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Windisch R, Soliman S, Hoffmann A, Chen-Wichmann L, Danese A, Vosberg S, Bravo J, Lutz S, Kellner C, Fischer A, Gebhard C, Redondo Monte E, Hartmann L, Schneider S, Beier F, Strobl CD, Weigert O, Peipp M, Schündeln M, Stricker SH, Rehli M, Bernhagen J, Humpe A, Klump H, Brendel C, Krause DS, Greif PA, Wichmann C. Engineering an inducible leukemia-associated fusion protein enables large-scale ex vivo production of functional human phagocytes. Proc Natl Acad Sci U S A 2024; 121:e2312499121. [PMID: 38857395 PMCID: PMC11194515 DOI: 10.1073/pnas.2312499121] [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: 08/01/2023] [Accepted: 03/20/2024] [Indexed: 06/12/2024] Open
Abstract
Ex vivo expansion of human CD34+ hematopoietic stem and progenitor cells remains a challenge due to rapid differentiation after detachment from the bone marrow niche. In this study, we assessed the capacity of an inducible fusion protein to enable sustained ex vivo proliferation of hematopoietic precursors and their capacity to differentiate into functional phagocytes. We fused the coding sequences of an FK506-Binding Protein 12 (FKBP12)-derived destabilization domain (DD) to the myeloid/lymphoid lineage leukemia/eleven nineteen leukemia (MLL-ENL) fusion gene to generate the fusion protein DD-MLL-ENL and retrovirally expressed the protein switch in human CD34+ progenitors. Using Shield1, a chemical inhibitor of DD fusion protein degradation, we established large-scale and long-term expansion of late monocytic precursors. Upon Shield1 removal, the cells lost self-renewal capacity and spontaneously differentiated, even after 2.5 y of continuous ex vivo expansion. In the absence of Shield1, stimulation with IFN-γ, LPS, and GM-CSF triggered terminal differentiation. Gene expression analysis of the obtained phagocytes revealed marked similarity with naïve monocytes. In functional assays, the novel phagocytes migrated toward CCL2, attached to VCAM-1 under shear stress, produced reactive oxygen species, and engulfed bacterial particles, cellular particles, and apoptotic cells. Finally, we demonstrated Fcγ receptor recognition and phagocytosis of opsonized lymphoma cells in an antibody-dependent manner. Overall, we have established an engineered protein that, as a single factor, is useful for large-scale ex vivo production of human phagocytes. Such adjustable proteins have the potential to be applied as molecular tools to produce functional immune cells for experimental cell-based approaches.
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Affiliation(s)
- Roland Windisch
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Sarah Soliman
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Adrian Hoffmann
- Vascular Biology, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Linping Chen-Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Anna Danese
- Biomedical Center, Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz8010, Austria
| | - Jimena Bravo
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main60596, Germany
| | - Sebastian Lutz
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Christian Kellner
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg93053, Germany
| | - Claudia Gebhard
- Leibniz Institute for Immunotherapy, Regensburg93053, Germany
| | - Enric Redondo Monte
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Luise Hartmann
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Stephanie Schneider
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen52074, Germany
| | - Carolin Dorothea Strobl
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Medicine II, Christian Albrechts University of Kiel, Kiel24105, Germany
| | - Michael Schündeln
- Pediatric Hematology and Oncology, Department of Pediatrics III, University Hospital Essen and the University of Duisburg-Essen, Essen45147, Germany
| | - Stefan H. Stricker
- Biomedical Center, Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg93053, Germany
- Leibniz Institute for Immunotherapy, Regensburg93053, Germany
| | - Jürgen Bernhagen
- Vascular Biology, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München, Munich81377, Germany
- Munich Cluster for Systems Neurology, Munich81377, Germany
| | - Andreas Humpe
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, Essen45147, Germany
- Institute for Transfusion Medicine and Cell Therapeutics, University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen52074, Germany
| | - Christian Brendel
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA02115
| | - Daniela S. Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main60596, Germany
- Institute of General Pharmacology and Toxicology, University Hospital Frankfurt, Goethe-University, Frankfurt am Main60596, Germany
| | - Philipp A. Greif
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
- German Cancer Consortium, Partner site Munich, Munich81377, Germany
- German Cancer Research Center, Heidelberg69120, Germany
| | - Christian Wichmann
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, Ludwig-Maximilians-Universität München, Munich81377, Germany
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2
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Ding Y, Zhang C, Zuo Q, Jin K, Li B. lncCPSET1 acts as a scaffold for MLL2/COMPASS to regulate Bmp4 and promote the formation of chicken primordial germ cells. Mol Genet Genomics 2024; 299:41. [PMID: 38551742 DOI: 10.1007/s00438-024-02127-4] [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: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
Primordial germ cells (PGCs) are the ancestors of female and male germ cells. Recent studies have shown that long non-coding RNA (lncRNA) and histone methylation are key epigenetic factors affecting PGC formation; however, their joint regulatory mechanisms have rarely been studied. Here, we explored the mechanism by which lncCPSET1 and H3K4me2 synergistically regulate the formation of chicken PGCs for the first time. Combined with chromatin immunoprecipitation (CHIP) sequencing and RNA-seq of PGCs transfected with the lncCPSET1 overexpression vector, GO annotation and KEGG enrichment analysis revealed that Wnt and TGF-β signaling pathways were significantly enriched, and Fzd2, Id1, Id4, and Bmp4 were identified as candidate genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that ASH2L, DPY30, WDR5, and RBBP5 overexpression significantly increased the expression of Bmp4, which was up-regulated after lncCPSET1 overexpression as well. It indicated that Bmp4 is a target gene co-regulated by lncCPSET1 and MLL2/COMPASS. Interestingly, co-immunoprecipitation results showed that ASH2L, DPY30 and WDR5 combined and RBBP5 weakly combined with DPY30 and WDR5. lncCPSET1 overexpression significantly increased Dpy30 expression and co-immunoprecipitation showed that interference/overexpression of lncCPSET1 did not affect the binding between the proteins in the complexes, but interference with lncCPSET1 inhibited DPY30 expression, which was confirmed by RNA immunoprecipitation that lncCPSET1 binds to DPY30. Additionally, CHIP-qPCR results showed that DPY30 enriched in the Bmp4 promoter region promoted its transcription, thus promoting the formation of PGCs. This study demonstrated that lncCPSET1 and H3K4me2 synergistically promote PGC formation, providing a reference for the study of the regulatory mechanisms between lncRNA and histone methylation, as well as a molecular basis for elucidating the formation mechanism of PGCs in chickens.
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Affiliation(s)
- Ying Ding
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chen Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- RNA Medicine Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
| | - Qisheng Zuo
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kai Jin
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Bichun Li
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China.
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3
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Ahmad M, Imran A, Movileanu L. Overlapping characteristics of weak interactions of two transcriptional regulators with WDR5. Int J Biol Macromol 2024; 258:128969. [PMID: 38158065 PMCID: PMC10922662 DOI: 10.1016/j.ijbiomac.2023.128969] [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: 08/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The WD40 repeat protein 5 (WDR5) is a nuclear hub that critically influences gene expression by interacting with transcriptional regulators. Utilizing the WDR5 binding motif (WBM) site, WDR5 interacts with the myelocytomatosis (MYC), an oncoprotein transcription factor, and the retinoblastoma-binding protein 5 (RbBP5), a scaffolding element of an epigenetic complex. Given the clinical significance of these protein-protein interactions (PPIs), there is a pressing necessity for a quantitative assessment of these processes. Here, we use biolayer interferometry (BLI) to examine interactions of WDR5 with consensus peptide ligands of MYC and RbBP5. We found that both interactions exhibit relatively weak affinities arising from a fast dissociation process. Remarkably, live-cell imaging identified distinctive WDR5 localizations in the absence and presence of full-length binding partners. Although WDR5 tends to accumulate within nucleoli, WBM-mediated interactions with MYC and RbBP5 require their localization outside nucleoli. We utilize fluorescence resonance energy transfer (FRET) microscopy to confirm these weak interactions through a low FRET efficiency of the MYC-WDR5 and RbBP5-WDR5 complexes in living cells. In addition, we evaluate the impact of peptide and small-molecule inhibitors on these interactions. These outcomes form a fundamental basis for further developments to clarify the multitasking role of the WBM binding site of WDR5.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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4
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Blatter M, Meylan C, Cléry A, Giambruno R, Nikolaev Y, Heidecker M, Solanki JA, Diaz MO, Gabellini D, Allain FHT. RNA binding induces an allosteric switch in Cyp33 to repress MLL1-mediated transcription. SCIENCE ADVANCES 2023; 9:eadf5330. [PMID: 37075125 PMCID: PMC10115415 DOI: 10.1126/sciadv.adf5330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mixed-lineage leukemia 1 (MLL1) is a transcription activator of the HOX family, which binds to specific epigenetic marks on histone H3 through its third plant homeodomain (PHD3) domain. Through an unknown mechanism, MLL1 activity is repressed by cyclophilin 33 (Cyp33), which binds to MLL1 PHD3. We determined solution structures of Cyp33 RNA recognition motif (RRM) free, bound to RNA, to MLL1 PHD3, and to both MLL1 and the histone H3 lysine N6-trimethylated. We found that a conserved α helix, amino-terminal to the RRM domain, adopts three different positions facilitating a cascade of binding events. These conformational changes are triggered by Cyp33 RNA binding and ultimately lead to MLL1 release from the histone mark. Together, our mechanistic findings rationalize how Cyp33 binding to MLL1 can switch chromatin to a transcriptional repressive state triggered by RNA binding as a negative feedback loop.
