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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024:1-49. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [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: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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2
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Li Z, Ning Z. Neonatal Kabuki syndrome caused by KMT2D mutation: A case report. Medicine (Baltimore) 2023; 102:e36681. [PMID: 38115267 PMCID: PMC10727567 DOI: 10.1097/md.0000000000036681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is an autosomal dominant inherited syndrome that involves multiple organs and systems. Gene mutation is the main cause of KS. The reported mutations in X-linked histone H3 lysine 4 methylase (KMT2D) and KDM6A genes are 2 relatively clear pathogenic pathways. In this paper, we report a case of KS with neonatal hypoglycemia and special features caused by KMT2D gene mutation confirmed by whole exome sequencing, it enriched the clinical phenotype spectrum and gene mutation spectrum of KS, which helps to improve the understanding of the disease. CASE REPORT Through whole exome sequencing, we performed gene diagnosis of a newborn child with special facial features and multiple malformations, which revealed heterozygous mutation of NM_003482.3:c.755dupA(p.His252Glnfs*21) in KMT2D gene. It is consistent with the pathogenesis of KS, an autosomal dominat genetic disease caused by KMT2D gene mutation. This pathogenic mutation has not been prebiously reported. DISCUSSION KS has strong clinical characteristics and biological heterogeneity. Genetic diagnosis can help identify mutant gene types. However, the relationship between genotype and phenotype has not been fully clarified. The molecular etiological mechanism still needs to be further explored and elucidated.
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Affiliation(s)
- Zhang Li
- The Second Affiliated Hospital of Dalian Medical University, Dalian City, Liaoning Province, China
| | - Zou Ning
- The Second Affiliated Hospital of Dalian Medical University, Dalian City, Liaoning Province, China
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3
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Cordeiro-Spinetti E, Rothbart SB. Lysine methylation signaling in skeletal muscle biology: from myogenesis to clinical insights. Biochem J 2023; 480:1969-1986. [PMID: 38054592 DOI: 10.1042/bcj20230223] [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: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Lysine methylation signaling is well studied for its key roles in the regulation of transcription states through modifications on histone proteins. While histone lysine methylation has been extensively studied, recent discoveries of lysine methylation on thousands of non-histone proteins has broadened our appreciation for this small chemical modification in the regulation of protein function. In this review, we highlight the significance of histone and non-histone lysine methylation signaling in skeletal muscle biology, spanning development, maintenance, regeneration, and disease progression. Furthermore, we discuss potential future implications for its roles in skeletal muscle biology as well as clinical applications for the treatment of skeletal muscle-related diseases.
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Affiliation(s)
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan 49503, U.S.A
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4
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Namitz KEW, Tan S, Cosgrove MS. Hierarchical assembly of the MLL1 core complex regulates H3K4 methylation and is dependent on temperature and component concentration. J Biol Chem 2023; 299:102874. [PMID: 36623730 PMCID: PMC9939731 DOI: 10.1016/j.jbc.2023.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023] Open
Abstract
Enzymes of the mixed lineage leukemia (MLL) family of histone H3 lysine 4 (H3K4) methyltransferases are critical for cellular differentiation and development and are regulated by interaction with a conserved subcomplex consisting of WDR5, RbBP5, Ash2L, and DPY30. While pairwise interactions between complex subunits have been determined, the mechanisms regulating holocomplex assembly are unknown. In this investigation, we systematically characterized the biophysical properties of a reconstituted human MLL1 core complex and found that the MLL1-WDR5 heterodimer interacts with the RbBP5-Ash2L-DPY30 subcomplex in a hierarchical assembly pathway that is highly dependent on concentration and temperature. Surprisingly, we found that the disassembled state is favored at physiological temperature, where the enzyme rapidly becomes irreversibly inactivated, likely because of complex components becoming trapped in nonproductive conformations. Increased protein concentration partially overcomes this thermodynamic barrier for complex assembly, suggesting a potential regulatory mechanism for spatiotemporal control of H3K4 methylation. Together, these results are consistent with the hypothesis that regulated assembly of the MLL1 core complex underlies an important mechanism for establishing different H3K4 methylation states in mammalian genomes.
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Affiliation(s)
- Kevin E W Namitz
- State University of New York (SUNY) Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, NY, USA
| | - Song Tan
- Penn State University, Department of Biochemistry and Molecular Biology, University Park, PA, USA
| | - Michael S Cosgrove
- State University of New York (SUNY) Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, NY, USA.
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5
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Pan H, Wang H, Zhang X, Yang F, Fan X, Zhang H. Chromosomal instability-associated MAT1 lncRNA insulates MLL1-guided histone methylation and accelerates tumorigenesis. Cell Rep 2022; 41:111829. [PMID: 36516779 DOI: 10.1016/j.celrep.2022.111829] [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: 08/05/2022] [Revised: 09/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Acquired chromosomal instability, especially copy number variations (CNVs), has been considered an important determinant of cancer progression and clinical survival. However, the functional role of aberrant CNV-induced lncRNAs in tumorigenesis remains unexplored. Here, we identify a CNV-induced MSC-antisense-transcript 1 (MAT1) lncRNA that plays an oncogenic role in promoting tumorigenesis of uveal melanoma in orthotopic and metastatic xenografts. In addition, our data suggest that MAT1 interrupts the interaction between the MLL1 complex and the PCDH20 promoter by forming an RNA-DNA triplex structure, subsequently abolishing H3K4 trimethylation and inactivating transcription of tumor suppressor PCDH20 to accelerate tumorigenesis. Our data show an intriguing insulation pattern of H3K4 histone modification in tumorigenesis mediated by a lncRNA, thereby providing an alternative mechanism for noncoding blockers in gene regulation.
