEATS domains and AHD on both wild-type proteins and when fused to MLL. We summarized the drug development efforts and their therapeutic potential and assess ongoing research that has refined our understanding of how these proteins function, which continues to reveal new therapeutic avenues.
Collapse
Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI.
| |
Collapse
|
4
|
Hu H, Saha N, Yang Y, Ahmad E, Lachowski L, Shrestha U, Premkumar V, Ropa J, Chen L, Teahan B, Grigsby S, Marschalek R, Nikolovska-Coleska Z, Muntean AG. The ENL YEATS epigenetic reader domain critically links MLL-ENL to leukemic stem cell frequency in t(11;19) Leukemia. Leukemia 2023; 37:190-201. [PMID: 36435883 PMCID: PMC11246743 DOI: 10.1038/s41375-022-01765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
MLL (KMT2a) translocations are found in ~10% of acute leukemia patients, giving rise to oncogenic MLL-fusion proteins. A common MLL translocation partner is ENL and associated with a poor prognosis in t(11;19) patients. ENL contains a highly conserved N-terminal YEATS domain that binds acetylated histones and interacts with the PAF1c, an epigenetic regulator protein complex essential for MLL-fusion leukemogenesis. Recently, wild-type ENL, and specifically the YEATS domain, was shown to be essential for leukemic cell growth. However, the inclusion and importance of the YEATS domain in MLL-ENL-mediated leukemogenesis remains unexplored. We found the YEATS domain is retained in 84.1% of MLL-ENL patients and crucial for MLL-ENL-mediated leukemogenesis in mouse models. Mechanistically, deletion of the YEATS domain impaired MLL-ENL fusion protein binding and decreased expression of pro-leukemic genes like Eya1 and Meis1. Point mutations that disrupt YEATS domain binding to acetylated histones decreased stem cell frequency and increased MLL-ENL-mediated leukemia latency. Therapeutically, YEATS containing MLL-ENL leukemic cells display increased sensitivity to the YEATS inhibitor SGC-iMLLT compared to control AML cells. Our results demonstrate that the YEATS domain is important for MLL-ENL fusion protein-mediated leukemogenesis and exposes an "Achilles heel" that may be therapeutically targeted for treating t(11;19) patients.
Collapse
Affiliation(s)
- Hsiangyu Hu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nirmalya Saha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yuting Yang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lauren Lachowski
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Uttar Shrestha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vidhya Premkumar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James Ropa
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA
| | - Lili Chen
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Blaine Teahan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sierrah Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology / Diagnostic Center of Acute Leukemia, University of Frankfurt, Frankfurt/Main, Germany
| | | | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
5
|
Arnold O, Barbosa K, Deshpande AJ, Zhu N. The Role of DOT1L in Normal and Malignant Hematopoiesis. Front Cell Dev Biol 2022; 10:917125. [PMID: 35712672 PMCID: PMC9197164 DOI: 10.3389/fcell.2022.917125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
Disruptor of telomeric silencing 1 (DOT1) was first identified in yeast (DOT1p) and is the sole methyltransferase responsible for histone three lysine 79 (H3K79) mono-, di-, and tri-methylation. Mammalian DOT1 (DOT1-like protein or DOT1L) has been implicated in many cellular processes, such as cell cycle progression, DNA damage response, and development. A notable developmental process reliant on DOT1L function is normal hematopoiesis, as DOT1L knockout leads to impairment in blood lineage formation. Aberrant activity of DOT1L has been implicated in hematopoietic malignancies as well, especially those with high expression of the homeobox (HOX) genes, as genetic or pharmacological DOT1L inhibition causes defects in leukemic transformation and maintenance. Recent studies have uncovered methyltransferase-independent functions and a novel mechanism of DOT1L function. Here, we summarize the roles of DOT1L in normal and malignant hematopoiesis and the potential mechanism behind DOT1L function in hematopoiesis, in light of recent discoveries.
Collapse
Affiliation(s)
- Olivia Arnold
- Blood Research Institute, Versiti, Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Karina Barbosa
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Aniruddha J. Deshpande
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Nan Zhu
- Blood Research Institute, Versiti, Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Nan Zhu,
| |
Collapse
|
6
|
Yuan Y, Du L, Tan R, Yu Y, Jiang J, Yao A, Luo J, Tang R, Xiao Y, Sun H. Design, Synthesis, and Biological Evaluations of DOT1L Peptide Mimetics Targeting the Protein-Protein Interactions between DOT1L and MLL-AF9/MLL-ENL. J Med Chem 2022; 65:7770-7785. [PMID: 35612819 DOI: 10.1021/acs.jmedchem.2c00083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
On the basis of a previously identified DOT1L peptide mimetic (compound 3), a series of novel peptide mimetics were designed and synthesized. These compounds can potently bind to AF9 and ENL either in cell-free binding assays or in leukemia cells, and selectively inhibit the growth of leukemia cells containing mixed lineage leukemia (MLL) fusion proteins. The most potent compound 12 exhibited comparable anticancer cellular activities to those of EPZ5676, a clinical stage enzymatic inhibitor of DOT1L in several leukemia cell lines containing MLL fusion proteins. Mechanism studies for compound 12 indicated that it did not affect the global methylation of H3K79 catalyzed by DOT1L but could effectively suppress the methylation of H3K79 at MLL fusion proteins targeted genes and inhibit the expressions of these genes. Our studies thus demonstrated that inhibiting the protein-protein interactions between DOT1L and MLL fusion proteins is a potentially effective strategy for the treatment of MLL rearranged leukemias.