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Affiliation(s)
- Markus Blatter
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Corresponding author. (F.H.-T.A.); (M.B.)
| | - Charlotte Meylan
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Antoine Cléry
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Roberto Giambruno
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Yaroslav Nikolaev
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Michel Heidecker
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jessica Arvindbhai Solanki
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago Medical Center, University of Chicago, Chicago, IL, USA
| | - Manuel O. Diaz
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago Medical Center, University of Chicago, Chicago, IL, USA
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Frédéric H.-T. Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Corresponding author. (F.H.-T.A.); (M.B.)
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5
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Structural insights on the KMT2-NCP interaction. Biochem Soc Trans 2023; 51:427-434. [PMID: 36695549 DOI: 10.1042/bst20221155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
The MLL/KMT2 family enzymes are frequently mutated in human cancers and congenital diseases. They deposit the majority of histone 3 lysine 4 (H3K4) mono-, di-, or tri-methylation in mammals and are tightly associated with gene activation. Structural and biochemical studies in recent years provide in-depth understanding of how the MLL1 and homologous yeast SET1 complexes interact with the nucleosome core particle (NCP) and how their activities for H3K4 methylation are regulated by the conserved core components. Here, we will discuss the recent single molecule cryo-EM studies on the MLL1 and ySET1 complexes bound on the NCP. These studies highlight the dynamic regulation of the MLL/SET1 family lysine methyltransferases with unique features as compared with other histone lysine methyltransferases. These studies provide insights for loci-specific regulation of H3K4 methylation states in cells. The mechanistic studies on the MLL1 complex have already led to the development of the MLL1 inhibitors that show efficacy in acute leukemia and metastatic breast cancers. Future studies on the MLL/SET1 family enzymes will continue to bring to light potential therapeutic opportunities.
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6
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Windisch R, Kreissig S, Wichmann C. Defined Human Leukemic CD34+ Liquid Cultures to Study HDAC/Transcriptional Repressor Complexes. Methods Mol Biol 2023; 2589:27-49. [PMID: 36255616 DOI: 10.1007/978-1-0716-2788-4_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Defined human primary cell model systems with growth dependence on oncogenes are highly requested to investigate tumor pathogenesis and to validate pharmacological inhibitors that specifically target oncoproteins and their executing protein complex partners. In acute myeloid leukemia (AML), transcription factors such as RUNX1 and MLL1, which are important for normal blood cell development, frequently harbor mutations including chromosomal translocations with other coding genes, resulting in tumor-promoting gain-of-function fusion proteins. These oncoproteins completely modify transcriptional programs, thereby inducing malignant cell phenotypes. A common theme of the chimeric gene products is their physical interaction with a variety of chromatin-modifying effector molecules, including histone acetyltransferases (HATs) and histone deacetylases (HDACs). These aberrant multiprotein machineries disturb gene expression and promote malignant cell growth. In this chapter, we briefly summarize the current understanding regarding AML-associated oncogene-driven human CD34+ blood progenitor cell expansion in ex vivo liquid cultures. We provide a step-by-step protocol to establish oncogene-induced human CD34+ blood progenitor cell cultures suitable to analyze the impact of transcriptional repressor/HDAC activity in these human AML cell models.
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Affiliation(s)
- Roland Windisch
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Sophie Kreissig
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, University Hospital, LMU Munich, Munich, Germany.
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7
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Ellis RJ, Bara A, Vargas CA, Frick AL, Loh E, Landry J, Uzamere TO, Callens JE, Martin Q, Rajarajan P, Brennand K, Ramakrishnan A, Shen L, Szutorisz H, Hurd YL. Prenatal Δ 9-Tetrahydrocannabinol Exposure in Males Leads to Motivational Disturbances Related to Striatal Epigenetic Dysregulation. Biol Psychiatry 2022; 92:127-138. [PMID: 34895699 PMCID: PMC8957623 DOI: 10.1016/j.biopsych.2021.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Cannabis remains one of the most widely abused drugs during pregnancy. In utero exposure to its principal psychoactive component, Δ9-tetrahydrocannabinol (THC), can result in long-term neuropsychiatric risk for the progeny. This study investigated epigenetic signatures underlying these enduring consequences. METHODS Rat dams were exposed daily to THC (0.15 mg/kg) during pregnancy, and adult male offspring were examined for reward and depressive-like behavioral endophenotypes. Using unbiased sequencing approaches, we explored transcriptional and epigenetic profiles in the nucleus accumbens (NAc), a brain area central to reward and emotional processing. An in vitro CRISPR (clustered regularly interspaced short palindromic repeats) activation model coupled with RNA sequencing was also applied to study specific consequences of epigenetic dysregulation, and altered molecular signatures were compared with human major depressive disorder transcriptome datasets. RESULTS Prenatal THC exposure induced increased motivation for food, heightened learned helplessness and anhedonia, and altered stress sensitivity. We identified a robust increase specific to males in the expression of Kmt2a (histone-lysine N-methyltransferase 2A) that targets H3K4 (lysine 4 on histone H3) in cellular chromatin. Normalizing Kmt2a in the NAc rescued the motivational phenotype of prenatally THC-exposed animals. Comparison of RNA- and H3K4me3-sequencing datasets from the NAc of rat offspring with the in vitro model of Kmt2a upregulation revealed overlapping, significant disturbances in pathways that mediate synaptic plasticity. Similar transcriptional alterations were detected in human major depressive disorder. CONCLUSIONS These studies provide direct evidence for the persistent effects of prenatal cannabis exposure on transcriptional and epigenetic deviations in the NAc via Kmt2a dysregulation and associated psychiatric vulnerability.
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Affiliation(s)
- Randall J. Ellis
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Addiction Institute of Mount Sinai, New York, NY, USA
| | - Anissa Bara
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Friedman Brain Institute, Department of Psychiatry, New York, NY, USA
| | - Claudia A. Vargas
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA
| | - Amy L. Frick
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA
| | - Eddie Loh
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA
| | - Joseph Landry
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Addiction Institute of Mount Sinai, New York, NY, USA
| | - Teddy O. Uzamere
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Addiction Institute of Mount Sinai, New York, NY, USA
| | - James E. Callens
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Addiction Institute of Mount Sinai, New York, NY, USA
| | - Qammarah Martin
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Addiction Institute of Mount Sinai, New York, NY, USA
| | - Prashanth Rajarajan
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA
| | - Kristen Brennand
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA,Addiction Institute of Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA
| | - Li Shen
- Icahn School of Medicine at Mount Sinai, Friedman Brain Institute, Department of Neuroscience, New York, NY, USA
| | - Henrietta Szutorisz
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Yasmin L Hurd
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Addiction Institute of Mount Sinai, New York, New York.
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8
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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9
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Bai H, Zhang SQ, Lei H, Wang F, Ma M, Xin M. Menin-MLL protein-protein interaction inhibitors: a patent review (2014-2021). Expert Opin Ther Pat 2022; 32:507-522. [PMID: 35202550 DOI: 10.1080/13543776.2022.2045947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Chromosomal translocations involving the mixed-lineage leukemia (MLL, KMT2A, MLL1) genes result in the production of MLL fusion proteins, which cause abnormal transcriptional regulation leading to acute leukemia (AL). Menin (MEN1) protein is essential for MLL to regulate the expression of related target genes. High affinity interactions between the amino terminus of MLL proteins and Menin proteins are required to mediate the oncogenic transformation of MLL fusion proteins. Therefore, inhibition of Menin and MLL interaction is a potential therapeutic strategy for MLL rearrangement (MLL-r) leukemia and can provide a new choice for treatment of other diseases. Therefore, researchers have made great efforts to explore small molecule Menin-MLL interaction inhibitors. AREAS COVERED This review is to provide an overview of the patented Menin-MLL protein protein interaction inhibitors from 2014 to 2021. EXPERT OPINION Menin-MLL interaction inhibitors have therapeutic potential in the treatment of acute leukemia, such as acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Nowadays, SNDX-5613 and KO-539 have been granted orphan drug designation by the FDA for treatment of refractory/relapsed leukemia and AML, respectively. In addition, they are undergoing clinical evaluation for other indications. It is clear that Menin-MLL interaction inhibitors have promising benefits in the clinical treatment of acute leukemia and other diseases.