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Affiliation(s)
- Hui Pan
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Huixue Wang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xiaoyu Zhang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Fan Yang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China.
| | - He Zhang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
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6
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Parallel functional annotation of cancer-associated missense mutations in histone methyltransferases. Sci Rep 2022; 12:18487. [PMID: 36323913 PMCID: PMC9630446 DOI: 10.1038/s41598-022-23229-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Abstract
Using exome sequencing for biomarker discovery and precision medicine requires connecting nucleotide-level variation with functional changes in encoded proteins. However, for functionally annotating the thousands of cancer-associated missense mutations, or variants of uncertain significance (VUS), purifying variant proteins for biochemical and functional analysis is cost-prohibitive and inefficient. We describe parallel functional annotation (PFA) of large numbers of VUS using small cultures and crude extracts in 96-well plates. Using members of a histone methyltransferase family, we demonstrate high-throughput structural and functional annotation of cancer-associated mutations. By combining functional annotation of paralogs, we discovered two phylogenetic and clustering parameters that improve the accuracy of sequence-based functional predictions to over 90%. Our results demonstrate the value of PFA for defining oncogenic/tumor suppressor functions of histone methyltransferases as well as enhancing the accuracy of sequence-based algorithms in predicting the effects of cancer-associated mutations.
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7
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Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C. Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Proc Natl Acad Sci U S A 2022; 119:e2205691119. [PMID: 36095189 PMCID: PMC9499523 DOI: 10.1073/pnas.2205691119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.
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Affiliation(s)
- Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas A. Hoffmann
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Evan J. Worden
- Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503
| | - Marissa L. Smith
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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8
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Histone H3K4 Methyltransferases as Targets for Drug-Resistant Cancers. BIOLOGY 2021; 10:biology10070581. [PMID: 34201935 PMCID: PMC8301125 DOI: 10.3390/biology10070581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022]
Abstract
The KMT2 (MLL) family of proteins, including the major histone H3K4 methyltransferase found in mammals, exists as large complexes with common subunit proteins and exhibits enzymatic activity. SMYD, another H3K4 methyltransferase, and SET7/9 proteins catalyze the methylation of several non-histone targets, in addition to histone H3K4 residues. Despite these structural and functional commonalities, H3K4 methyltransferase proteins have specificity for their target genes and play a role in the development of various cancers as well as in drug resistance. In this review, we examine the overall role of histone H3K4 methyltransferase in the development of various cancers and in the progression of drug resistance. Compounds that inhibit protein-protein interactions between KMT2 family proteins and their common subunits or the activity of SMYD and SET7/9 are continuously being developed for the treatment of acute leukemia, triple-negative breast cancer, and castration-resistant prostate cancer. These H3K4 methyltransferase inhibitors, either alone or in combination with other drugs, are expected to play a role in overcoming drug resistance in leukemia and various solid cancers.
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9
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Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [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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10
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Abay-Nørgaard S, Attianese B, Boreggio L, Salcini AE. Regulators of H3K4 methylation mutated in neurodevelopmental disorders control axon guidance in Caenorhabditis elegans. Development 2020; 147:dev.190637. [PMID: 32675280 PMCID: PMC7420840 DOI: 10.1242/dev.190637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
Abstract
Post-translational histone modifications regulate chromatin compaction and gene expression to control many aspects of development. Mutations in genes encoding regulators of H3K4 methylation are causally associated with neurodevelopmental disorders characterized by intellectual disability and deficits in motor functions. However, it remains unclear how H3K4 methylation influences nervous system development and contributes to the aetiology of disease. Here, we show that the catalytic activity of set-2, the Caenorhabditis elegans homologue of the H3K4 methyltransferase KMT2F/G (SETD1A/B) genes, controls embryonic transcription of neuronal genes and is required for establishing proper axon guidance, and for neuronal functions related to locomotion and learning. Moreover, we uncover a striking correlation between components of the H3K4 regulatory machinery mutated in neurodevelopmental disorders and the process of axon guidance in C. elegans. Thus, our study supports an epigenetic-based model for the aetiology of neurodevelopmental disorders, based on an aberrant axon guidance process originating from deregulated H3K4 methylation. Summary: Analysis of mutants lacking many known H3K4 regulators reveals the role of H3K4 methylation in C. elegans neuronal functions and suggests that aberrant axon guidance is a shared trait in neurodevelopmental diseases.
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Affiliation(s)
- Steffen Abay-Nørgaard
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Benedetta Attianese
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Laura Boreggio
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
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11
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Soderquist CR, Hsiao S, Mansukhani MM, Alobeid B, Green PH, Bhagat G. Refractory celiac disease type II: An atypical case highlighting limitations of the current classification system. Hematol Oncol 2020; 38:399-405. [PMID: 32010998 DOI: 10.1002/hon.2720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
Abstract
Refractory celiac disease (RCD) is a rare condition associated with high morbidity that develops in individuals with celiac disease. It is known to be biologically heterogeneous, and currently two types are recognized based on immunophenotypic and molecular features, type I (RCD I) and type II (RCD II). Differentiating between RCD I and RCD II is critical, as patients with RCD II have substantially worse outcomes and a high risk of developing enteropathy-associated T-cell lymphoma. However, the current RCD classification is limited in scope, and atypical presentations and immunophenotypes are not recognized at present. Herein, we describe a unique case of RCD II with atypical clinical (primarily neurologic manifestations and lack of significant gastrointestinal symptoms), histopathologic (no villous atrophy), immunophenotypic (virtual absence of cytoplasmic CD3 expression), and molecular features (absence of clonal TR rearrangement and identification of pathogenic STAT3 and KMT2D mutations). This case highlights limitations of the current RCD classification system and the utility of next generation sequencing (NGS) studies in the diagnostic workup of RCD. Future algorithms need to recognize extraintestinal manifestations and incorporate atypical histopathologic and immunophenotypic features, as well as results of NGS analysis for RCD II classification.