Collapse
Affiliation(s)
- Yinan Yuan
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Du
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Rongliang Tan
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yifan Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinxin Jiang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Aihong Yao
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jiajun Luo
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Rui Tang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
7
|
Yi Y, Ge S. Targeting the histone H3 lysine 79 methyltransferase DOT1L in MLL-rearranged leukemias. J Hematol Oncol 2022; 15:35. [PMID: 35331314 PMCID: PMC8944089 DOI: 10.1186/s13045-022-01251-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/09/2022] [Indexed: 01/28/2023] Open
Abstract
Disrupting the methylation of telomeric silencing 1-like (DOT1L)-mediated histone H3 lysine 79 has been implicated in MLL fusion-mediated leukemogenesis. Recently, DOT1L has become an attractive therapeutic target for MLL-rearranged leukemias. Rigorous studies have been performed, and much progress has been achieved. Moreover, one DOT1L inhibitor, EPZ-5676, has entered clinical trials, but its clinical activity is modest. Here, we review the recent advances and future trends of various therapeutic strategies against DOT1L for MLL-rearranged leukemias, including DOT1L enzymatic activity inhibitors, DOT1L degraders, protein-protein interaction (PPI) inhibitors, and combinatorial interventions. In addition, the limitations, challenges, and prospects of these therapeutic strategies are discussed. In summary, we present a general overview of DOT1L as a target in MLL-rearranged leukemias to provide valuable guidance for DOT1L-associated drug development in the future. Although a variety of DOT1L enzymatic inhibitors have been identified, most of them require further optimization. Recent advances in the development of small molecule degraders, including heterobifunctional degraders and molecular glues, provide valuable insights and references for DOT1L degraders. However, drug R&D strategies and platforms need to be developed and preclinical experiments need to be performed with the purpose of blocking DOT1L-associated PPIs. DOT1L epigenetic-based combination therapy is worth considering and exploring, but the therapy should be based on a thorough understanding of the regulatory mechanism of DOT1L epigenetic modifications.
Collapse
Affiliation(s)
- Yan Yi
- Departments of Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Shenglei Ge
- Departments of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Street, Changsha, 410011, Hunan, People's Republic of China.
| |
Collapse
|
8
|
Yeewa R, Chaiya P, Jantrapirom S, Shotelersuk V, Lo Piccolo L. Multifaceted roles of YEATS domain-containing proteins and novel links to neurological diseases. Cell Mol Life Sci 2022; 79:183. [PMID: 35279775 PMCID: PMC11071958 DOI: 10.1007/s00018-022-04218-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
The so-called Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain-containing proteins, hereafter referred to as YD proteins, take control over the transcription by multiple steps of regulation either involving epigenetic remodelling of chromatin or guiding the processivity of RNA polymerase II to facilitate elongation-coupled mRNA 3' processing. Interestingly, an increasing amount of evidence suggest a wider repertoire of YD protein's functions spanning from non-coding RNA regulation, RNA-binding proteins networking, post-translational regulation of a few signalling transduction proteins and the spindle pole formation. However, such a large set of non-canonical roles is still poorly characterized. Notably, four paralogous of human YEATS domain family members, namely eleven-nineteen-leukaemia (ENL), ALL1-fused gene from chromosome 9 protein (AF9), YEATS2 and glioma amplified sequence 41 (GAS41), have a strong link to cancer yet new findings also highlight a potential novel role in neurological diseases. Here, in an attempt to more comprehensively understand the complexity of four YD proteins and to gain more insight into the novel functions they may accomplish in the neurons, we summarized the YD protein's networks, systematically searched and reviewed the YD genetic variants associated with neurodevelopmental disorders and finally interrogated the model organism Drosophila melanogaster.
Collapse
Affiliation(s)
- Ranchana Yeewa
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pawita Chaiya
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Salinee Jantrapirom
- Drosophila Centre for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Vorasuk Shotelersuk
- Centre of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Centre for Genomics and Precision Medicine, The Thai Red Cross Society, King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Luca Lo Piccolo
- Centre of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Musculoskeletal Science and Translational Research Centre (MSTR), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai, 50200, Thailand.
| |
Collapse
|
9
|
Chi SG, Minami Y. Emerging Targeted Therapy for Specific Genomic Abnormalities in Acute Myeloid Leukemia. Int J Mol Sci 2022; 23:2362. [PMID: 35216478 PMCID: PMC8879537 DOI: 10.3390/ijms23042362] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
We describe recent updates of existing molecular-targeting agents and emerging novel gene-specific strategies. FLT3 and IDH inhibitors are being tested in combination with conventional chemotherapy for both medically fit patients and patients who are ineligible for intensive therapy. FLT3 inhibitors combined with non-cytotoxic agents, such as BCL-2 inhibitors, have potential therapeutic applicability. The menin-MLL complex pathway is an emerging therapeutic target. The pathway accounts for the leukemogenesis in AML with MLL-rearrangement, NPM1 mutation, and NUP98 fusion genes. Potent menin-MLL inhibitors have demonstrated promising anti-leukemic effects in preclinical studies. The downstream signaling molecule SYK represents an additional target. However, the TP53 mutation continues to remain a challenge. While the p53 stabilizer APR-246 in combination with azacitidine failed to show superiority compared to azacitidine monotherapy in a phase 3 trial, next-generation p53 stabilizers are now under development. Among a number of non-canonical approaches to TP53-mutated AML, the anti-CD47 antibody magrolimab in combination with azacitidine showed promising results in a phase 1b trial. Further, the efficacy was somewhat better in patients with the TP53 mutation. Although clinical evidence has not been accumulated sufficiently, targeting activating KIT mutations and RAS pathway-related molecules can be a future therapeutic strategy.
Collapse
Affiliation(s)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 2778577, Japan;
| |
Collapse
|
10
|
Song T, Zou Q, Yan Y, Lv S, Li N, Zhao X, Ma X, Liu H, Tang B, Sun L. DOT1L O-GlcNAcylation promotes its protein stability and MLL-fusion leukemia cell proliferation. Cell Rep 2021; 36:109739. [PMID: 34551297 DOI: 10.1016/j.celrep.2021.109739] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/08/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Histone lysine methylation functions at the interface of the extracellular environment and intracellular gene expression. DOT1L is a versatile histone H3K79 methyltransferase with a prominent role in MLL-fusion leukemia, yet little is known about how DOT1L responds to extracellular stimuli. Here, we report that DOT1L protein stability is regulated by the extracellular glucose level through the hexosamine biosynthetic pathway (HBP). Mechanistically, DOT1L is O-GlcNAcylated at evolutionarily conserved S1511 in its C terminus. We identify UBE3C as a DOT1L E3 ubiquitin ligase promoting DOT1L degradation whose interaction with DOT1L is susceptible to O-GlcNAcylation. Consequently, HBP enhances H3K79 methylation and expression of critical DOT1L target genes such as HOXA9/MEIS1, promoting cell proliferation in MLL-fusion leukemia. Inhibiting HBP or O-GlcNAc transferase (OGT) increases cellular sensitivity to DOT1L inhibitor. Overall, our work uncovers O-GlcNAcylation and UBE3C as critical determinants of DOT1L protein abundance, revealing a mechanism by which glucose metabolism affects malignancy progression through histone methylation.