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Affiliation(s)
- Huanrong Bai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - San-Qi Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Hao Lei
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Fang Wang
- Hebei Chemical & Pharmaceutical College, Shijiazhuang 050000, P.R. China
| | - Mengyan Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Minhang Xin
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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10
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Foroutan A, Haghshenas S, Bhai P, Levy MA, Kerkhof J, McConkey H, Niceta M, Ciolfi A, Pedace L, Miele E, Genevieve D, Heide S, Alders M, Zampino G, Merla G, Fradin M, Bieth E, Bonneau D, Dieterich K, Fergelot P, Schaefer E, Faivre L, Vitobello A, Maitz S, Fischetto R, Gervasini C, Piccione M, van de Laar I, Tartaglia M, Sadikovic B, Lebre AS. Clinical Utility of a Unique Genome-Wide DNA Methylation Signature for KMT2A-Related Syndrome. Int J Mol Sci 2022; 23:ijms23031815. [PMID: 35163737 PMCID: PMC8836705 DOI: 10.3390/ijms23031815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/28/2022] Open
Abstract
Wiedemann–Steiner syndrome (WDSTS) is a Mendelian syndromic intellectual disability (ID) condition associated with hypertrichosis cubiti, short stature, and characteristic facies caused by pathogenic variants in the KMT2A gene. Clinical features can be inconclusive in mild and unusual WDSTS presentations with variable ID (mild to severe), facies (typical or not) and other associated malformations (bone, cerebral, renal, cardiac and ophthalmological anomalies). Interpretation and classification of rare KMT2A variants can be challenging. A genome-wide DNA methylation episignature for KMT2A-related syndrome could allow functional classification of variants and provide insights into the pathophysiology of WDSTS. Therefore, we assessed genome-wide DNA methylation profiles in a cohort of 60 patients with clinical diagnosis for WDSTS or Kabuki and identified a unique highly sensitive and specific DNA methylation episignature as a molecular biomarker of WDSTS. WDSTS episignature enabled classification of variants of uncertain significance in the KMT2A gene as well as confirmation of diagnosis in patients with clinical presentation of WDSTS without known genetic variants. The changes in the methylation profile resulting from KMT2A mutations involve global reduction in methylation in various genes, including homeobox gene promoters. These findings provide novel insights into the molecular etiology of WDSTS and explain the broad phenotypic spectrum of the disease.
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Affiliation(s)
- Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (L.P.); (E.M.)
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (L.P.); (E.M.)
| | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Groupe DI, Inserm U1183—Institute for Regenerative Medicine and Biotherapy, Montpellier University, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France;
| | - Solveig Heide
- Department of Genetics, Referral Center for Intellectual Disabilities, APHP Sorbonne University, Pitié Salpêtrière Hospital, 75013 Paris, France;
| | - Mariëlle Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy;
- Facoltà di Medicina e Chirurgia, Università Cattolica del S. Cuore, 20123 Roma, Italy
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, Università di Napoli “Federico II”, 80131 Naples, Italy;
- Laboratory of Regulatory and Functional Genomics, Fondazione Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Mélanie Fradin
- Service de Génétique, CHU de Rennes, 35203 Rennes, France;
| | - Eric Bieth
- Medical Genetics Department, University of Angers, CHU Angers, 49000 Angers, France;
| | - Dominique Bonneau
- Department of genetics, CHU d’Angers, 49000 Angers, France and MitoVasc, UMR CNRS 6015-INSERM 1083, University of Angers, 49055 Angers, France;
| | - Klaus Dieterich
- CHU Grenoble Alpes, Inserm, U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, 38000 Grenoble, France;
| | - Patricia Fergelot
- Medical Genetics Department, Inserm U1211, Reference Center AD SOOR, AnDDI-RARE, Bordeaux University, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France;
| | - Elise Schaefer
- Service de Génétique Médicale—Institut de Génétique Médicale d’Alsace—Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg, France;
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, 15 boulevard du Maréchal de Lattre de Tassigny, 21000 Dijon, France; (L.F.); (A.V.)
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, Department of Medical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Antonio Vitobello
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, 15 boulevard du Maréchal de Lattre de Tassigny, 21000 Dijon, France; (L.F.); (A.V.)
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, Department of Medical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, 20900 Monza, Italy;
| | - Rita Fischetto
- Clinical Genetics Unit, Department of Pediatric Medicine, Giovanni XXIII Children’s Hospital, 02115 Bari, Italy;
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy;
| | - Maria Piccione
- Department of Sciences for Health Promotion and Mother and Child Care “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
- Correspondence: (B.S.); (A.-S.L.)
| | - Anne-Sophie Lebre
- Team Physiopathologie des Maladies Psychiatriques, GDR3557-Institut de Psychiatrie, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, 75006 Paris, France
- Centre Hospitalier Universitaire de Reims, Pôle de Biologie Médicale et Pathologie, Service de GénéTique, 51100 Reims, France
- Correspondence: (B.S.); (A.-S.L.)
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11
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Ayoub A, Park SH, Lee YT, Cho US, Dou Y. Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes. Biochemistry 2021; 61:1-9. [DOI: 10.1021/acs.biochem.1c00603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sang Ho Park
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Young-Tae Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
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12
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Chen W, Chen X, Li D, Wang X, Long G, Jiang Z, You Q, Guo X. Discovery of a potent MLL1 and WDR5 protein-protein interaction inhibitor with in vivo antitumor activity. Eur J Med Chem 2021; 223:113677. [PMID: 34225179 DOI: 10.1016/j.ejmech.2021.113677] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 10/21/2022]
Abstract
MLL1-WDR5 interaction is essential for the formation of MLL core complex and its H3K4 methyltransferase activity. Disrupting MLL1-WDR5 interaction has been proposed as a potential therapeutic approach in the treatment of leukemia. A "toolkit" of well-characterized chemical probe will allow exploring animal studies. Based on a specific MLL1-WDR5 PPI inhibitor (DDO-2117), which was previously reported by our group, we conducted a bioisosterism approach by click chemistry to discover novel phenyltriazole scaffold MLL1-WDR5 interaction blockers. Here, our efforts resulted in the best inhibitor 24 (DDO-2093) with high binding affinity (Kd = 11.6 nM) and with improved drug-like properties. Both in vitro and in vivo assays revealed 24 could efficiently block the MLL1-WDR5 interaction. Furthermore, 24 significantly suppressed tumor growth in the MV4-11 xenograft mouse model and showed a favorable safety profile. We propose 24 as a chemical probe that is suitable for in vivo pharmacodynamic and biological studies of MLL1-WDR5 interaction.
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Affiliation(s)
- Weilin Chen
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Xin Chen
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Dongdong Li
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Xianghan Wang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Guanlu Long
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengyu Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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13
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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14
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Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin. Nat Commun 2021; 12:2953. [PMID: 34012049 PMCID: PMC8134635 DOI: 10.1038/s41467-021-23268-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show that DPY30 and the intrinsically disordered regions (IDRs) of ASH2L work together in restricting the rotational dynamics of the MLL1 complex on the NCP. We show that DPY30 binding to ASH2L leads to stabilization and integration of ASH2L IDRs into the MLL1 complex and establishes new ASH2L-NCP contacts. The significance of ASH2L-DPY30 interactions is demonstrated by requirement of both ASH2L IDRs and DPY30 for dramatic increase of processivity and activity of the MLL1 complex. This DPY30 and ASH2L-IDR dependent regulation is NCP-specific and applies to all members of the MLL/SET1 family of enzymes. We further show that DPY30 is causal for de novo establishment of H3K4me3 in ESCs. Our study provides a paradigm of how H3K4me3 is regulated on chromatin and how H3K4me3 heterogeneity can be modulated by ASH2L IDR interacting proteins. Regulation of the MLL family of histone H3K4 methyltransferases on the nucleosome core particle (NCP) remains largely unknown. Here the authors show that intrinsically disordered regions of ASH2L and DPY30 restrict the rotational dynamics of MLL1 on the NCP, allowing more efficient enzyme-substrate engagement and higher H3K4 trimethylation activity.
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15
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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16
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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.
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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.
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17
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Fallah MS, Szarics D, Robson CM, Eubanks JH. Impaired Regulation of Histone Methylation and Acetylation Underlies Specific Neurodevelopmental Disorders. Front Genet 2021; 11:613098. [PMID: 33488679 PMCID: PMC7820808 DOI: 10.3389/fgene.2020.613098] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic processes are critical for governing the complex spatiotemporal patterns of gene expression in neurodevelopment. One such mechanism is the dynamic network of post-translational histone modifications that facilitate recruitment of transcription factors or even directly alter chromatin structure to modulate gene expression. This is a tightly regulated system, and mutations affecting the function of a single histone-modifying enzyme can shift the normal epigenetic balance and cause detrimental developmental consequences. In this review, we will examine select neurodevelopmental conditions that arise from mutations in genes encoding enzymes that regulate histone methylation and acetylation. The methylation-related conditions discussed include Wiedemann-Steiner, Kabuki, and Sotos syndromes, and the acetylation-related conditions include Rubinstein-Taybi, KAT6A, genitopatellar/Say-Barber-Biesecker-Young-Simpson, and brachydactyly mental retardation syndromes. In particular, we will discuss the clinical/phenotypic and genetic basis of these conditions and the model systems that have been developed to better elucidate cellular and systemic pathological mechanisms.
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Affiliation(s)
- Merrick S Fallah
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Dora Szarics
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Clara M Robson
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - James H Eubanks
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.,Department of Surgery (Neurosurgery), University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada
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18
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Ye X, Chen G, Jin J, Zhang B, Wang Y, Cai Z, Ye F. The Development of Inhibitors Targeting the Mixed Lineage Leukemia 1 (MLL1)-WD Repeat Domain 5 Protein (WDR5) Protein- Protein Interaction. Curr Med Chem 2020; 27:5530-5542. [PMID: 31132972 DOI: 10.2174/0929867326666190528080514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Mixed Lineage Leukemia 1 (MLL1), an important member of Histone Methyltransferases (HMT) family, is capable of catalyzing mono-, di-, and trimethylation of Histone 3 lysine 4 (H3K4). The optimal catalytic activity of MLL1 requires the formation of a core complex consisting of MLL1, WDR5, RbBP5, and ASH2L. The Protein-Protein Interaction (PPI) between WDR5 and MLL1 plays an important role in abnormal gene expression during tumorigenesis, and disturbing this interaction may have a potential for the treatment of leukemia harboring MLL1 fusion proteins. In this review, we will summarize recent progress in the development of inhibitors targeting MLL1- WDR5 interaction.