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Affiliation(s)
- Craig R Soderquist
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Susan Hsiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Bachir Alobeid
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Peter H Green
- Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
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12
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Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [K CDCOM-ADs]: an emerging class of congenital regulopathies. Clin Epigenetics 2020; 12:10. [PMID: 31924266 PMCID: PMC6954584 DOI: 10.1186/s13148-019-0802-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
The type 2 lysine methyltransferases KMT2C and KMT2D are large, enzymatically active scaffold proteins that form the core of nuclear regulatory structures known as KMT2C/D COMPASS complexes (complex of proteins associating with Set1). These evolutionarily conserved proteins regulate DNA promoter and enhancer elements, modulating the activity of diverse cell types critical for embryonic morphogenesis, central nervous system development, and post-natal survival. KMT2C/D COMPASS complexes and their binding partners enhance active gene expression of specific loci via the targeted modification of histone-3 tail residues, in general promoting active euchromatic conformations. Over the last 20 years, mutations in five key COMPASS complex genes have been linked to three human congenital syndromes: Kabuki syndrome (type 1 [KMT2D] and 2 [KDM6A]), Rubinstein-Taybi syndrome (type 1 [CBP] and 2 [EP300]), and Kleefstra syndrome type 2 (KMT2C). Here, we review the composition and biochemical function of the KMT2 complexes. The specific cellular and embryonic roles of the KMT2C/D COMPASS complex are highlight with a focus on clinically relevant mechanisms sensitive to haploinsufficiency. The phenotypic similarities and differences between the members of this new family of disorders are outlined and emerging therapeutic strategies are detailed.
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Affiliation(s)
- William J Lavery
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
- Division of Human Genetics, CCHMC, Cincinnati, OH, USA
| | - Susan Wiley
- Division of Developmental and Behavioral Pediatrics, CCHMC, Cincinnati, OH, USA
| | | | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA.
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13
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Wang YR, Xu NX, Wang J, Wang XM. Kabuki syndrome: review of the clinical features, diagnosis and epigenetic mechanisms. World J Pediatr 2019; 15:528-535. [PMID: 31587141 DOI: 10.1007/s12519-019-00309-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 08/07/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Kabuki syndrome (KS), is a infrequent inherited malformation syndrome caused by mutations in a H3 lysine 4 methylase (KMT2D) or an X-linked histone H3 lysine 27 demethylase (UTX/KDM6A). The characteristics in patients with KS have not yet been well recognized. DATA SOURCES We used databases including PubMed and Google Scholar to search for publications about the clinical features and the etiology of Kabuki syndrome. The most relevant articles to the scope of this review were chosen for analysis. RESULTS Clinical diagnosis of KS is challenging in initial period, because many clinical characteristics become apparent only in subsequent years. Recently, the genetic and functional interaction between KS-associated genes and their products have been elucidated. New clinical findings were reported including nervous system and intellectual performance, endocrine-related disorders and immune deficiency and autoimmune disease. Cancer risks of Kabuki syndrome was reviewed. Meanwhile, we discussed the Kabuki-like syndrome. Digital clinical genetic service, such as dysmorphology database can improve availability and provide high-quality diagnostic services. Given the significant clinical relevance of KS-associated genes and epigenetic modifications crosstalk, efforts in the research for new mechanisms are thus of maximum interest. CONCLUSIONS Kabuki syndrome has a strong clinical and biological heterogeneity. The main pathogenesis of Kabuki syndrome is the imbalance between switch-on and -off of the chromatin. The direction of drug research may be to regulate the normal opening of chromatin. Small molecule inhibitors of histone deacetylases maybe helpful in treatment of mental retardation and reduce cancer risk in KS.
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Affiliation(s)
- Yi-Rou Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Nai-Xin Xu
- Huaxi Medical College School of Sichuan University, Sichuan, China
| | - Jian Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiu-Min Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China. .,Department of Genetics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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14
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Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng N. Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS. Mol Cell 2019; 76:712-723.e4. [PMID: 31733991 DOI: 10.1016/j.molcel.2019.10.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/03/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
The COMPASS (complex of proteins associated with Set1) complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well known as a prerequisite histone mark for COMPASS activity, how H2Bub activates COMPASS remains unclear. Here, we report the cryoelectron microscopy (cryo-EM) structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that autoinhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By delineating the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.
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Affiliation(s)
- Peter L Hsu
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Hui Shi
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Calvin Leonen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jianming Kang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Ning Zheng
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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15
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Kong X, Ma L, Chen E, Shaw CA, Edelstein LC. Identification of the Regulatory Elements and Target Genes of Megakaryopoietic Transcription Factor MEF2C. Thromb Haemost 2019; 119:716-725. [PMID: 30731491 PMCID: PMC6932631 DOI: 10.1055/s-0039-1678694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Megakaryopoiesis produces specialized haematopoietic stem cells in the bone marrow that give rise to megakaryocytes which ultimately produce platelets. Defects in megakaryopoiesis can result in altered platelet counts and physiology, leading to dysfunctional haemostasis and thrombosis. Additionally, dysregulated megakaryopoiesis is also associated with myeloid pathologies. Transcription factors play critical roles in cell differentiation by regulating the temporal and spatial patterns of gene expression which ultimately decide cell fate. Several transcription factors have been described as regulating megakaryopoiesis including myocyte enhancer factor 2C (MEF2C); however, the genes regulated by MEF2C that influence megakaryopoiesis have not been reported. Using chromatin immunoprecipitation-sequencing and Gene Ontology data we identified five candidate genes that are bound by MEF2C and regulate megakaryopoiesis: MOV10, AGO3, HDAC1, RBBP5 and WASF2. To study expression of these genes, we silenced MEF2C gene expression in the Meg01 megakaryocytic cell line and in induced pluripotent stem cells by CRISPR/Cas9 editing. We also knocked down MEF2C expression in cord blood-derived haematopoietic stem cells by siRNA. We found that absent or reduced MEF2C expression resulted in defects in megakaryocytic differentiation and reduced levels of the candidate target genes. Luciferase assays confirmed that genomic sequences within the target genes are regulated by MEF2C levels. Finally, we demonstrate that small deletions linked to a platelet count-associated single nucleotide polymorphism alter transcriptional activity, suggesting a mechanism by which genetic variation in MEF2C alters platelet production. These data help elucidate the mechanism behind MEF2C regulation of megakaryopoiesis and genetic variation driving platelet production.