Collapse
Affiliation(s)
- Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China.
| | - Qingli Zou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yingying Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Neng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Xuefeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Xianyun Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Haigang Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Borui Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China.
| |
Collapse
|
11
|
Li X, Song Y. Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins. J Hematol Oncol 2021; 14:56. [PMID: 33823889 PMCID: PMC8022399 DOI: 10.1186/s13045-021-01057-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia 1 (MLL1, also known as MLL or KMT2A) is an important transcription factor and histone-H3 lysine-4 (H3K4) methyltransferase. It is a master regulator for transcription of important genes (e.g., Hox genes) for embryonic development and hematopoiesis. However, it is largely dispensable in matured cells. Dysregulation of MLL1 leads to overexpression of certain Hox genes and eventually leukemia initiation. Chromosome translocations involving MLL1 cause ~ 75% of acute leukemia in infants and 5–10% in children and adults with a poor prognosis. Targeted therapeutics against oncogenic fusion MLL1 (onco-MLL1) are therefore needed. Onco-MLL1 consists of the N-terminal DNA-interacting domains of MLL1 fused with one of > 70 fusion partners, among which transcription cofactors AF4, AF9 and its paralog ENL, and ELL are the most frequent. Wild-type (WT)- and onco-MLL1 involve numerous protein–protein interactions (PPI), which play critical roles in regulating gene expression in normal physiology and leukemia. Moreover, WT-MLL1 has been found to be essential for MLL1-rearranged (MLL1-r) leukemia. Rigorous studies of such PPIs have been performed and much progress has been achieved in understanding their structures, structure–function relationships and the mechanisms for activating gene transcription as well as leukemic transformation. Inhibition of several critical PPIs by peptides, peptidomimetic or small-molecule compounds has been explored as a therapeutic approach for MLL1-r leukemia. This review summarizes the biological functions, biochemistry, structure and inhibition of the critical PPIs involving MLL1 and its fusion partner proteins. In addition, challenges and perspectives of drug discovery targeting these PPIs for the treatment of MLL1-r leukemia are discussed.
Collapse
Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
12
|
Grigsby SM, Friedman A, Chase J, Waas B, Ropa J, Serio J, Shen C, Muntean AG, Maillard I, Nikolovska-Coleska Z. Elucidating the Importance of DOT1L Recruitment in MLL-AF9 Leukemia and Hematopoiesis. Cancers (Basel) 2021; 13:642. [PMID: 33562706 PMCID: PMC7914713 DOI: 10.3390/cancers13040642] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/27/2021] [Accepted: 01/31/2021] [Indexed: 12/14/2022] Open
Abstract
MLL1 (KMT2a) gene rearrangements underlie the pathogenesis of aggressive MLL-driven acute leukemia. AF9, one of the most common MLL-fusion partners, recruits the histone H3K79 methyltransferase DOT1L to MLL target genes, constitutively activating transcription of pro-leukemic targets. DOT1L has emerged as a therapeutic target in patients with MLL-driven leukemia. However, global DOT1L enzymatic inhibition may lead to off-target toxicities in non-leukemic cells that could decrease the therapeutic index of DOT1L inhibitors. To bypass this problem, we developed a novel approach targeting specific protein-protein interactions (PPIs) that mediate DOT1L recruitment to MLL target genes, and compared the effects of enzymatic and PPIs inhibition on leukemic and non-leukemic hematopoiesis. MLL-AF9 cell lines were engineered to carry mutant DOT1L constructs with a defective AF9 interaction site or lacking enzymatic activity. In cell lines expressing a DOT1L mutant with defective AF9 binding, we observed complete disruption of DOT1L recruitment to critical target genes and inhibition of leukemic cell growth. To evaluate the overall impact of DOT1L loss in non-leukemic hematopoiesis, we first assessed the impact of acute Dot1l inactivation in adult mouse bone marrow. We observed a rapid reduction in myeloid progenitor cell numbers within 7 days, followed by a loss of long-term hematopoietic stem cells. Furthermore, WT and PPI-deficient DOT1L mutants but not an enzymatically inactive DOT1L mutant were able to rescue sustained hematopoiesis. These data show that the AF9-DOT1L interaction is dispensable in non-leukemic hematopoiesis. Our findings support targeting of the MLL-AF9-DOT1L interaction as a promising therapeutic strategy that is selectively toxic to MLL-driven leukemic cells.
Collapse
Affiliation(s)
- Sierrah M. Grigsby
- Molecular and Celular Graduate Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (S.M.G.); (J.R.); (J.S.); (C.S.); (A.G.M.)
| | - Ann Friedman
- Department of Internal Medicine, Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (A.F.); (J.C.); (B.W.); (I.M.)
| | - Jennifer Chase
- Department of Internal Medicine, Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (A.F.); (J.C.); (B.W.); (I.M.)
| | - Bridget Waas
- Department of Internal Medicine, Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (A.F.); (J.C.); (B.W.); (I.M.)
| | - James Ropa
- Molecular and Celular Graduate Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (S.M.G.); (J.R.); (J.S.); (C.S.); (A.G.M.)
| | - Justin Serio
- Molecular and Celular Graduate Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (S.M.G.); (J.R.); (J.S.); (C.S.); (A.G.M.)
| | - Chenxi Shen
- Molecular and Celular Graduate Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (S.M.G.); (J.R.); (J.S.); (C.S.); (A.G.M.)
| | - Andrew G. Muntean
- Molecular and Celular Graduate Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (S.M.G.); (J.R.); (J.S.); (C.S.); (A.G.M.)
- Rogel Cancer Center, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI 48104, USA
| | - Ivan Maillard
- Department of Internal Medicine, Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (A.F.); (J.C.); (B.W.); (I.M.)
| | - Zaneta Nikolovska-Coleska
- Molecular and Celular Graduate Program, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48104, USA; (S.M.G.); (J.R.); (J.S.); (C.S.); (A.G.M.)