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Affiliation(s)
- Xiaoqing Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gang Chen
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Jia Jin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Binzhong Zhang
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yinda Wang
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Zhenhai Cai
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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19
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Huxham J, Tabariès S, Siegel PM. Afadin (AF6) in cancer progression: A multidomain scaffold protein with complex and contradictory roles. Bioessays 2020; 43:e2000221. [PMID: 33165933 DOI: 10.1002/bies.202000221] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 11/09/2022]
Abstract
Adherens (AJ) and tight junctions (TJ) maintain cell-cell adhesions and cellular polarity in normal tissues. Afadin, a multi-domain scaffold protein, is commonly found in both adherens and tight junctions, where it plays both structural and signal-modulating roles. Afadin is a complex modulator of cellular processes implicated in cancer progression, including signal transduction, migration, invasion, and apoptosis. In keeping with the complexities associated with the roles of adherens and tight junctions in cancer, afadin exhibits both tumor suppressive and pro-metastatic functions. In this review, we will explore the dichotomous roles that afadin plays during cancer progression.
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Affiliation(s)
- Jennifer Huxham
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.,Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Sébastien Tabariès
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.,Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Peter M Siegel
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada.,Department of Medicine, McGill University, Montréal, Québec, Canada.,Department of Biochemistry, McGill University, Montréal, Québec, Canada.,Department of Anatomy & Cell Biology, McGill University, Montréal, Québec, Canada.,Department of Oncology, McGill University, Montréal, Québec, Canada
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20
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Dcona MM, Mitra K, Hartman MCT. Photocontrolled activation of small molecule cancer therapeutics. RSC Med Chem 2020; 11:982-1002. [PMID: 33479692 PMCID: PMC7513389 DOI: 10.1039/d0md00107d] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/19/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer remains one of the leading causes of death worldwide. Conventional treatment of the disease is comprised of chemotherapy, radiation and surgery among other treatment approaches. Chemotherapy is plagued by multiple side-effects caused due to non-specific drug action. Light-based therapies offer an alternative treatment approach that can be fine tuned to achieve the desired effect to treat the disease and address challenges posed by chemotherapeutic side-effects. Photodynamic therapy (PDT) is one of the light mediated treatment modalities that has been successfully applied to treat superficial malignancies with high-efficiency, although its dependence on normoxic conditions limits its efficiency to treat deep-seated tumors. On the other hand, light-sensitive drug-mimetics and drug-release platforms have been deemed efficient in preclinical settings to induce cancer cell death with minimal collateral damage. Drawing from about a decade's worth of examples, we highlight the application of photosensitive molecules as an alternative therapeutic option to PDT and describe their designs that influence the biology of the cancer cells, in turn affecting their viability with high spatio-temporal control.
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Affiliation(s)
- M Michael Dcona
- Department of Internal Medicine , Virginia Commonwealth University , 1201 East Marshall Street , Richmond , 23298 , Virginia , USA .
- Massey Cancer Center , 401 College St. , Richmond , 23219 , Virginia , USA
| | - Koushambi Mitra
- Massey Cancer Center , 401 College St. , Richmond , 23219 , Virginia , USA
- Department of Chemistry , Virginia Commonwealth University , 1001 W Main St , Richmond , 23284 , Virginia , USA
| | - Matthew C T Hartman
- Massey Cancer Center , 401 College St. , Richmond , 23219 , Virginia , USA
- Department of Chemistry , Virginia Commonwealth University , 1001 W Main St , Richmond , 23284 , Virginia , USA
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21
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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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22
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Delgado RN, Mansky B, Ahanger SH, Lu C, Andersen RE, Dou Y, Alvarez-Buylla A, Lim DA. Maintenance of neural stem cell positional identity by mixed-lineage leukemia 1. Science 2020; 368:48-53. [PMID: 32241942 DOI: 10.1126/science.aba5960] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022]
Abstract
Neural stem cells (NSCs) in the developing and postnatal brain have distinct positional identities that dictate the types of neurons they generate. Although morphogens initially establish NSC positional identity in the neural tube, it is unclear how such regional differences are maintained as the forebrain grows much larger and more anatomically complex. We found that the maintenance of NSC positional identity in the murine brain requires a mixed-lineage leukemia 1 (Mll1)-dependent epigenetic memory system. After establishment by sonic hedgehog, ventral NSC identity became independent of this morphogen. Even transient MLL1 inhibition caused a durable loss of ventral identity, resulting in the generation of neurons with the characteristics of dorsal NSCs in vivo. Thus, spatial information provided by morphogens can be transitioned to epigenetic mechanisms that maintain regionally distinct developmental programs in the forebrain.
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Affiliation(s)
- Ryan N Delgado
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin Mansky
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sajad Hamid Ahanger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.,San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Changqing Lu
- Department of Human Anatomy, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, P.R. China
| | - Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.,Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arturo Alvarez-Buylla
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.,San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA
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23
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Insights on the regulation of the MLL/SET1 family histone methyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194561. [PMID: 32304759 DOI: 10.1016/j.bbagrm.2020.194561] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/07/2020] [Accepted: 04/09/2020] [Indexed: 01/09/2023]
Abstract
In eukaryotes, histone H3K4 methylation by the MLL/SET1 family histone methyltransferases is enriched at transcription regulatory elements including gene promoters and enhancers. The level of H3K4 methylation is highly correlated with transcription activation and is one of the most frequently used histone post-translational modifications to predict transcriptional outcome. Recently, it has been shown that rearrangement of the cellular landscape of H3K4 mono-methylation at distal enhancers precedes cell fate transition and is used for identification of novel regulatory elements for development and disease progression. Similarly, broad H3K4 tri-methylation regions have also been used to predict intrinsic tumor suppression properties of regulator regions in a variety of cellular models. Understanding the regulation for how H3K4 methylation is deposited and regulated is of paramount importance. In this review, we will discuss new findings on how the MLL/SET1 family enzymes are regulated on chromatin and their potential functional and regulatory implications. This article is part of a Special Issue entitled: The MLL family of proteins in normal development and disease edited by Thomas A Milne.
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24
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DNMT3A mutants provide proliferating advantage with augmentation of self-renewal activity in the pathogenesis of AML in KMT2A-PTD-positive leukemic cells. Oncogenesis 2020; 9:7. [PMID: 32015320 PMCID: PMC6997180 DOI: 10.1038/s41389-020-0191-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/11/2019] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) with partial tandem duplication of histone-lysine N-methyltransferase 2A (KMT2A-PTD) is a subtype of AML and is associated with adverse survival, yet the molecular pathogenesis of KMT2A-PTD is not fully understood. DNA methyltransferase 3A (DNMT3A) is mutated in various myeloid neoplasms including AML, especially at the Arg882. Recently, it has been found that DNMT3A mutations frequently coexisted with KMT2A-PTD and are associated with inferior outcomes. We aimed to understand the biological role of DNMT3A mutation in KMT2A-PTD-positive cells. Herein, we found that overexpression of DNMT3A mutants (MT) in KMT2A-PTD-positive EOL-1 cells augmented cell proliferation and clonogenicity. Serial colony replating assays indicated that DNMT3A-MT increased the self-renewal ability of Kmt2a-PTD-expressing mouse bone marrow cells with immature morphology. At 10 months post bone marrow transplantation, mice with the combined Kmt2a-PTD and DNMT3A-MT showed hepatosplenomegaly and leukocytosis with a shorter latency compared to control and DNMT3A-wild-type. Gene expression microarray analyses of bone marrow samples from human AML with KMT2A-PTD/DNMT3A-MT showed a stem cell signature and myeloid hematopoietic lineage with dysregulation of HOXB gene expression. In addition, human bone marrow AML cells carrying KMT2A-PTD/DNMT3A-MT showed abnormal growth and augmented self-renewal activity in primary cell culture. The present study provides information underlying the pathogenic role of DNMT3A-MT with KMT2A-PTD in proliferating advantage with augmentation of self-renewal activity in human leukemia, which may help to better understand the disease and to design better therapy for AML patients with these mutations.