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Affiliation(s)
- Xianguo Kong
- Cardeza Foundation for Hematologic Research and Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA
| | - Lin Ma
- Cardeza Foundation for Hematologic Research and Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA
| | - Edward Chen
- Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, TX
| | - Chad A. Shaw
- Department of Human & Molecular Genetics, Baylor College of Medicine, Houston, TX
- Department of Statistics, Rice University, Houston, TX
| | - Leonard C. Edelstein
- Cardeza Foundation for Hematologic Research and Department of Medicine, Sidney Kimmel Medical School at Thomas Jefferson University, Philadelphia, PA
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16
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Skvortsova K, Masle-Farquhar E, Luu PL, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters TJ, Colino-Sanguino Y, Pidsley R, Nair SS, Khoury A, Smith GC, Miosge LA, Reed JH, Kench JG, Rubin MA, Horvath L, Bogdanovic O, Lim SM, Polo JM, Goodnow CC, Stirzaker C, Clark SJ. DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns. Cancer Cell 2019; 35:297-314.e8. [PMID: 30753827 DOI: 10.1016/j.ccell.2019.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 11/14/2018] [Accepted: 01/07/2019] [Indexed: 01/20/2023]
Abstract
Promoter CpG islands are typically unmethylated in normal cells, but in cancer a proportion are subject to hypermethylation. Using methylome sequencing we identified CpG islands that display partial methylation encroachment across the 5' or 3' CpG island borders. CpG island methylation encroachment is widespread in prostate and breast cancer and commonly associates with gene suppression. We show that the pattern of H3K4me1 at CpG island borders in normal cells predicts the different modes of cancer CpG island hypermethylation. Notably, genetic manipulation of Kmt2d results in concordant alterations in H3K4me1 levels and CpG island border DNA methylation encroachment. Our findings suggest a role for H3K4me1 in the demarcation of CpG island methylation borders in normal cells, which become eroded in cancer.
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Affiliation(s)
- Ksenia Skvortsova
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; Developmental Epigenomics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Etienne Masle-Farquhar
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Jenny Z Song
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Wenjia Qu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Elena Zotenko
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Cathryn M Gould
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Qian Du
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Timothy J Peters
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Yolanda Colino-Sanguino
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Shalima S Nair
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Amanda Khoury
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Grady C Smith
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Lisa A Miosge
- Immunogenomics Laboratory, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Joanne H Reed
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2010, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2010, Australia; Cancer Division, The Kinghorn Cancer Centre, Sydney, NSW 2010, Australia
| | - Mark A Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York 10021, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, USA; Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York 10065, USA; Department for Biomedical Research, University of Bern, Bern, CH-3012, Switzerland; Bern Center for Precision Medicine, Inselspital, Bern University Hospital, Bern, CH-3012, Switzerland
| | - Lisa Horvath
- Sydney Medical School, University of Sydney, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia; Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW 2050, Australia; Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia; Cancer Division, The Kinghorn Cancer Centre, Sydney, NSW 2010, Australia
| | - Ozren Bogdanovic
- St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia; Developmental Epigenomics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Sue Mei Lim
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Jose M Polo
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Christopher C Goodnow
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia.
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17
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A comparative analysis of KMT2D missense variants in Kabuki syndrome, cancers and the general population. J Hum Genet 2018; 64:161-170. [PMID: 30459467 DOI: 10.1038/s10038-018-0536-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/10/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Determining the clinical significance of germline and somatic KMT2D missense variants (MVs) in Kabuki syndrome (KS) and cancers can be challenging. We analysed 1920 distinct KMT2D MVs that included 1535 germline MVs in controls (Control-MVs), 584 somatic MVs in cancers (Cancer-MVs) and 201 MV in individuals with KS (KS-MVs). The proportion of MVs likely to affect splicing was significantly higher for Cancer-MVs and KS-MVs than in Control-MVs (p = 0.000018). Our analysis identified significant clustering of Cancer-MVs and KS-MVs in the PHD#3 and #4, RING#4 and SET domains. Areas of enrichment restricted to just Cancer-MVs (FYR-C and between amino acids 3043-3248) or KS-MVs (coiled-coil#5, FYR-N and between amino acids 4995-5090) were also found. Cancer-MVs and KS-MVs tended to affect more conserved residues (lower BLOSUM scores, p < 0.001 and p = 0.007). KS-MVs are more likely to increase the energy for protein folding (higher ELASPIC ∆∆G scores, p = 0.03). Cancer-MVs are more likely to disrupt protein interactions (higher StructMAn scores, p = 0.019). We reclassify several presumed pathogenic MVs as benign or as variants of uncertain significance. We raise the possibility of as yet unrecognised 'non-KS' phenotype(s) associated with some germline pathogenic KMT2D MVs. Overall, this work provides insights into the disease mechanism of KMT2D variants and can be extended to other genes, mutations in which also cause developmental syndromes and cancer.
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18
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Cocciadiferro D, Augello B, De Nittis P, Zhang J, Mandriani B, Malerba N, Squeo GM, Romano A, Piccinni B, Verri T, Micale L, Pasqualucci L, Merla G. Dissecting KMT2D missense mutations in Kabuki syndrome patients. Hum Mol Genet 2018; 27:3651-3668. [PMID: 30107592 PMCID: PMC6488975 DOI: 10.1093/hmg/ddy241] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
Kabuki syndrome is a rare autosomal dominant condition characterized by facial features, various organs malformations, postnatal growth deficiency and intellectual disability. The discovery of frequent germline mutations in the histone methyltransferase KMT2D and the demethylase KDM6A revealed a causative role for histone modifiers in this disease. However, the role of missense mutations has remained unexplored. Here, we expanded the mutation spectrum of KMT2D and KDM6A in KS by identifying 37 new KMT2D sequence variants. Moreover, we functionally dissected 14 KMT2D missense variants, by investigating their impact on the protein enzymatic activity and the binding to members of the WRAD complex. We demonstrate impaired H3K4 methyltransferase activity in 9 of the 14 mutant alleles and show that this reduced activity is due in part to disruption of protein complex formation. These findings have relevant implications for diagnostic and counseling purposes in this disease.