- Rogel Cancer Center, Michigan Medicine, University of Michigan Medical School, Ann Arbor, MI 48104, USA
| |
Collapse
|
13
|
Affiliation(s)
- Susan E Bates
- From the Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center and James J. Peters Veterans Affairs Medical Center, New York
| |
Collapse
|
14
|
Gibbons GS, Chakraborty A, Grigsby SM, Umeano AC, Liao C, Moukha-Chafiq O, Pathak V, Mathew B, Lee YT, Dou Y, Schürer SC, Reynolds RC, Snowden TS, Nikolovska-Coleska Z. Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library. Eur J Med Chem 2020; 189:112023. [PMID: 31978781 DOI: 10.1016/j.ejmech.2019.112023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/27/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023]
Abstract
Disruptor of Telomeric Silencing 1-Like (DOT1L), the sole histone H3 lysine 79 (H3K79) methyltransferase, is required for leukemogenic transformation in a subset of leukemias bearing chromosomal translocations of the Mixed Lineage Leukemia (MLL) gene, as well as other cancers. Thus, DOT1L is an attractive therapeutic target and discovery of small molecule inhibitors remain of high interest. Herein, we are presenting screening results for a unique focused library of 1200 nucleoside analogs originally produced under the aegis of the NIH Pilot Scale Library Program. The complete nucleoside set was screened virtually against DOT1L, resulting in 210 putative hits. In vitro screening of the virtual hits resulted in validation of 11 compounds as DOT1L inhibitors clustered into two distinct chemical classes, adenosine-based inhibitors and a new chemotype that lacks adenosine. Based on the developed DOT1L ligand binding model, a structure-based design strategy was applied and a second-generation of non-nucleoside DOT1L inhibitors was developed. Newly synthesized compound 25 was the most potent DOT1L inhibitor in the new series with an IC50 of 1.0 μM, showing 40-fold improvement in comparison with hit 9 and exhibiting reasonable on target effects in a DOT1L dependent murine cell line. These compounds represent novel chemical probes with a unique non-nucleoside scaffold that bind and compete with the SAM binding site of DOT1L, thus providing foundation for further medicinal chemistry efforts to develop more potent compounds.
Collapse
Affiliation(s)
- Garrett S Gibbons
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Amarraj Chakraborty
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Sierrah M Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Afoma C Umeano
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Chenzhong Liao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Omar Moukha-Chafiq
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Vibha Pathak
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Bini Mathew
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Young-Tae Lee
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA; Center for Computational Science, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Robert C Reynolds
- Division of Hematology and Oncology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Timothy S Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA.
| | - Zaneta Nikolovska-Coleska
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Rogel Cancer Center at University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
15
|
Cao L, Mitra P, Gonda TJ. The mechanism of MYB transcriptional regulation by MLL-AF9 oncoprotein. Sci Rep 2019; 9:20084. [PMID: 31882723 PMCID: PMC6934848 DOI: 10.1038/s41598-019-56426-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/08/2019] [Indexed: 11/18/2022] Open
Abstract
Acute leukaemias express high levels of MYB which are required for the initiation and maintenance of the disease. Inhibition of MYB expression or activity has been shown to suppress MLL-fusion oncoprotein-induced acute myeloid leukaemias (AML), which are among the most aggressive forms of AML, and indeed MYB transcription has been reported to be regulated by the MLL-AF9 oncoprotein. This highlights the importance of understanding the mechanism of MYB transcriptional regulation in these leukaemias. Here we have demonstrated that the MLL-AF9 fusion protein regulates MYB transcription directly at the promoter region, in part by recruiting the transcriptional regulator kinase CDK9, and CDK9 inhibition effectively suppresses MYB expression as well as cell proliferation. However, MYB regulation by MLL-AF9 does not require H3K79 methylation mediated by the methyltransferase DOT1L, which has also been shown to be a key mediator of MLL-AF9 leukemogenicity. The identification of specific, essential and druggable transcriptional regulators may enable effective targeting of MYB expression, which in turn could potentially lead to new therapeutic approaches for acute myeloid leukaemia with MLL-AF9.
Collapse
Affiliation(s)
- Lu Cao
- School of Pharmacy, University of Queensland, Brisbane, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Gallipoli Medical Research Institute, Greenslopes Private Hospital, Brisbane, QLD, Australia
| | - Partha Mitra
- School of Pharmacy, University of Queensland, Brisbane, QLD, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, TRI, Woolloongabba, QLD, Australia
| | - Thomas J Gonda
- School of Pharmacy, University of Queensland, Brisbane, QLD, Australia. .,University of South Australia Cancer Research Institute, Adelaide, SA, Australia.
| |
Collapse
|
16
|
Chan AKN, Chen CW. Rewiring the Epigenetic Networks in MLL-Rearranged Leukemias: Epigenetic Dysregulation and Pharmacological Interventions. Front Cell Dev Biol 2019; 7:81. [PMID: 31157223 PMCID: PMC6529847 DOI: 10.3389/fcell.2019.00081] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022] Open
Abstract
Leukemias driven by chromosomal translocation of the mixed-lineage leukemia gene (MLL or KMT2A) are highly prevalent in pediatric oncology. The poor survival rate and lack of an effective targeted therapy for patients with MLL-rearranged (MLL-r) leukemias emphasize an urgent need for improved knowledge and novel therapeutic approaches for these malignancies. The resulting chimeric products of MLL gene rearrangements, i.e., MLL-fusion proteins (MLL-FPs), are capable of transforming hematopoietic stem/progenitor cells (HSPCs) into leukemic blasts. The ability of MLL-FPs to reprogram HSPCs toward leukemia requires the involvement of multiple chromatin effectors, including the histone 3 lysine 79 methyltransferase DOT1L, the chromatin epigenetic reader BRD4, and the super elongation complex. These epigenetic regulators constitute a complicated network that dictates maintenance of the leukemia program, and therefore represent an important cluster of therapeutic opportunities. In this review, we will discuss the role of MLL and its fusion partners in normal HSPCs and hematopoiesis, including the links between chromatin effectors, epigenetic landscapes, and leukemia development, and summarize current approaches to therapeutic targeting of MLL-r leukemias.