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25
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Xie W, Tang G, Wang E, Kim Y, Cloe A, Shen Q, Zhou Y, Garcia-Manero G, Loghavi S, Hu AY, Wang S, Bueso-Ramos CE, Kantarjian HM, Medeiros LJ, Hu S. t(11;16)(q23;p13)/KMT2A-CREBBP in hematologic malignancies: presumptive evidence of myelodysplasia or therapy-related neoplasm? Ann Hematol 2020; 99:487-500. [PMID: 32006151 DOI: 10.1007/s00277-020-03909-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
Fusion partners of KMT2A affect disease phenotype and influence the current World Health Organization classification of hematologic neoplasms. The t(11;16)(q23;p13)/KMT2A-CREBBP is considered presumptive evidence of a myelodysplastic syndrome (MDS) and a MDS-related cytogenetic abnormality in the classification of acute myeloid leukemia (AML). Here, we report 18 cases of hematologic neoplasms with t(11;16). There were 8 males and 10 females with a median age of 51.9 years at time of detection of t(11;16). Of 17 patients with enough clinical information and pathological materials for review, 16 had a history of cytotoxic therapies for various malignancies including 12/15 patients who received topoisomerase II inhibitors, and 15 were classified as having therapy-related neoplasms. The median interval from the diagnosis of primary malignancy to the detection of t(11;16) was 23.2 months. Dysplasia, usually mild, was observed in 7/17 patients. Blasts demonstrated monocytic differentiation in 8/8 patients who developed AML at the time or following detection of t(11;16). t(11;16) was observed as the sole chromosomal abnormality in 10/18 patients. KMT2A rearrangement was confirmed in 11/11 patients. The median survival from the detection of t(11;16) was 15.4 months. In summary, t(11;16)(q23;p13) is rare and overwhelmingly associated with prior exposure of cytotoxic therapy. Instead of being considered presumptive evidence of myelodysplasia, we suggest that the detection of t(11;16) should automatically prompt a search for a history of malignancy and cytotoxic therapy so that proper risk stratification and clinical management are made accordingly. The dismal outcome of patients with t(11;16) is in keeping with that of therapy-related neoplasms.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- CREB-Binding Protein/genetics
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 16/genetics
- Databases, Factual
- Female
- Hematologic Neoplasms/drug therapy
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/mortality
- Histone-Lysine N-Methyltransferase/genetics
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Male
- Middle Aged
- Myelodysplastic Syndromes/drug therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/mortality
- Myeloid-Lymphoid Leukemia Protein/genetics
- Neoplasms, Second Primary/drug therapy
- Neoplasms, Second Primary/genetics
- Neoplasms, Second Primary/mortality
- Oncogene Proteins, Fusion/genetics
- Risk Assessment
- Topoisomerase II Inhibitors/administration & dosage
- Translocation, Genetic
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Affiliation(s)
- Wei Xie
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Guiling Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Endi Wang
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Young Kim
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Adam Cloe
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Qi Shen
- Department of Pathology, Florida Hospital, Orlando, FL, USA
| | - Yi Zhou
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Sanam Loghavi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Aileen Y Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Sa Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Carlos E Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Hagop M Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA
| | - Shimin Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 0072, Houston, TX, 77030, USA.
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26
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Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nat Commun 2019; 10:5540. [PMID: 31804488 PMCID: PMC6895043 DOI: 10.1038/s41467-019-13550-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity. MLL family histone methyltransferases deposit histone H3 Lys4 mono-/di-/tri-methylation and regulate gene expression in mammals. Here the authors report the single-particle cryo-EM structure of the NCP-bound human MLL1 core complex, shedding light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.
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Affiliation(s)
- Sang Ho Park
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Young-Tae Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Wei Zheng
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Biao Zhang
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Liang Sha
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Sojin An
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yang Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yali Dou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA. .,Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.
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27
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Beurton F, Stempor P, Caron M, Appert A, Dong Y, Chen RAJ, Cluet D, Couté Y, Herbette M, Huang N, Polveche H, Spichty M, Bedet C, Ahringer J, Palladino F. Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans. Nucleic Acids Res 2019; 47:11164-11180. [PMID: 31602465 PMCID: PMC6868398 DOI: 10.1093/nar/gkz880] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/13/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022] Open
Abstract
The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between Caenorhabditis elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex. Supporting a functional connection, we find that mutants of COMPASS and SIN3 complex components genetically interact and have similar phenotypic defects including misregulation of common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3S HDAC complex at promoters.
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Affiliation(s)
- Flore Beurton
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthieu Caron
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ron A-j Chen
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - David Cluet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Marion Herbette
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hélène Polveche
- INSERM UMR 861, I-STEM, 28, Rue Henri Desbruères, 91100 Corbeil-Essonnes, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Cécile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
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28
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Ul-Haq A, Jin ML, Jeong KW, Kim HM, Chun KH. Isolation of MLL1 Inhibitory RNA Aptamers. Biomol Ther (Seoul) 2019; 27:201-209. [PMID: 30419633 PMCID: PMC6430220 DOI: 10.4062/biomolther.2018.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 11/23/2022] Open
Abstract
Mixed lineage leukemia proteins (MLL) are the key histone lysine methyltransferases that regulate expression of diverse genes. Aberrant activation of MLL promotes leukemia as well as solid tumors in humans, highlighting the urgent need for the development of an MLL inhibitor. We screened and isolated MLL1-binding ssRNAs using SELEX (Systemic Evolution of Ligands by Exponential enrichment) technology. When sequences in sub-libraries were obtained using next-generation sequencing (NGS), the most enriched aptamers—APT1 and APT2—represented about 30% and 26% of sub-library populations, respectively. Motif analysis of the top 50 sequences provided a highly conserved sequence: 5′-A[A/C][C/G][G/U][U/A]ACAGAGGG[U/A]GG[A/C] GAGUGGGU-3′. APT1, APT2, and APT5 embracing this motif generated secondary structures with similar topological characteristics. We found that APT1 and APT2 have a good binding activity and the analysis using mutated aptamer variants showed that the site information in the central region was critical for binding. In vitro enzyme activity assay showed that APT1 and APT2 had MLL1 inhibitory activity. Three-dimensional structure prediction of APT1-MLL1 complex indicates multiple weak interactions formed between MLL1 SET domain and APT1. Our study confirmed that NGS-assisted SELEX is an efficient tool for aptamer screening and that aptamers could be useful in diagnosis and treatment of MLL1-mediated diseases.
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Affiliation(s)
- Asad Ul-Haq
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Ming Li Jin
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Kwang Won Jeong
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Hwan-Mook Kim
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Kwang-Hoon Chun
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
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29
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TRIB2 regulates the differentiation of MLL-TET1 transduced myeloid progenitor cells. J Mol Med (Berl) 2018; 96:1267-1277. [PMID: 30324339 DOI: 10.1007/s00109-018-1700-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/23/2022]
Abstract
The function and mechanism of action of MLL-TET1 (MT1) fusion protein in hematological cells are unclear and require further investigation. In the present study, we found that the MT1 fusion protein attenuated the expression of Cebpa, Csf1r, and Cd11b and inhibited the differentiation of myeloid progenitor cells. Increased binding of the MT1 fusion protein to the Trib2 promoter upregulated Trib2 mRNA and protein expression and downregulated Cebpa expression. Trib2 knockdown relieved the inhibition of myeloid cell differentiation induced by the MT1 fusion protein. Thus, TRIB2 is important for the survival of leukemia cells during MT1-related leukemogenesis and is important in maintaining differentiation blockade of leukemic cells. KEY MESSAGES: • MLL-TET1 fusion decreases the 5-hmC levels in the myeloid progenitor cells. • MLL-TET1 fusion inhibits myeloid differentiation through decreased expression of Cebpa. • MLL-TET1 fusion blocks the differentiation of the myeloid progenitor cells by overexpressing Trib2. • Knockdown of Trib2 in MLL-TET1 transduced cells induces myeloid differentiation.
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RNA Sequencing and Pathway Analysis Identify Important Pathways Involved in Hypertrichosis and Intellectual Disability in Patients with Wiedemann-Steiner Syndrome. Neuromolecular Med 2018; 20:409-417. [PMID: 30014449 DOI: 10.1007/s12017-018-8502-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/11/2018] [Indexed: 01/10/2023]
Abstract
A growing number of histone modifiers are involved in human neurodevelopmental disorders, suggesting that proper regulation of chromatin state is essential for the development of the central nervous system. Among them, heterozygous de novo variants in KMT2A, a gene coding for histone methyltransferase, have been associated with Wiedemann-Steiner syndrome (WSS), a rare developmental disorder mainly characterized by intellectual disability (ID) and hypertrichosis. As KMT2A is known to regulate the expression of multiple target genes through methylation of lysine 4 of histone 3 (H3K4me), we sought to investigate the transcriptomic consequences of KMT2A variants involved in WSS. Using fibroblasts from four WSS patients harboring loss-of-function KMT2A variants, we performed RNA sequencing and identified a number of genes for which transcription was altered in KMT2A-mutated cells compared to the control ones. Strikingly, analysis of the pathways and biological functions significantly deregulated between patients with WSS and healthy individuals revealed a number of processes predicted to be altered that are relevant for hypertrichosis and intellectual disability, the cardinal signs of this disease.
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31
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Zhang X, Zheng X, Yang H, Yan J, Fu X, Wei R, Xu X, Zhang Z, Yu A, Zhou K, Ding J, Geng M, Huang X. Piribedil disrupts the MLL1-WDR5 interaction and sensitizes MLL-rearranged acute myeloid leukemia (AML) to doxorubicin-induced apoptosis. Cancer Lett 2018; 431:150-160. [PMID: 29857126 DOI: 10.1016/j.canlet.2018.05.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 12/13/2022]
Abstract
Targeting WT MLL for the treatment of MLL-r leukemia, which is highly aggressive and resistant to chemotherapy, has been shown to be a promising strategy. However, drug treatments targeting WT MLL are lacking. We used an in vitro histone methyltransferase assay to screen a library consists of 592 FDA-approved drugs for MLL1 inhibitors by measuring alterations in HTRF signal and found that Piribedil represented a potent activity. Piribedil specifically inhibited the proliferation of MLL-r cells by inducing cell-cycle arrest, apoptosis and myeloid differentiation with little toxicity to the non-MLL cells. Mechanism study showed Piribedil blocked the MLL1-WDR5 interaction and thus selectively reduced MLL1-dependent H3K4 methylation. Importantly, MLL1 depletion induced gene expression that was similar to that induced by Piribedil and rendered the MLL-r cells resistant to Piribedil-induced toxicity, revealing Piribedil exerted anti-leukemia effects by targeting MLL1. Furthermore, both the Piribedil treatment and MLL1 depletion sensitized the MLL-r cells to doxorubicin-induced apoptosis. Our study support the hypothesis that Piribedil could serve as a new drug for the treatment of MLL-r AML and provide new insight for further optimization of targeting MLL1 HMT activity.