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Affiliation(s)
- Dario Cocciadiferro
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
- PhD Program in Experimental and Regenerative Medicine, Faculty of Medicine, University of Foggia, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | | | - Jiyuan Zhang
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Barbara Mandriani
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, Naples, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
- PhD Program in Experimental and Regenerative Medicine, Faculty of Medicine, University of Foggia, Italy
| | - Gabriella M Squeo
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Alessandro Romano
- Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Piccinni
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Lucia Micale
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Laura Pasqualucci
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
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19
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Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module. Cell 2018; 174:1106-1116.e9. [PMID: 30100181 PMCID: PMC6108940 DOI: 10.1016/j.cell.2018.06.038] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/07/2023]
Abstract
The SET1/MLL family of histone methyltransferases is conserved in eukaryotes and regulates transcription by catalyzing histone H3K4 mono-, di-, and tri-methylation. These enzymes form a common five-subunit catalytic core whose assembly is critical for their basal and regulated enzymatic activities through unknown mechanisms. Here, we present the crystal structure of the intact yeast COMPASS histone methyltransferase catalytic module consisting of Swd1, Swd3, Bre2, Sdc1, and Set1. The complex is organized by Swd1, whose conserved C-terminal tail not only nucleates Swd3 and a Bre2-Sdc1 subcomplex, but also joins Set1 to construct a regulatory pocket next to the catalytic site. This inter-subunit pocket is targeted by a previously unrecognized enzyme-modulating motif in Swd3 and features a doorstop-style mechanism dictating substrate selectivity among SET1/MLL family members. By spatially mapping the functional components of COMPASS, our results provide a structural framework for understanding the multifaceted functions and regulation of the H3K4 methyltransferase family.
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20
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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21
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Cui Z, Li H, Liang F, Mu C, Mu Y, Zhang X, Liu J. Effect of high WDR5 expression on the hepatocellular carcinoma prognosis. Oncol Lett 2018; 15:7864-7870. [PMID: 29731905 PMCID: PMC5921231 DOI: 10.3892/ol.2018.8298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 02/22/2018] [Indexed: 01/22/2023] Open
Abstract
WD repeat domain 5 (WDR5) serves an important role in various biological functions through the epigenetic regulation of gene transcription. Aberrant expression of WDR5 has been observed in various types of human cancer, including prostate cancer, breast cancer and leukemia. However, the role of WDR5 expression and its clinical implications in hepatocellular carcinoma (HCC) remain largely unknown. The present study investigated the WDR5 expression pattern in HCC. It was demonstrated that the mRNA and protein levels of WDR5 were upregulated in HCC cancer tissues compared with normal adjacent tissues using reverse transcription-quantitative polymerase chain reaction and western blotting. Furthermore, the elevated WDR5 protein level was significantly associated with the histological grade (P=0.038), tumor size (P=0.023), tumor-node-metastasis stage (P=0.035) and reduced long-term survival time. Additionally, it was demonstrated through the shRNA-mediated knockdown of WDR5 in HCC cells in vitro that WDR5 expression promotes cell proliferation using an MTT assay. Taken together, the results suggested that WDR5 overexpression may have an oncogenic effect in HCC, and may be a promising biomarker for the diagnosis and prognosis of HCC.
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Affiliation(s)
- Zhoujun Cui
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Hongbo Li
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Feng Liang
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Cuiling Mu
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Yuhua Mu
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Xuegong Zhang
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
| | - Jundong Liu
- Department of General Surgery, People's Hospital of Rizhao, Rizhao, Shandong 276800, P.R. China
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22
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Porntaveetus T, Abid MF, Theerapanon T, Srichomthong C, Ohazama A, Kawasaki K, Kawasaki M, Suphapeetiporn K, Sharpe PT, Shotelersuk V. Expanding the Oro-Dental and Mutational Spectra of Kabuki Syndrome and Expression of KMT2D and KDM6A in Human Tooth Germs. Int J Biol Sci 2018; 14:381-389. [PMID: 29725259 PMCID: PMC5930470 DOI: 10.7150/ijbs.23517] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
Kabuki syndrome is a rare genetic disorder characterized by distinct dysmorphic facial features, intellectual disability, and multiple developmental abnormalities. Despite more than 350 documented cases, the oro-dental spectrum associated with kabuki syndrome and expression of KMT2D (histone-lysine N-methyltransferase 2D) or KDM6A (lysine-specific demethylase 6A) genes in tooth development have not been well defined. Here, we report seven unrelated Thai patients with Kabuki syndrome having congenital absence of teeth, malocclusion, high-arched palate, micrognathia, and deviated tooth shape and size. Exome sequencing successfully identified that six patients were heterozygous for mutations in KMT2D, and one in KDM6A. Six were novel mutations, of which five were in KMT2D and one in KDM6A. They were truncating mutations including four frameshift deletions and two nonsense mutations. The predicted non-functional KMT2D and KDM6A proteins are expected to cause disease by haploinsufficiency. Our study expands oro-dental, medical, and mutational spectra associated with Kabuki syndrome. We also demonstrate for the first time that KMT2D and KDM6A are expressed in the dental epithelium of human tooth germs.