Collapse
Affiliation(s)
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
| |
Collapse
|
17
|
Yokoyama A. RNA Polymerase II-Dependent Transcription Initiated by Selectivity Factor 1: A Central Mechanism Used by MLL Fusion Proteins in Leukemic Transformation. Front Genet 2019; 9:722. [PMID: 30693017 PMCID: PMC6339877 DOI: 10.3389/fgene.2018.00722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/21/2018] [Indexed: 11/13/2022] Open
Abstract
Cancer cells transcribe RNAs in a characteristic manner in order to maintain their oncogenic potentials. In eukaryotes, RNA is polymerized by three distinct RNA polymerases, RNA polymerase I, II, and III (RNAP1, RNAP2, and RNAP3, respectively). The transcriptional machinery that initiates each transcription reaction has been purified and characterized. Selectivity factor 1 (SL1) is the complex responsible for RNAP1 pre-initiation complex formation. However, whether it plays any role in RNAP2-dependent transcription remains unclear. Our group previously found that SL1 specifically associates with AF4 family proteins. AF4 family proteins form the AEP complex with ENL family proteins and the P-TEFb elongation factor. Similar complexes have been independently characterized by several different laboratories and are often referred to as super elongation complex. The involvement of AEP in RNAP2-dependent transcription indicates that SL1 must play an important role in RNAP2-dependent transcription. To date, this role of SL1 has not been appreciated. In leukemia, AF4 and ENL family genes are frequently rearranged to form chimeric fusion genes with MLL. The resultant MLL fusion genes produce chimeric MLL fusion proteins comprising MLL and AEP components. The MLL portion functions as a targeting module, which specifically binds chromatin containing di-/tri-methylated histone H3 lysine 36 and non-methylated CpGs. This type of chromatin is enriched at the promoters of transcriptionally active genes which allows MLL fusion proteins to selectively bind to transcriptionally-active/CpG-rich gene promoters. The fusion partner portion, which recruits other AEP components and SL1, is responsible for activation of RNAP2-dependent transcription. Consequently, MLL fusion proteins constitutively activate the transcription of previously-transcribed MLL target genes. Structure/function analysis has shown that the ability of MLL fusion proteins to transform hematopoietic progenitors depends on the recruitment of AEP and SL1. Thus, the AEP/SL1-mediated gene activation pathway appears to be the central mechanism of MLL fusion-mediated transcriptional activation. However, the molecular mechanism by which SL1 activates RNAP2-dependent transcription remains largely unclear. This review aims to cover recent discoveries of the mechanism of transcriptional activation by MLL fusion proteins and to introduce novel roles of SL1 in RNAP2-dependent transcription by discussing how the RNAP1 machinery may be involved in RNAP2-dependent gene regulation.
Collapse
Affiliation(s)
- Akihiko Yokoyama
- Tsuruoka Meatabolomics Laboratory, National Cancer Center, Yamagata, Japan
| |
Collapse
|
18
|
Parameswaran S, Vizeacoumar FS, Kalyanasundaram Bhanumathy K, Qin F, Islam MF, Toosi BM, Cunningham CE, Mousseau DD, Uppalapati MC, Stirling PC, Wu Y, Bonham K, Freywald A, Li H, Vizeacoumar FJ. Molecular characterization of an MLL1 fusion and its role in chromosomal instability. Mol Oncol 2018; 13:422-440. [PMID: 30548174 PMCID: PMC6360371 DOI: 10.1002/1878-0261.12423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/06/2018] [Accepted: 11/26/2018] [Indexed: 01/02/2023] Open
Abstract
Chromosomal rearrangements involving the mixed‐lineage leukemia (MLL1) gene are common in a unique group of acute leukemias, with more than 100 fusion partners in this malignancy alone. However, do these fusions occur or have a role in solid tumors? We performed extensive network analyses of MLL1‐fusion partners in patient datasets, revealing that multiple MLL1‐fusion partners exhibited significant interactions with the androgen‐receptor signaling pathway. Further exploration of tumor sequence data from TCGA predicts the presence of MLL1 fusions with truncated SET domain in prostate tumors. To investigate the physiological relevance of MLL1 fusions in solid tumors, we engineered a truncated version of MLL1 by fusing it with one of its known fusion partners, ZC3H13, to use as a model system. Functional characterization with cell‐based assays revealed that MLL1‐ZC3H13 fusion induced chromosomal instability, affected mitotic progression, and enhanced tumorsphere formation. The MLL1‐ZC3H13 chimera consistently increased the expression of a cancer stem cell marker (CD44); in addition, we detected potential collateral lethality between DOT1L and MLL1 fusions. Our work reveals that MLL1 fusions are likely prevalent in solid tumors and exhibit a potential pro‐tumorigenic role.
Collapse
Affiliation(s)
- Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Md Fahmid Islam
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Behzad M Toosi
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Chelsea E Cunningham
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Darrell D Mousseau
- Cell Signaling Laboratory, Departments of Psychiatry and Physiology, University of Saskatchewan, Saskatoon, Canada
| | - Maruti C Uppalapati
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Yuliang Wu
- Department of Biochemistry, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Keith Bonham
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Canada.,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Canada
| |
Collapse
|
19
|
Du L, Grigsby SM, Yao A, Chang Y, Johnson G, Sun H, Nikolovska-Coleska Z. Peptidomimetics for Targeting Protein-Protein Interactions between DOT1L and MLL Oncofusion Proteins AF9 and ENL. ACS Med Chem Lett 2018; 9:895-900. [PMID: 30258537 DOI: 10.1021/acsmedchemlett.8b00175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/06/2018] [Indexed: 01/08/2023] Open
Abstract
MLL-fusion proteins, AF9 and ENL, play an essential role in the recruitment of DOT1L and the H3K79 hypermethylation of MLL target genes, which is pivotal for leukemogenesis. Blocking these interactions may represent a novel therapeutic approach for MLL-rearranged leukemia. Based on the 7 mer DOT1L peptide, a class of peptidomimetics was designed. Compound 21 with modified middle residues, achieved significantly improved binding affinities to AF9 and ENL, with KD values of 15 nM and 57 nM, respectively. Importantly, 21 recognizes and binds to the cellular AF9 protein and effectively inhibits the AF9-DOT1L interactions in cells. Modifications of the N- and C-termini of 21 resulted in 28 with 2-fold improved binding affinity to AF9 and much decreased peptidic characteristics. Our study provides a proof-of-concept for development of nonpeptidic compounds to inhibit DOT1L activity by targeting its recruitment and the interactions between DOT1L and MLL-oncofusion proteins AF9 and ENL.