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Affiliation(s)
- Xiong Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xingling Zheng
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hong Yang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Juan Yan
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Xuhong Fu
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Rongrui Wei
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Xiaowei Xu
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Zhuqing Zhang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Aisong Yu
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Kaixin Zhou
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China
| | - Jian Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China; Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China.
| | - Meiyu Geng
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China.
| | - Xun Huang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing, 100049, China.
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Zhang H, Zhou B, Qin S, Xu J, Harding R, Tempel W, Nayak V, Li Y, Loppnau P, Dou Y, Min J. Structural and functional analysis of the DOT1L-AF10 complex reveals mechanistic insights into MLL-AF10-associated leukemogenesis. Genes Dev 2018; 32:341-346. [PMID: 29563185 PMCID: PMC5900708 DOI: 10.1101/gad.311639.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/01/2018] [Indexed: 11/24/2022]
Abstract
The mixed-lineage leukemia (MLL)-AF10 fusion oncoprotein recruits DOT1L to the homeobox A (HOXA) gene cluster through its octapeptide motif leucine zipper (OM-LZ), thereby inducing and maintaining the MLL-AF10-associated leukemogenesis. However, the recognition mechanism between DOT1L and MLL-AF10 is unclear. Here, we present the crystal structures of both apo AF10OM-LZ and its complex with the coiled-coil domain of DOT1L. Disruption of the DOT1L-AF10 interface abrogates MLL-AF10-associated leukemic transformation. We further show that zinc stabilizes the DOT1L-AF10 complex and may be involved in the regulation of the HOXA gene expression. Our studies may also pave the way for the rational design of therapeutic drugs against MLL-rearranged leukemia.
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Affiliation(s)
- Heng Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Life Science Research Center, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rachel Harding
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Vinod Nayak
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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33
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Lebrun N, Giurgea I, Goldenberg A, Dieux A, Afenjar A, Ghoumid J, Diebold B, Mietton L, Briand-Suleau A, Billuart P, Bienvenu T. Molecular and cellular issues of KMT2A variants involved in Wiedemann-Steiner syndrome. Eur J Hum Genet 2017; 26:107-116. [PMID: 29203834 DOI: 10.1038/s41431-017-0033-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/06/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022] Open
Abstract
Variants in KMT2A, encoding the histone methyltransferase KMT2A, are a growing cause of intellectual disability (ID). Up to now, the majority of KMT2A variants are non-sense and frameshift variants causing a typical form of Wiedemann-Steiner syndrome. We studied KMT2A gene in a cohort of 200 patients with unexplained syndromic and non-syndromic ID and identified four novel variants, one splice and three missense variants, possibly deleterious. We used primary cells from the patients and molecular approaches to determine the deleterious effects of those variants on KMT2A expression and function. For the putative splice variant c.11322-1G>A, we showed that it led to only one nucleotide deletion and loss of the C-terminal part of the protein. For two studied KMT2A missense variants, c.3460C>T (p.(Arg1154Trp)) and c.8558T>G (p.(Met2853Arg)), located at the cysteine-rich CXXC domain and the transactivation domain of the protein, respectively, we found altered KMT2A target genes expression in patient's fibroblasts compared to controls. Furthermore, we found a disturbed subcellular distribution of KMT2A for the c.3460C>T mutant. Taken together, our results demonstrated the deleterious impact of the splice variant and of the missense variants located at two different functional domains and suggested reduction of KMT2A function as the disease-causing mechanism.
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Affiliation(s)
- Nicolas Lebrun
- Inserm, Institut Cochin, U1016, Paris, France.,Cnrs, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Irina Giurgea
- Service de Génétique, Hôpital Trousseau, Paris, France
| | - Alice Goldenberg
- Service de génétique, CHU de Rouen et Inserm U1079, Université de Rouen, Center Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Anne Dieux
- Service de génétique clinique Guy Fontaine CHRU de Lille - Hôpital Jeanne de Flandre Avenue Eugène Avinée, 59037, LILLE, France
| | - Alexandra Afenjar
- GRC Concer-LD, Sorbonne universités, Département de Génétique et Embryologie Médicale, Hôpital Trousseau, Paris, France
| | - Jamal Ghoumid
- Service de génétique clinique Guy Fontaine CHRU de Lille - Hôpital Jeanne de Flandre Avenue Eugène Avinée, 59037, LILLE, France
| | - Bertrand Diebold
- Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France
| | - Léo Mietton
- Inserm, Institut Cochin, U1016, Paris, France.,Cnrs, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Audrey Briand-Suleau
- Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France
| | - Pierre Billuart
- Inserm, Institut Cochin, U1016, Paris, France.,Cnrs, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Thierry Bienvenu
- Inserm, Institut Cochin, U1016, Paris, France. .,Cnrs, UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne Paris Cité, Paris, France. .,Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France.
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34
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Ali A, Veeranki SN, Chinchole A, Tyagi S. MLL/WDR5 Complex Regulates Kif2A Localization to Ensure Chromosome Congression and Proper Spindle Assembly during Mitosis. Dev Cell 2017. [PMID: 28633016 DOI: 10.1016/j.devcel.2017.05.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mixed-lineage leukemia (MLL), along with multisubunit (WDR5, RbBP5, ASH2L, and DPY30) complex catalyzes the trimethylation of H3K4, leading to gene activation. Here, we characterize a chromatin-independent role for MLL during mitosis. MLL and WDR5 localize to the mitotic spindle apparatus, and loss of function of MLL complex by RNAi results in defects in chromosome congression and compromised spindle formation. We report interaction of MLL complex with several kinesin and dynein motors. We further show that the MLL complex associates with Kif2A, a member of the Kinesin-13 family of microtubule depolymerase, and regulates the spindle localization of Kif2A during mitosis. We have identified a conserved WDR5 interaction (Win) motif, so far unique to the MLL family, in Kif2A. The Win motif of Kif2A engages in direct interactions with WDR5 for its spindle localization. Our findings highlight a non-canonical mitotic function of MLL complex, which may have a direct impact on chromosomal stability, frequently compromised in cancer.
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Affiliation(s)
- Aamir Ali
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India; Graduate Studies, Manipal University, Manipal, India
| | - Sailaja Naga Veeranki
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India
| | - Akash Chinchole
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India; Graduate Studies, Manipal University, Manipal, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad 500001, India.
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35
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Albert L, Xu J, Wan R, Srinivasan V, Dou Y, Vázquez O. Controlled inhibition of methyltransferases using photoswitchable peptidomimetics: towards an epigenetic regulation of leukemia. Chem Sci 2017; 8:4612-4618. [PMID: 28970883 PMCID: PMC5618341 DOI: 10.1039/c7sc00137a] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/09/2017] [Indexed: 12/28/2022] Open
Abstract
Shine light on epigenetics: we describe how photoswitchable peptidomimetics modulate the activity of the MLLl enzyme affecting epigenetic states.
We describe a cell-permeable photoswitchable probe capable of modulating epigenetic cellular states by disruption of an essential protein–protein interaction within the MLL1 methyltransferase core complex. Our azobenzene-containing peptides selectively block the WDR5-MLL1 interaction by binding to WDR5 with high affinity (Ki = 1.25 nM). We determined the co-crystal structure of this photoswitchable peptiomimetic with WDR5 to understand the interaction at the atomic level. Importantly, the photoswitchable trans and cis conformers of the probe display a clear difference in their inhibition of MLL1. We further demonstrate that the designed photo-controllable azo-peptidomimetics affect the transcription of the MLL1-target gene Deptor, which regulates hematopoiesis and leukemogenesis, and inhibit the growth of leukemia cells. This strategy demonstrates the potential of photopharmacological inhibition of methyltransferase protein–protein interactions as a novel method for external epigenetic control, providing a new toolbox for controlling epigenetic states.
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Affiliation(s)
- Lea Albert
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Strasse 4 , 35043 Marburg , Germany .
| | - Jing Xu
- Department of Pathology , University of Michigan , Ann Arbor , Michigan 48109 , USA
| | - Ruiwei Wan
- Department of Pathology , University of Michigan , Ann Arbor , Michigan 48109 , USA
| | - Vasundara Srinivasan
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro , Philipps-Universität Marburg , Hans-Meerwein-Strasse 4 , 35043 Marburg , Germany
| | - Yali Dou
- Department of Pathology , University of Michigan , Ann Arbor , Michigan 48109 , USA
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Strasse 4 , 35043 Marburg , Germany .
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36
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Ali A, Tyagi S. Diverse roles of WDR5-RbBP5-ASH2L-DPY30 (WRAD) complex in the functions of the SET1 histone methyltransferase family. J Biosci 2017; 42:155-159. [PMID: 28229975 DOI: 10.1007/s12038-017-9666-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
WD repeat containing protein 5 (WDR5), Retinoblastoma Binding Protein 5 (RbBP5), Absent-Small-Homeotic-2- Like protein (ASH2L), and Dumpy-30 (Dpy30) have been reported to be the integral and shared components of all the SET1 family of histone 3 lysine 4 histone methyltransferase (HMT) complexes. Collectively called the WRAD complex, these proteins are pivotal to the HMT activity of the SET1 complexes. Recent reports highlight the novel non-canonical functions of WRAD in cellular processes other than its well-studied role in histone methylation and gene expression. In this review, we examine the diversity in emerging transcription-independent functions of WRAD.