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Affiliation(s)
- Thantrira Porntaveetus
- Craniofacial Genetics and Stem Cells Research Group, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mushriq F Abid
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Thanakorn Theerapanon
- Excellence Center in Regenerative Dentistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Atsushi Ohazama
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | | | - Maiko Kawasaki
- Division of Oral Anatomy, Niigata University, Niigata 951-8514, Japan
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Dental Institute, King's College London, London, SE1 9RT, UK
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
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23
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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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24
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 657] [Impact Index Per Article: 93.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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25
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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: 20] [Impact Index Per Article: 2.9] [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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Weirich S, Kudithipudi S, Jeltsch A. Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex. Mol Oncol 2017; 11:373-387. [PMID: 28182322 PMCID: PMC5527479 DOI: 10.1002/1878-0261.12041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/28/2017] [Accepted: 02/02/2017] [Indexed: 12/19/2022] Open
Abstract
Somatic missense mutations in the mixed lineage leukemia 1 (MLL1) histone H3K4 methyltransferase are often observed in cancers. MLL1 forms a complex with WDR5, RBBP5, and ASH2L (WRA) which stimulates its activity. The MM‐102 compound prevents the interaction between MLL1 and WDR5 and functions as an MLL1 inhibitor. We have studied the effects of four cancer mutations in the catalytic SET domain of MLL1 on the enzymatic activity of MLL1 and MLL1–WRA complexes. In addition, we studied the interaction of the MLL1 mutants with the WRA proteins and inhibition of MLL1–WRA complexes by MM‐102. All four investigated mutations had strong effects on the activity of MLL1. R3903H was inactive and S3865F showed reduced activity both alone and in complex with WRA, but its activity was stimulated by the WRA complex. By contrast, R3864C and R3841W were both more active than wild‐type MLL1, but still less active than the wild‐type MLL1–WRA complex. Both mutants were not stimulated by complex formation with WRA, although no differences in the interaction with the complex proteins were observed. These results indicate that both mutants are in an active conformation even in the absence of the WRA complex and their normal control of activity by the WRA complex is altered. In agreement with this observation, the activity of R3864C and R3841W was not reduced by addition of the MM‐102 inhibitor. We show that different cancer mutations in MLL1 lead to a loss or increase in activity, illustrating the complex and tumor‐specific role of MLL1 in carcinogenesis. Our data exemplify that biochemical investigations of somatic tumor mutations are required to decipher their pathological role. Moreover, our data indicate that MM‐102 may not be used as an MLL1 inhibitor if the R3864C and R3841W mutations are present. More generally, the efficacy of any enzyme inhibitor must be experimentally confirmed for mutant enzymes before an application can be considered.
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Affiliation(s)
- Sara Weirich
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
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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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Liu H, Ding L, Shen Y, Zhong F, Wang Q, Xu X. RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance. Int J Biol Macromol 2016; 91:115-22. [PMID: 27189701 DOI: 10.1016/j.ijbiomac.2016.05.050] [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: 02/26/2016] [Revised: 05/13/2016] [Accepted: 05/13/2016] [Indexed: 12/21/2022]
Abstract
Cell adhesion mediated drug resistance (CAM-DR) is a major factor that impedes the effect of chemotherapy in multiple myeloma (MM). RBQ3, which is a RB-binding protein, played a crucial role in cell cycle process. Here, we reported that RBQ3 expression was increased gradually during the proliferation process of myeloma cells. Knocking down of RBQ3 resulted in cell cycle arrest in G1 phase and increased myeloma cells adherent to fibronectin or bone marrow stromal cells (BMSCs). Furthermore, silencing of RBQ3 reduced sensitivity to chemotherapeutic drugs in myeloma cell lines adherent to BMSCs and reduced two apoptotic marker proteins cleaved caspase-3 and cleaved PARP expression. Besides, we also found that RBQ3 participated in MAPK/ERK signal transduction pathway. In summary, these results may shed new insights into the role of RBQ3 in the development of multiple myeloma.
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Affiliation(s)
- Hong Liu
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, Jiangsu Province, People's Republic of China
| | - Linlin Ding
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, Jiangsu Province, People's Republic of China; Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, Jiangsu Province, People's Republic of China
| | - Yaodong Shen
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, Jiangsu Province, People's Republic of China
| | - Fei Zhong
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, Jiangsu Province, People's Republic of China
| | - Qiru Wang
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, Jiangsu Province, People's Republic of China
| | - Xiaohong Xu
- Department of Oncology, Affiliated Cancer Hospital of Nantong University, Nantong 226361, Jiangsu Province, People's Republic of China.
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Shinsky SA, Cosgrove MS. Unique Role of the WD-40 Repeat Protein 5 (WDR5) Subunit within the Mixed Lineage Leukemia 3 (MLL3) Histone Methyltransferase Complex. J Biol Chem 2015; 290:25819-33. [PMID: 26324722 PMCID: PMC4646236 DOI: 10.1074/jbc.m115.684142] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 12/29/2022] Open
Abstract
The MLL3 (mixed lineage leukemia 3) protein is a member of the human SET1 family of histone H3 lysine 4 methyltransferases and contains the conserved WDR5 interaction (Win) motif and the catalytic suppressor of variegation, enhancer of zeste, trithorax (SET) domain. The human SET1 family includes MLL1-4 and SETd1A/B, which all interact with a conserved subcomplex containing WDR5, RbBP5, Ash2L, and DPY-30 (WRAD) to form the minimal core complex required for full methyltransferase activity. However, recent evidence suggests that the WDR5 subunit may not be utilized in an identical manner within all SET1 family core complexes. Although the roles of WDR5 within the MLL1 core complex have been extensively studied, not much is known about the roles of WDR5 in other SET1 family core complexes. In this investigation, we set out to characterize the roles of the WDR5 subunit in the MLL3 core complex. We found that unlike MLL1, the MLL3 SET domain assembles with the RbBP5/Ash2L heterodimer independently of the Win motif-WDR5 interaction. Furthermore, we observed that WDR5 inhibits the monomethylation activity of the MLL3 core complex, which is dependent on the Win motif. We also found evidence suggesting that the WRAD subcomplex catalyzes weak H3K4 monomethylation within the context of the MLL3 core complex. Furthermore, solution structures of the MLL3 core complex assembled with and without WDR5 by small angle x-ray scattering show similar overall topologies. Together, this work demonstrates a unique role for WDR5 in modulating the enzymatic activity of the MLL3 core complex.