Collapse
Affiliation(s)
- Lei Du
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | | | - Aihong Yao
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Yujie Chang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | | | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | | |
Collapse
|
20
|
Krivtsov AV, Hoshii T, Armstrong SA. Mixed-Lineage Leukemia Fusions and Chromatin in Leukemia. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026658. [PMID: 28242784 DOI: 10.1101/cshperspect.a026658] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent studies have shown the importance of chromatin-modifying complexes in the maintenance of developmental gene expression and human disease. The mixed lineage leukemia gene (MLL1) encodes a chromatin-modifying protein and was discovered as a result of the cloning of translocations involved in human leukemias. MLL1 is a histone lysine 4 (H3K4) methyltransferase that supports transcription of genes that are important for normal development including homeotic (Hox) genes. MLL1 rearrangements result in expression of fusion proteins without H3K4 methylation activity but may gain the ability to recruit other chromatin-associated complexes such as the H3K79 methyltransferase DOT1L and the super elongation complex. Therefore, chromosomal translocations involving MLL1 appear to directly perturb the regulation of multiple chromatin-associated complexes to allow inappropriate expression of developmentally regulated genes and thus drive leukemia development.
Collapse
Affiliation(s)
- Andrei V Krivtsov
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02215
| | - Takayuki Hoshii
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02215
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02215
| |
Collapse
|
21
|
Evolution of AF6-RAS association and its implications in mixed-lineage leukemia. Nat Commun 2017; 8:1099. [PMID: 29062045 PMCID: PMC5653649 DOI: 10.1038/s41467-017-01326-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/09/2017] [Indexed: 12/31/2022] Open
Abstract
Elucidation of activation mechanisms governing protein fusions is essential for therapeutic development. MLL undergoes rearrangement with numerous partners, including a recurrent translocation fusing the epigenetic regulator to a cytoplasmic RAS effector, AF6/afadin. We show here that AF6 employs a non-canonical, evolutionarily conserved α-helix to bind RAS, unique to AF6 and the classical RASSF effectors. Further, all patients with MLL-AF6 translocations express fusion proteins missing only this helix from AF6, resulting in exposure of hydrophobic residues that induce dimerization. We provide evidence that oligomerization is the dominant mechanism driving oncogenesis from rare MLL translocation partners and employ our mechanistic understanding of MLL-AF6 to examine how dimers induce leukemia. Proteomic data resolve association of dimerized MLL with gene expression modulators, and inhibiting dimerization disrupts formation of these complexes while completely abrogating leukemogenesis in mice. Oncogenic gene translocations are thus selected under pressure from protein structure/function, underscoring the complex nature of chromosomal rearrangements. Several rearrangements of the MLL gene are associated with acute leukemia, including the fusion of MLL with a RAS effector protein, AF6. Here the authors show that the truncated AF6 can induce AF6-MLL dimerization and drive its oncogenic activity.
Collapse
|
22
|
Möbitz H, Machauer R, Holzer P, Vaupel A, Stauffer F, Ragot C, Caravatti G, Scheufler C, Fernandez C, Hommel U, Tiedt R, Beyer KS, Chen C, Zhu H, Gaul C. Discovery of Potent, Selective, and Structurally Novel Dot1L Inhibitors by a Fragment Linking Approach. ACS Med Chem Lett 2017; 8:338-343. [PMID: 28337327 DOI: 10.1021/acsmedchemlett.6b00519] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/14/2017] [Indexed: 02/07/2023] Open
Abstract
Misdirected catalytic activity of histone methyltransferase Dot1L is believed to be causative for a subset of highly aggressive acute leukemias. Targeting the catalytic domain of Dot1L represents a potential therapeutic approach for these leukemias. In the context of a comprehensive Dot1L hit finding strategy, a knowledge-based virtual screen of the Dot1L SAM binding pocket led to the discovery of 2, a non-nucleoside fragment mimicking key interactions of SAM bound to Dot1L. Fragment linking of 2 and 3, an induced back pocket binder identified in earlier studies, followed by careful ligand optimization led to the identification of 7, a highly potent, selective and structurally novel Dot1L inhibitor.
Collapse
Affiliation(s)
- Henrik Möbitz
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Rainer Machauer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Philipp Holzer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Andrea Vaupel
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Frédéric Stauffer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Christian Ragot
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Giorgio Caravatti
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Clemens Scheufler
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Cesar Fernandez
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Ulrich Hommel
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Ralph Tiedt
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Kim S. Beyer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Chao Chen
- Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Hugh Zhu
- Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Christoph Gaul
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| |
Collapse
|
23
|
Dafflon C, Craig VJ, Méreau H, Gräsel J, Schacher Engstler B, Hoffman G, Nigsch F, Gaulis S, Barys L, Ito M, Aguadé-Gorgorió J, Bornhauser B, Bourquin JP, Proske A, Stork-Fux C, Murakami M, Sellers WR, Hofmann F, Schwaller J, Tiedt R. Complementary activities of DOT1L and Menin inhibitors in MLL-rearranged leukemia. Leukemia 2016; 31:1269-1277. [PMID: 27840424 DOI: 10.1038/leu.2016.327] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/16/2016] [Accepted: 10/21/2016] [Indexed: 12/16/2022]
Abstract
Chromosomal rearrangements of the mixed lineage leukemia (MLL/KMT2A) gene leading to oncogenic MLL-fusion proteins occur in ~10% of acute leukemias and are associated with poor clinical outcomes, emphasizing the need for new treatment modalities. Inhibition of the DOT1-like histone H3K79 methyltransferase (DOT1L) is a specific therapeutic approach for such leukemias that is currently being tested in clinical trials. However, in most MLL-rearranged leukemia models responses to DOT1L inhibitors are limited. Here, we performed deep-coverage short hairpin RNA sensitizer screens in DOT1L inhibitor-treated MLL-rearranged leukemia cell lines and discovered that targeting additional nodes of MLL complexes concomitantly with DOT1L inhibition bears great potential for superior therapeutic results. Most notably, combination of a DOT1L inhibitor with an inhibitor of the MLL-Menin interaction markedly enhanced induction of differentiation and cell killing in various MLL disease models including primary leukemia cells, while sparing normal hematopoiesis and leukemias without MLL rearrangements. Gene expression analysis on human and murine leukemic cells revealed that target genes of MLL-fusion proteins and MYC were suppressed more profoundly upon combination treatment. Our findings provide a strong rationale for a novel targeted combination therapy that is expected to improve therapeutic outcomes in patients with MLL-rearranged leukemia.