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Affiliation(s)
- Aamir Ali
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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37
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Alicea-Velázquez NL, Shinsky SA, Loh DM, Lee JH, Skalnik DG, Cosgrove MS. Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes. J Biol Chem 2016; 291:22357-22372. [PMID: 27563068 DOI: 10.1074/jbc.m116.752626] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 08/23/2016] [Indexed: 11/06/2022] Open
Abstract
MLL1 belongs to the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, composed of MLL1-4 and SETd1A/B. MLL1 translocations are present in acute leukemias, and mutations in several family members are associated with cancer and developmental disorders. MLL1 associates with a subcomplex containing WDR5, RbBP5, ASH2L, and DPY-30 (WRAD), forming the MLL1 core complex required for H3K4 mono- and dimethylation and transcriptional activation. Core complex assembly requires interaction of WDR5 with the MLL1 Win (WDR5 interaction) motif, which is conserved across the SET1 family. Agents that mimic the SET1 family Win motif inhibit the MLL1 core complex and have become an attractive approach for targeting MLL1 in cancers. Like MLL1, other SET1 family members interact with WRAD, but the roles of the Win motif in complex assembly and enzymatic activity remain unexplored. Here, we show that the Win motif is necessary for interaction of WDR5 with all members of the human SET1 family. Mutation of the Win motif-WDR5 interface severely disrupts assembly and activity of MLL1 and SETd1A complexes but only modestly disrupts MLL2/4 and SETd1B complexes without significantly altering enzymatic activity in vitro Notably, in the absence of WDR5, MLL3 interacts with RAD and shows enhanced activity. To further probe the role of the Win motif-WDR5 interaction, we designed a peptidomimetic that binds WDR5 (Kd ∼3 nm) and selectively inhibits activity of MLL1 and SETd1A core complexes within the SET1 family. Our results reveal that SET1 family complexes with the weakest Win motif-WDR5 interaction are more susceptible to Win motif-based inhibitors.
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Affiliation(s)
- Nilda L Alicea-Velázquez
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Daniel M Loh
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Jeong-Heon Lee
- the Biology Department, School of Science, Indiana University-Purdue University, Indianapolis, Indiana 46202
| | - David G Skalnik
- the Biology Department, School of Science, Indiana University-Purdue University, Indianapolis, Indiana 46202
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
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38
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Evolving Catalytic Properties of the MLL Family SET Domain. Structure 2015; 23:1921-1933. [PMID: 26320581 PMCID: PMC4597100 DOI: 10.1016/j.str.2015.07.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/20/2015] [Accepted: 07/27/2015] [Indexed: 12/25/2022]
Abstract
Methylation of histone H3 lysine-4 is a hallmark of chromatin associated with active gene expression. The activity of H3K4-specific modification enzymes, in higher eukaryotes the MLL (or KMT2) family, is tightly regulated. The MLL family has six members, each with a specialized function. All contain a catalytic SET domain that associates with a core multiprotein complex for activation. These SET domains segregate into three classes that correlate with the arrangement of targeting domains that populate the rest of the protein. Here we show that, unlike MLL1, the MLL4 SET domain retains significant activity without the core complex. We also present the crystal structure of an inactive MLL4-tagged SET domain construct and describe conformational changes that account for MLL4 intrinsic activity. Finally, our structure explains how the MLL SET domains are able to add multiple methyl groups to the target lysine, despite having the sequence characteristics of a classical monomethylase. MLL4 SET domain has significant H3K4 methyltransferase activity without WRAD MLL4 SET domain structure (inactivated by tag) reveals differences to MLL1 The postSET loop region contributes to the intrinsic methyltransferase activity MLL4 can catalyze multiple methylations on H3K4 but prefers monomethylation
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Bina M, Wyss P. Impact of the MLL1 morphemes on codon utilization and preservation in CpG Islands. Biopolymers 2015; 103:480-90. [PMID: 25991579 DOI: 10.1002/bip.22681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Phillip Wyss
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
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Eriksson A, Lennartsson A, Lehmann S. Epigenetic aberrations in acute myeloid leukemia: Early key events during leukemogenesis. Exp Hematol 2015; 43:609-24. [PMID: 26118500 DOI: 10.1016/j.exphem.2015.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 12/17/2022]
Abstract
As a result of the introduction of new sequencing technologies, the molecular landscape of acute myeloid leukemia (AML) is rapidly evolving. From karyotyping, which detects only large genomic aberrations of metaphase chromosomes, we have moved into an era when sequencing of each base pair allows us to define the AML genome at highest resolution. This has revealed a new complex landscape of genetic aberrations where addition of mutations in epigenetic regulators has been one of the most important contributions to the understanding of the pathogenesis of AML. These findings, together with new insights into epigenetic mechanisms, have placed dysregulated epigenetic mechanisms at the forefront of AML development. Not only have several new mutations in genes directly involved in epigenetic regulatory mechanisms been discovered, but also previously well-known gene fusions have been found to exert aberrant effects through epigenetic mechanisms. In addition, mutations in epigenetic regulators such as DNMT3A, TET2, and ASXL1 have recently been found to be the earliest known events during AML evolution and to be present as preleukemic lesions before the onset of AML. In this article, we review epigenetic changes in AML also in relation to what is known about their mechanism of action and their prognostic role.
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Affiliation(s)
- Anna Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Centre of Hematology, HERM, Department of Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.
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41
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Wang X, Ju L, Fan J, Zhu Y, Liu X, Zhu K, Wu M, Li L. Histone H3K4 methyltransferase Mll1 regulates protein glycosylation and tunicamycin-induced apoptosis through transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2592-602. [PMID: 24983772 DOI: 10.1016/j.bbamcr.2014.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 01/03/2023]
Abstract
Disrupting protein glycosylation induces ER (endoplasmic reticulum) stress, resulting in the activation of UPR (unfolded protein response) pathways. A key function of the UPR is to restore ER homeostasis, but prolonged or unsolved ER stress can lead to apoptosis. MLL1 (Mixed Lineage Leukemia 1, also named ALL-1 or HRX), a histone H3K4 methyltransferase in mammals, plays important roles in leukemogenesis, transcriptional regulation, cell cycle and development. Here, we find that Mll1 deficiency enhances UPR and apoptosis induced by the glycosylation inhibitor TM (tunicamycin). The abnormal regulation of the UPR appears to be caused by a defect in protein glycosylation. Furthermore, Mll1 directly binds to the promoters of H6pd, Galnt12 and Ugp2, which regulates H3K4 trimethylation and the subsequent expression of these genes. The knockdown of H6pd, Galnt12 or Ugp2 enhances TM-induced apoptosis in Mll1(+/+)MEF cells, whereas the ectopic expression of these proteins inhibits TM-induced apoptosis in Mll1(-/-) MEF cells. Together, our data suggest that the maturation of glycoproteins in the ER is subject to regulation at the epigenetic level by a histone methyltransferase whose abnormality can lead to cancer and developmental defects.
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Affiliation(s)
- Xiang Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Lingao Ju
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiadong Fan
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuan Zhu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaolan Liu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Kun Zhu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Min Wu
- College of Life Sciences, Wuhan University, Wuhan, China.
| | - Lianyun Li
- College of Life Sciences, Wuhan University, Wuhan, China.
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42
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Chopra M, Bohlander SK. Disturbing the histone code in leukemia: translocations and mutations affecting histone methyl transferases. Cancer Genet 2014; 208:192-205. [PMID: 25592767 DOI: 10.1016/j.cancergen.2014.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/01/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Leukemia is characterized by increased numbers of blasts originating from transformed early hematopoietic stem and progenitor cells. Genetic alterations are widely recognized as the main drivers of oncogenic transformation. Of considerable interest are mutations affecting the writers of epigenetic marks. In this review, we focus on histone methyltransferases--enzymes that catalyze the methylation of lysine residues in core histones. Histone methylation is a tightly controlled mechanism that is responsible for both activating as well as repressing gene expression in a site-specific manner, depending on which lysine residue is methylated. Histone methyltransferases, including MLL1, DOT1L, EZH2, and SETD2 are recurrently deregulated in human leukemia, either directly by gene mutations or balanced translocations, or indirectly as components of protein complexes that are disturbed in leukemia due to alterations of the other components in these complexes. Several small molecule inhibitors of histone methyltransferases are currently being clinically evaluated for their therapeutic potential in human leukemia. These drugs reverse some of the adverse effects of aberrant histone methylation, and can induce differentiation and cell death in leukemic blasts.
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Affiliation(s)
- Martin Chopra
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
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43
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Yamagishi J, Natori A, Tolba MEM, Mongan AE, Sugimoto C, Katayama T, Kawashima S, Makalowski W, Maeda R, Eshita Y, Tuda J, Suzuki Y. Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum. Genome Res 2014; 24:1433-44. [PMID: 25091627 PMCID: PMC4158759 DOI: 10.1101/gr.158980.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To understand the molecular mechanisms of parasitism in vivo, it is essential to elucidate how the transcriptomes of the human hosts and the infecting parasites affect one another. Here we report the RNA-seq analysis of 116 Indonesian patients infected with the malaria parasite Plasmodium falciparum (Pf). We extracted RNAs from their peripheral blood as a mixture of host and parasite transcripts and mapped the RNA-seq tags to the human and Pf reference genomes to separate the respective tags. We were thus able to simultaneously analyze expression patterns in both humans and parasites. We identified human and parasite genes and pathways that correlated with various clinical data, which may serve as primary targets for drug developments. Of particular importance, we revealed characteristic expression changes in the human innate immune response pathway genes including TLR2 and TICAM2 that correlated with the severity of the malaria infection. We also found a group of transcription regulatory factors, JUND, for example, and signaling molecules, TNFAIP3, for example, that were strongly correlated in the expression patterns of humans and parasites. We also identified several genetic variations in important anti-malaria drug resistance-related genes. Furthermore, we identified the genetic variations which are potentially associated with severe malaria symptoms both in humans and parasites. The newly generated data should collectively lay a unique foundation for understanding variable behaviors of the field malaria parasites, which are far more complex than those observed under laboratory conditions.