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Affiliation(s)
- Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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30
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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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Lindsley AW, Saal HM, Burrow TA, Hopkin RJ, Shchelochkov O, Khandelwal P, Xie C, Bleesing J, Filipovich L, Risma K, Assa'ad AH, Roehrs PA, Bernstein JA. Defects of B-cell terminal differentiation in patients with type-1 Kabuki syndrome. J Allergy Clin Immunol 2015; 137:179-187.e10. [PMID: 26194542 DOI: 10.1016/j.jaci.2015.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/28/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Kabuki syndrome (KS) is a complex multisystem developmental disorder associated with mutation of genes encoding histone-modifying proteins. In addition to craniofacial, intellectual, and cardiac defects, KS is also characterized by humoral immune deficiency and autoimmune disease, yet no detailed molecular characterization of the KS-associated immune phenotype has been reported. OBJECTIVE We sought to characterize the humoral immune defects found in patients with KS with lysine methyltransferase 2D (KMT2D) mutations. METHODS We comprehensively characterized B-cell function in a cohort (n = 13) of patients with KS (age, 4 months to 27 years). RESULTS Three quarters (77%) of the cohort had a detectable heterozygous KMT2D mutation (50% nonsense, 20% splice site, and 30% missense mutations), and 70% of the reported mutations are novel. Among the patients with KMT2D mutations (KMT2D(Mut/+)), hypogammaglobulinemia was detected in all but 1 patient, with IgA deficiency affecting 90% of patients and a deficiency in at least 1 other isoform seen in 40% of patients. Numbers of total memory (CD27(+)) and class-switched memory B cells (IgM(-)) were significantly reduced in patients with KMT2D(Mut/+) mutations compared with numbers in control subjects (P < .001). Patients with KMT2D(Mut/+) mutations also had significantly reduced rates of somatic hypermutation in IgG (P = .003) but not IgA or IgM heavy chain sequences. Impaired terminal differentiation was noted in primary B cells from patients with KMT2D(Mut/+) mutations. Autoimmune pathology was observed in patients with missense mutations affecting the SET domain and its adjacent domains. CONCLUSIONS In patients with KS, autosomal dominant KMT2D mutations are associated with dysregulation of terminal B-cell differentiation, leading to humoral immune deficiency and, in some cases, autoimmunity. All patients with KS should undergo serial clinical immune evaluations.
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Affiliation(s)
- Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio.
| | - Howard M Saal
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Thomas A Burrow
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Robert J Hopkin
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Oleg Shchelochkov
- Division of Genetics, Stead Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Pooja Khandelwal
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Division of Bone Marrow Transplantation, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Changchun Xie
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
| | - Jack Bleesing
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Division of Bone Marrow Transplantation, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lisa Filipovich
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Division of Bone Marrow Transplantation, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kimberly Risma
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - Amal H Assa'ad
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - Phillip A Roehrs
- Division of Pediatric Hematology/Oncology, University of North Carolina, Chapel Hill, NC
| | - Jonathan A Bernstein
- Division of Immunology, Allergy and Rheumatology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
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32
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Chen CW, Armstrong SA. Targeting DOT1L and HOX gene expression in MLL-rearranged leukemia and beyond. Exp Hematol 2015; 43:673-84. [PMID: 26118503 DOI: 10.1016/j.exphem.2015.05.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/28/2015] [Accepted: 05/28/2015] [Indexed: 01/05/2023]
Abstract
Leukemias harboring mixed-lineage leukemia gene (MLL1) abnormalities are associated with poor clinical outcomes, and new therapeutic approaches are desperately needed. Rearrangement of the MLL1 gene generates chimeric proteins that fuse the NH3 terminus of MLL1 to the COOH terminus of its translocation partners. These MLL1 fusion oncoproteins drive the expression of homeobox genes such as HOXA cluster genes and myeloid ecotropic viral integration site 1 homolog (MEIS1), which are known to induce leukemic transformation of hematopoietic progenitors. Genomewide histone methylation studies have revealed that the abnormal expression of MLL1 fusion target genes is associated with high levels of H3K79 methylation at these gene loci. The only known enzyme that catalyzes methylation of H3K79 is disruptor of telomeric-silencing 1-like (DOT1L). Loss-of-function mouse models, as well as small molecular inhibitors of DOT1L, illustrate that leukemias driven by MLL1 translocations are dependent on DOT1L enzymatic activity for proliferation and for the maintenance of HOXA gene expression. Furthermore, DOT1L also appears to be important for HOXA gene expression in other settings including leukemias with select genetic abnormalities. These discoveries have established a foundation for disease-specific therapies that target chromatin modifications in highly malignant leukemias harboring specific genetic abnormalities. This review focuses on the molecular mechanisms underlying MLL1 translocation-driven leukemogenesis and the latest progress on DOT1L-targeted epigenetic therapies for MLL1-rearranged and other leukemias.
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Affiliation(s)
- Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Abstract
Histone-lysine N-methyltransferase 2 (KMT2) family proteins methylate lysine 4 on the histone H3 tail at important regulatory regions in the genome and thereby impart crucial functions through modulating chromatin structures and DNA accessibility. Although the human KMT2 family was initially named the mixed-lineage leukaemia (MLL) family, owing to the role of the first-found member KMT2A in this disease, recent exome-sequencing studies revealed KMT2 genes to be among the most frequently mutated genes in many types of human cancers. Efforts to integrate the molecular mechanisms of KMT2 with its roles in tumorigenesis have led to the development of first-generation inhibitors of KMT2 function, which could become novel cancer therapies.