Collapse
Affiliation(s)
- C Dafflon
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - V J Craig
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - H Méreau
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - J Gräsel
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - B Schacher Engstler
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - G Hoffman
- Novartis Institutes for BioMedical Research, Developmental and Molecular Pathways, Cambridge, MA, USA
| | - F Nigsch
- Novartis Institutes for BioMedical Research, Developmental and Molecular Pathways, Basel, Switzerland
| | - S Gaulis
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - L Barys
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - M Ito
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - J Aguadé-Gorgorió
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | - B Bornhauser
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | - J-P Bourquin
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | - A Proske
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - C Stork-Fux
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - M Murakami
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - W R Sellers
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Cambridge, MA, USA
| | - F Hofmann
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| | - J Schwaller
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - R Tiedt
- Novartis Institutes for BioMedical Research, Disease Area Oncology, Basel, Switzerland
| |
Collapse
|
24
|
Saito Y, Nakagawa T, Kakihana A, Nakamura Y, Nabika T, Kasai M, Takamori M, Yamagishi N, Kuga T, Hatayama T, Nakayama Y. Yeast Two-Hybrid and One-Hybrid Screenings Identify Regulators ofhsp70Gene Expression. J Cell Biochem 2016; 117:2109-17. [DOI: 10.1002/jcb.25517] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/10/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Youhei Saito
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Takanobu Nakagawa
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Ayana Kakihana
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Yoshia Nakamura
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Tomomi Nabika
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Michihiro Kasai
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Mai Takamori
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Nobuyuki Yamagishi
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Takahisa Kuga
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Takumi Hatayama
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| | - Yuji Nakayama
- Department of Biochemistry and Molecular Biology; Kyoto Pharmaceutical University; 5 Nakauchi-cho, Misasagi, Yamashina-ku Kyoto 607-8414 Japan
| |
Collapse
|
25
|
|
26
|
Wong M, Polly P, Liu T. The histone methyltransferase DOT1L: regulatory functions and a cancer therapy target. Am J Cancer Res 2015; 5:2823-2837. [PMID: 26609488 PMCID: PMC4633909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/15/2015] [Indexed: 06/05/2023] Open
Abstract
DOT1L is a unique histone methyltransferase that targets the histone H3 lysine 79 (H3K79) residue for mono-, di- and tri- methylation. Histone H3K79 mono- and di-methylation results in active gene transcription, while H3K79 tri-methylation is associated with gene repression. DOT1L has a critical role in regulating gene transcription, development, cell cycle progression, somatic reprogramming and DNA damage repair. DOT1L interacts with Mixed Lineage Leukemia (MLL) fusion proteins, leading to enhanced H3K79 methylation, maintenance of open chromatin, overexpression of downstream oncogenes and leukemogenesis. Importantly, small molecule DOT1L inhibitors have been recently developed, and one of the DOT1L inhibitors is already under investigation in a Phase I clinical trial in patients with MLL fusion gene-driven leukemia.
Collapse
Affiliation(s)
- Matthew Wong
- Children’s Cancer Institute Australia for Medical ResearchRandwick NSW 2031, Australia
| | - Patsie Polly
- Department of Pathology and Inflammation and Infection Research Centre, School of Medical Sciences, UNSW AustraliaKensington NSW 2052, Australia
| | - Tao Liu
- Children’s Cancer Institute Australia for Medical ResearchRandwick NSW 2031, Australia
- School of Women’s & Children’s Health, University of New South WalesRandwick NSW 2031, Australia
| |
Collapse
|
27
|
Chen CW, Armstrong SA. Targeting DOT1L and HOX gene expression in MLL-rearranged leukemia and beyond. Exp Hematol 2015; 43:673-84. [PMID: 26118503 DOI: 10.1016/j.exphem.2015.05.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/28/2015] [Accepted: 05/28/2015] [Indexed: 01/05/2023]
Abstract
Leukemias harboring mixed-lineage leukemia gene (MLL1) abnormalities are associated with poor clinical outcomes, and new therapeutic approaches are desperately needed. Rearrangement of the MLL1 gene generates chimeric proteins that fuse the NH3 terminus of MLL1 to the COOH terminus of its translocation partners. These MLL1 fusion oncoproteins drive the expression of homeobox genes such as HOXA cluster genes and myeloid ecotropic viral integration site 1 homolog (MEIS1), which are known to induce leukemic transformation of hematopoietic progenitors. Genomewide histone methylation studies have revealed that the abnormal expression of MLL1 fusion target genes is associated with high levels of H3K79 methylation at these gene loci. The only known enzyme that catalyzes methylation of H3K79 is disruptor of telomeric-silencing 1-like (DOT1L). Loss-of-function mouse models, as well as small molecular inhibitors of DOT1L, illustrate that leukemias driven by MLL1 translocations are dependent on DOT1L enzymatic activity for proliferation and for the maintenance of HOXA gene expression. Furthermore, DOT1L also appears to be important for HOXA gene expression in other settings including leukemias with select genetic abnormalities. These discoveries have established a foundation for disease-specific therapies that target chromatin modifications in highly malignant leukemias harboring specific genetic abnormalities. This review focuses on the molecular mechanisms underlying MLL1 translocation-driven leukemogenesis and the latest progress on DOT1L-targeted epigenetic therapies for MLL1-rearranged and other leukemias.