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Affiliation(s)
- Junya Yamagishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8579, Japan; Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Anna Natori
- Department of Medical Genome Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | | | - Arthur E Mongan
- Department of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado, 95115, Indonesia
| | - Chihiro Sugimoto
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Toshiaki Katayama
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), The University of Tokyo Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shuichi Kawashima
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), The University of Tokyo Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, 48149 Munster, Germany
| | - Ryuichiro Maeda
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yuki Eshita
- Oita University, School of Medicine, Yufushi, Oita 879-5593, Japan
| | - Josef Tuda
- Department of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado, 95115, Indonesia
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan;
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Cheng X. Structural and functional coordination of DNA and histone methylation. Cold Spring Harb Perspect Biol 2014; 6:6/8/a018747. [PMID: 25085914 DOI: 10.1101/cshperspect.a018747] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and recognized. This central process in controlling gene expression includes coordinated covalent modifications of DNA and its associated histones. This article focuses on structural aspects of enzymatic activities of histone (arginine and lysine) methylation and demethylation and functional links between the methylation status of the DNA and histones. An interconnected network of methyltransferases, demethylases, and accessory proteins is responsible for changing or maintaining the modification status of specific regions of chromatin.
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Affiliation(s)
- Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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Ali A, Veeranki SN, Tyagi S. A SET-domain-independent role of WRAD complex in cell-cycle regulatory function of mixed lineage leukemia. Nucleic Acids Res 2014; 42:7611-24. [PMID: 24880690 PMCID: PMC4081079 DOI: 10.1093/nar/gku458] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular processes like cell-cycle regulation are not well studied. Here we show that the MLL has a regulatory role during multiple phases of the cell cycle. RNAi-mediated knockdown reveals that MLL regulates S-phase progression and, proper segregation and cytokinesis during M phase. Using deletions and mutations, we narrow the cell-cycle regulatory role to the C subunit of MLL. Our analysis reveals that the transactivation domain and not the SET domain is important for the S-phase function of MLL. Surprisingly, disruption of MLL–WRAD interaction is sufficient to disrupt proper mitotic progression. These mitotic functions of WRAD are independent of SET domain of MLL and, therefore, define a new role of WRAD in subset of MLL functions. Finally, we address the overlapping and unique roles of the different SET family members in the cell cycle.
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Affiliation(s)
- Aamir Ali
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Sailaja Naga Veeranki
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
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Cierpicki T, Grembecka J. Challenges and opportunities in targeting the menin-MLL interaction. Future Med Chem 2014; 6:447-62. [PMID: 24635524 PMCID: PMC4138051 DOI: 10.4155/fmc.13.214] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Menin is an essential co-factor of oncogenic MLL fusion proteins and the menin-MLL interaction is critical for development of acute leukemia in vivo. Targeting the menin-MLL interaction with small molecules represents an attractive strategy to develop new anticancer agents. Recent developments, including determination of menin crystal structure and development of potent small molecule and peptidomimetic inhibitors, demonstrate the feasibility of targeting the menin-MLL interaction. On the other hand, biochemical and structural studies revealed that MLL binds to menin in a complex bivalent mode engaging two MLL motifs, and therefore inhibition of this protein-protein interaction represents a challenge. This review summarizes the most recent achievements in targeting the menin-MLL interaction as well as discusses potential benefits of blocking menin in cancer.
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Affiliation(s)
- Tomasz Cierpicki
- Author for correspondence: Tel.: +1 734 615 9324, Fax: +1 734 615 0688,
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47
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Downregulation of RUNX1/CBFβ by MLL fusion proteins enhances hematopoietic stem cell self-renewal. Blood 2014; 123:1729-38. [PMID: 24449215 DOI: 10.1182/blood-2013-03-489575] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RUNX1/CBFβ (core binding factor [CBF]) is a heterodimeric transcription factor complex that is frequently involved in chromosomal translocations, point mutations, or deletions in acute leukemia. The mixed lineage leukemia (MLL) gene is also frequently involved in chromosomal translocations or partial tandem duplication in acute leukemia. The MLL protein interacts with RUNX1 and prevents RUNX1 from ubiquitin-mediated degradation. RUNX1/CBFβ recruits MLL to regulate downstream target genes. However, the functional consequence of MLL fusions on RUNX1/CBFβ activity has not been fully understood. In this report, we show that MLL fusion proteins and the N-terminal MLL portion of MLL fusions downregulate RUNX1 and CBFβ protein expression via the MLL CXXC domain and flanking regions. We confirmed this finding in Mll-Af9 knock-in mice and human M4/M5 acute myeloid leukemia (AML) cell lines, with or without MLL translocations, showing that MLL translocations cause a hypomorph phenotype of RUNX1/CBFβ. Overexpression of RUNX1 inhibits the development of AML in Mll-Af9 knock-in mice; conversely, further reducing Runx1/Cbfβ levels accelerates MLL-AF9-mediated AML in bone marrow transplantation assays. These data reveal a newly defined negative regulation of RUNX1/CBFβ by MLL fusion proteins and suggest that targeting RUNX1/CBFβ levels may be a potential therapy for MLLs.
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48
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Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia. Mol Cell 2014; 53:247-61. [PMID: 24389101 DOI: 10.1016/j.molcel.2013.12.001] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/03/2013] [Accepted: 11/26/2013] [Indexed: 12/22/2022]
Abstract
Here we report a comprehensive characterization of our recently developed inhibitor MM-401 that targets the MLL1 H3K4 methyltransferase activity. MM-401 is able to specifically inhibit MLL1 activity by blocking MLL1-WDR5 interaction and thus the complex assembly. This targeting strategy does not affect other mixed-lineage leukemia (MLL) family histone methyltransferases (HMTs), revealing a unique regulatory feature for the MLL1 complex. Using MM-401 and its enantiomer control MM-NC-401, we show that inhibiting MLL1 methyltransferase activity specifically blocks proliferation of MLL cells by inducing cell-cycle arrest, apoptosis, and myeloid differentiation without general toxicity to normal bone marrow cells or non-MLL cells. More importantly, transcriptome analyses show that MM-401 induces changes in gene expression similar to those of MLL1 deletion, supporting a predominant role of MLL1 activity in regulating MLL1-dependent leukemia transcription program. We envision broad applications for MM-401 in basic and translational research.
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49
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Bina M, Wyss P, Novorolsky E, Zulkelfi N, Xue J, Price R, Fay M, Gutmann Z, Fogler B, Wang D. Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin. BMC Genomics 2013; 14:927. [PMID: 24373511 PMCID: PMC3890651 DOI: 10.1186/1471-2164-14-927] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/16/2013] [Indexed: 11/10/2022] Open
Abstract
Background Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA. Results By analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven “bookmarked” regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands. Conclusion Our results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes during mitosis.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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50
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Patel A, Vought VE, Swatkoski S, Viggiano S, Howard B, Dharmarajan V, Monteith KE, Kupakuwana G, Namitz KE, Shinsky SA, Cotter RJ, Cosgrove MS. Automethylation activities within the mixed lineage leukemia-1 (MLL1) core complex reveal evidence supporting a "two-active site" model for multiple histone H3 lysine 4 methylation. J Biol Chem 2013; 289:868-84. [PMID: 24235145 PMCID: PMC3887211 DOI: 10.1074/jbc.m113.501064] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mixed lineage leukemia-1 (MLL1) core complex predominantly catalyzes mono- and dimethylation of histone H3 at lysine 4 (H3K4) and is frequently altered in aggressive acute leukemias. The molecular mechanisms that account for conversion of mono- to dimethyl H3K4 (H3K4me1,2) are not well understood. In this investigation, we report that the suppressor of variegation, enhancer of zeste, trithorax (SET) domains from human MLL1 and Drosophila Trithorax undergo robust intramolecular automethylation reactions at an evolutionarily conserved cysteine residue in the active site, which is inhibited by unmodified histone H3. The location of the automethylation in the SET-I subdomain indicates that the MLL1 SET domain possesses significantly more conformational plasticity in solution than suggested by its crystal structure. We also report that MLL1 methylates Ash2L in the absence of histone H3, but only when assembled within a complex with WDR5 and RbBP5, suggesting a restraint for the architectural arrangement of subunits within the complex. Using MLL1 and Ash2L automethylation reactions as probes for histone binding, we observed that both automethylation reactions are significantly inhibited by stoichiometric amounts of unmethylated histone H3, but not by histones previously mono-, di-, or trimethylated at H3K4. These results suggest that the H3K4me1 intermediate does not significantly bind to the MLL1 SET domain during the dimethylation reaction. Consistent with this hypothesis, we demonstrate that the MLL1 core complex assembled with a catalytically inactive SET domain variant preferentially catalyzes H3K4 dimethylation using the H3K4me1 substrate. Taken together, these results are consistent with a “two-active site” model for multiple H3K4 methylation by the MLL1 core complex.
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Affiliation(s)
- Anamika Patel
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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