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Affiliation(s)
- Rajesh C. Rao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI 48109
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
- Correspondence: , Tel: (734) 6151315, Fax: (734) 7636476
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Chen H, Wan D, Wang L, Peng A, Xiao H, Petersen RB, Liu C, Zheng L, Huang K. Apelin protects against acute renal injury by inhibiting TGF-β1. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1278-87. [PMID: 25748499 DOI: 10.1016/j.bbadis.2015.02.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/12/2015] [Accepted: 02/27/2015] [Indexed: 12/29/2022]
Abstract
Renal ischemia/reperfusion (I/R) injury is the most common cause of acute kidney injury, having a high rate of mortality and no effective therapy currently available. Apelin-13, a bioactive peptide, has been shown to inhibit the early lesions of diabetic nephropathy in several mouse models by us and others. To test whether apelin-13 protects against renal I/R induced injury, male rats were exposed to renal I/R injury with or without apelin-13 treatment for 3 days. Apelin-13 treatment markedly reduced the injury-induced tubular lesions, renal cell apoptosis, and normalized the injury induced renal dysfunction. Apelin-13 treatment inhibited the injury-induced elevation of inflammatory factors and Tgf-β1, as well as apoptosis. Apelin-13 treatment also inhibited the injury-induced elevation of histone methylation and Kmt2d, a histone methyltransferase of H3K4me2, following renal I/R injury. Furthermore, in cultured renal mesangial and tubular cells, apelin-13 suppressed the injury-induced elevation of Tgf-β1, apoptosis, H3K4me2 and Kmt2d under the in vitro hypoxia/reperfusion (H/R) conditions. Consistently, over-expression of apelin significantly inhibited H/R-induced elevation of TGF-β1, apoptosis, H3K4me2 and Kmt2d. The present study therefore suggests apelin-13 may be a therapeutic candidate for treating acute kidney injury.
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Affiliation(s)
- Hong Chen
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China, 430030; Centre for Biomedicine Research, Wuhan Institute of Biotechnology, Wuhan, China, 430074
| | - Danyang Wan
- College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Lin Wang
- College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Anlin Peng
- Wuhan the Third Hospital, Wuhan, China, 430060
| | - Hongdou Xiao
- College of Life Sciences, Wuhan University, Wuhan, China, 430072
| | - Robert B Petersen
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA, 44106; Department of Neuroscience, Case Western Reserve University, Cleveland, OH, USA, 44106; Department of Neurology, Case Western Reserve University, Cleveland, OH, USA, 44106
| | - Chengyu Liu
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China, 430030; Centre for Biomedicine Research, Wuhan Institute of Biotechnology, Wuhan, China, 430074
| | - Ling Zheng
- College of Life Sciences, Wuhan University, Wuhan, China, 430072.
| | - Kun Huang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China, 430030; Centre for Biomedicine Research, Wuhan Institute of Biotechnology, Wuhan, China, 430074.
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35
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Bailey JK, Fields AT, Cheng K, Lee A, Wagenaar E, Lagrois R, Schmidt B, Xia B, Ma D. WD repeat-containing protein 5 (WDR5) localizes to the midbody and regulates abscission. J Biol Chem 2015; 290:8987-9001. [PMID: 25666610 DOI: 10.1074/jbc.m114.623611] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 12/25/2022] Open
Abstract
Cytokinesis partitions the cytoplasm of a parent cell into two daughter cells and is essential for the completion of cell division. The final step of cytokinesis in animal cells is abscission, which is a process leading to the physical separation of two daughter cells. Abscission requires membrane traffic and microtubule disassembly at a specific midbody region called the secondary ingression. Here, we report that WD repeat-containing protein 5 (WDR5), a core subunit of COMPASS/MLL family histone H3 lysine 4 methyltransferase (H3K4MT) complexes, resides at the midbody and associates with a subset of midbody regulatory proteins, including PRC1 and CYK4/MKLP1. Knockdown of WDR5 impairs abscission and increases the incidence of multinucleated cells. Further investigation revealed that the abscission delay is primarily due to slower formation of secondary ingressions in WDR5 knockdown cells. Consistent with these defects, midbody microtubules in WDR5 knockdown cells also display enhanced resistance to depolymerization by nocodazole. Recruitment of WDR5 to the midbody dark zone appears to require integrity of the WDR5 central arginine-binding cavity, as mutations that disrupt histone H3 and MLL1 binding to this pocket also abolish the midbody localization of WDR5. Taken together, these data suggest that WDR5 is specifically targeted to the midbody in the absence of chromatin and that it promotes abscission, perhaps by facilitating midbody microtubule disassembly.
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Affiliation(s)
- Jeffrey K Bailey
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Alexander T Fields
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Kaijian Cheng
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Albert Lee
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Eric Wagenaar
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Remy Lagrois
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Bailey Schmidt
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Bin Xia
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Dzwokai Ma
- From the Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106
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The cancer COMPASS: navigating the functions of MLL complexes in cancer. Cancer Genet 2015; 208:178-91. [PMID: 25794446 DOI: 10.1016/j.cancergen.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/13/2022]
Abstract
The mixed-lineage leukemia family of histone methyltransferases (MLL1-4, or KMT2A-D) were previously linked to cancer through the founding member, MLL1/KMT2A, which is often involved in translocation-associated gene fusion events in childhood leukemias. However, in recent years, a multitude of tumor exome sequencing studies have revealed that orthologues MLL3/KMT2C and MLL2/KMT2D are mutated in a significant percentage of a large variety of malignancies, particularly solid tumors. These unexpected findings necessitate a deeper inspection into the activities and functional differences between the MLL/KMT2 family members. This review provides an overview of this protein family and its relation to cancers, focusing on the recent links between MLL3/KMT2C and MLL2/4/KMT2D and their potential roles as tumor suppressors in an assortment of cell types.
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37
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Shinsky SA, Monteith KE, Viggiano S, Cosgrove MS. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation. J Biol Chem 2015; 290:6361-75. [PMID: 25561738 DOI: 10.1074/jbc.m114.627646] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo.
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Affiliation(s)
- Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Kelsey E Monteith
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Susan Viggiano
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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Khorasanizadeh S, Ostankovitch M. Zooming into Epigenetic Regulatory Elements in Health and Disease. J Mol Biol 2014; 426:3327-9. [DOI: 10.1016/j.jmb.2014.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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