Collapse
Affiliation(s)
- Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
28
|
Kuntimaddi A, Achille NJ, Thorpe J, Lokken AA, Singh R, Hemenway CS, Adli M, Zeleznik-Le NJ, Bushweller JH. Degree of recruitment of DOT1L to MLL-AF9 defines level of H3K79 Di- and tri-methylation on target genes and transformation potential. Cell Rep 2015; 11:808-20. [PMID: 25921540 DOI: 10.1016/j.celrep.2015.04.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/18/2015] [Accepted: 03/30/2015] [Indexed: 12/16/2022] Open
Abstract
The MLL gene is a common target of chromosomal translocations found in human leukemia. MLL-fusion leukemia has a consistently poor outcome. One of the most common translocation partners is AF9 (MLLT3). MLL-AF9 recruits DOT1L, a histone 3 lysine 79 methyltransferase (H3K79me1/me2/me3), leading to aberrant gene transcription. We show that DOT1L has three AF9 binding sites and present the nuclear magnetic resonance (NMR) solution structure of a DOT1L-AF9 complex. We generate structure-guided point mutations and find that they have graded effects on recruitment of DOT1L to MLL-AF9. Chromatin immunoprecipitation sequencing (ChIP-seq) analyses of H3K79me2 and H3K79me3 show that graded reduction of the DOT1L interaction with MLL-AF9 results in differential loss of H3K79me2 and me3 at MLL-AF9 target genes. Furthermore, the degree of DOT1L recruitment is linked to the level of MLL-AF9 hematopoietic transformation.
Collapse
Affiliation(s)
- Aravinda Kuntimaddi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nicholas J Achille
- Oncology Institute, Department of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jeremy Thorpe
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Alyson A Lokken
- Oncology Institute, Department of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Ritambhara Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Charles S Hemenway
- Oncology Institute, Department of Pediatrics, Loyola University Chicago, Maywood, IL 60153, USA
| | - Mazhar Adli
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nancy J Zeleznik-Le
- Oncology Institute, Department of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
| |
Collapse
|
29
|
Chen CW, Koche RP, Sinha AU, Deshpande AJ, Zhu N, Eng R, Doench JG, Xu H, Chu SH, Qi J, Wang X, Delaney C, Bernt KM, Root DE, Hahn WC, Bradner JE, Armstrong SA. DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia. Nat Med 2015; 21:335-43. [PMID: 25822366 PMCID: PMC4390532 DOI: 10.1038/nm.3832] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/02/2015] [Indexed: 12/14/2022]
Abstract
MLL -rearrangements generate MLL-fusion proteins that bind DNA and drive leukemogenic gene expression. This gene expression program is dependent on the histone 3 lysine 79 (H3K79) methyltransferase DOT1L, and small molecule DOT1L inhibitors show promise as therapeutics for these leukemias. However, the mechanisms underlying this dependency are unclear. We conducted a genome-scale RNAi screen and found that the histone deacetylase SIRT1 is required for the establishment of a heterochromatin-like state around MLL-fusion target genes after DOT1L inhibition. DOT1L inhibits chromatin localization of a repressive complex composed of SIRT1 and SUV39H1, thereby maintaining an open chromatin state with elevated H3K9 acetylation and minimal H3K9 methylation at MLL-fusion target genes. Furthermore, the combination of SIRT1 activators and DOT1L inhibitors shows enhanced activity against MLL-rearranged leukemia cells. These results indicate that the dynamic interplay between chromatin regulators controlling activation and repression of gene expression could provide novel opportunities for combination therapy.
Collapse
Affiliation(s)
- Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard P Koche
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Amit U Sinha
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aniruddha J Deshpande
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nan Zhu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rowena Eng
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John G Doench
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Haiming Xu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Scott H Chu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Xi Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Christopher Delaney
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kathrin M Bernt
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - William C Hahn
- 1] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James E Bradner
- 1] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
30
|
Gibbons GS, Owens SR, Fearon ER, Nikolovska-Coleska Z. Regulation of Wnt signaling target gene expression by the histone methyltransferase DOT1L. ACS Chem Biol 2015; 10:109-14. [PMID: 25361163 DOI: 10.1021/cb500668u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The histone methyltransferase DOT1L, solely responsible for histone H3 lysine 79 (H3K79) methylation, is associated with gene activation. Human leukemias carrying MLL gene rearrangements aberrantly recruit DOT1L to leukemogenic genes leading to increased H3K79 methylation and their transcriptional activation. Recent studies suggest that Wnt-targeted genes also depend on H3K79 methylation. Employing a chemical biology approach, the requirement for H3K79 methylation was investigated in Wnt pathway-inducible HEK293 cells and human colon adenocarcinoma-derived cell lines by inhibiting DOT1L with EPZ004777, a selective and potent S-adenosylmethionine competitive inhibitor. Our findings indicate that H3K79 methylation is not essential for the canonical Wnt signaling pathway, in particular for maintenance or activation of Wnt pathway target gene expression. Furthermore, H3K79 methylation is not elevated in human colon carcinoma samples in comparison with normal colon tissue. Therefore, our findings indicate that inhibition of DOT1L histone methyltransferase activity is likely not a viable therapeutic strategy in colon cancer.
Collapse
Affiliation(s)
- Garrett S. Gibbons
- Department
of Pathology, ‡Departments of Internal Medicine and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Scott R. Owens
- Department
of Pathology, ‡Departments of Internal Medicine and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Eric R. Fearon
- Department
of Pathology, ‡Departments of Internal Medicine and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Zaneta Nikolovska-Coleska
- Department
of Pathology, ‡Departments of Internal Medicine and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
31
|
Abstract
Protein-protein interactions regulate many important cellular processes, including carbohydrate and lipid metabolism, cell cycle and cell death regulation, protein and nucleic acid metabolism, signal transduction, and cellular architecture. A complete understanding of cellular function depends on full characterization of the complex network of cellular protein-protein interactions, including measurements of their kinetic and binding properties. Surface plasmon resonance (SPR) is one of the commonly used technologies for detailed and quantitative studies of protein-protein interactions and determination of their equilibrium and kinetic parameters. SPR provides excellent instrumentation for a label-free, real-time investigation of protein-protein interactions. This chapter details the experimental design and proper use of the instrumentation for a kinetic experiment. It will provide readers with basic theory, assay setup, and the proper way of reporting this type of results with practical tips useful for SPR-based studies. A generic protocol for immobilizing ligands using amino coupling chemistry, also useful if an antibody affinity capture approach is used, performing kinetic studies, and collecting and analyzing data is described.
Collapse
Affiliation(s)
- Zaneta Nikolovska-Coleska
- Department of Pathology, University of Michigan Medical School, 4510E MSRB I, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA,
| |
Collapse
|