1
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BenDavid E, Yang C, Zhou Y, Pfaller CK, Samuel CE, Ma D. Host WD repeat-containing protein 5 inhibits protein kinase R-mediated integrated stress response during measles virus infection. J Virol 2024; 98:e0102024. [PMID: 39194235 PMCID: PMC11406981 DOI: 10.1128/jvi.01020-24] [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: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024] Open
Abstract
Some negative-sense RNA viruses, including measles virus (MeV), share the characteristic that during their infection cycle, cytoplasmic inclusion bodies (IBs) are formed where components of the viral replication machinery are concentrated. As a foci of viral replication, how IBs act to enhance the efficiency of infection by affecting virus-host interactions remains an important topic of investigation. We previously established that upon MeV infection, the epigenetic host protein, WD repeat-containing protein 5 (WDR5), translocates to cytoplasmic viral IBs and facilitates MeV replication. We now show that WDR5 is recruited to IBs by forming a complex with IB-associated MeV phosphoprotein via a conserved binding motif located on the surface of WDR5. Furthermore, we provide evidence that WDR5 promotes viral replication by suppressing a major innate immune response pathway, the double-stranded RNA-mediated activation of protein kinase R and integrated stress response. IMPORTANCE MeV is a pathogen that remains a global concern, with an estimated 9 million measles cases and 128,000 measles deaths in 2022 according to the World Health Organization. A large population of the world still has inadequate access to the effective vaccine against the exceptionally transmissible MeV. Measles disease is characterized by a high morbidity in children and in immunocompromised individuals. An important area of research for negative-sense RNA viruses, including MeV, is the characterization of the complex interactome between virus and host occurring at cytoplasmic IBs where viral replication occurs. Despite the progress made in understanding IB structures, little is known regarding the virus-host interactions within IBs and the role of these interactions in promoting viral replication and antagonizing host innate immunity. Herein we provide evidence suggesting a model by which MeV IBs utilize the host protein WDR5 to suppress the protein kinase R-integrated stress response pathway.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Chuyuan Yang
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Yuqin Zhou
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Charles E Samuel
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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2
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Grégoire S, Grégoire J, Yang Y, Capitani S, Joshi M, Sarvan S, Zaker A, Ning Z, Figeys D, Ulrich K, Brunzelle JS, Mer A, Couture JF. Structural insights into an atypical histone binding mechanism by a PHD finger. Structure 2024; 32:1498-1506.e4. [PMID: 39029460 DOI: 10.1016/j.str.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 07/21/2024]
Abstract
Complex associating with SET1 (COMPASS) is a histone H3K4 tri-methyltransferase controlled by several regulatory subunits including CXXC zinc finger protein 1 (Cfp1). Prior studies established the structural underpinnings controlling H3K4me3 recognition by the PHD domain of Cfp1's yeast homolog (Spp1). However, metazoans Cfp1PHD lacks structural elements important for H3K4me3 stabilization in Spp1, suggesting that in metazoans, Cfp1PHD domain binds H3K4me3 differently. The structure of Cfp1PHD in complex with H3K4me3 shows unique features such as non-canonical coordination of the first zinc atom and a disulfide bond forcing the reorientation of Cfp1PHD N-terminus, thereby leading to an atypical H3K4me3 binding pocket. This configuration minimizes Cfp1PHD reliance on canonical residues important for histone binding functions of other PHD domains. Cancer-related mutations in Cfp1PHD impair H3K4me3 binding, implying a potential impact on epigenetic signaling. Our work highlights a potential diversification of PHD histone binding modes and the impact of cancer mutations on Cfp1 functions.
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Affiliation(s)
- Sabrina Grégoire
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Janelle Grégoire
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Yidai Yang
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Sabrina Capitani
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Sabina Sarvan
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Arvin Zaker
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Kathrin Ulrich
- Institute of Biochemistry, Cellular Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Joseph S Brunzelle
- Life Sciences Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Arvind Mer
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada.
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3
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Wolf E, Herasymenko O, Kutera M, Lento C, Arrowsmith C, Ackloo S, Wilson D. Quantitative Hydrogen-Deuterium Exchange Mass Spectrometry for Simultaneous Structural Characterization and Affinity Indexing of Single Target Drug Candidate Libraries. Anal Chem 2024; 96:13015-13024. [PMID: 39074309 PMCID: PMC11326436 DOI: 10.1021/acs.analchem.4c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Hydrogen-deuterium eXchange mass spectrometry (HDX-MS) is increasingly used in drug development to locate binding sites and to identify allosteric effects in drug/target interactions. However, the potential of this technique to quantitatively analyze drug candidate libraries remains largely unexplored. Here, a collection of 13 WDR5-targeting small molecules with surface plasmon resonance (SPR) dissociation coefficients (KD) ranging from 20 nM to ∼116 μM were characterized using differential HDX-MS (ΔHDX-MS). Conventional qualitative analysis of the ΔHDX-MS data set revealed the binding interfaces for all compounds and allosteric effects where present. We then demonstrated that ΔHDX-MS signal-to-noise (S/N) not only can rank library-relative affinity but also can accurately predict KD from a calibration curve constructed from high-quality SPR data. Three methods for S/N calculation are explored, each suitable for libraries with different characteristics. Our results demonstrate the potential for ΔHDX-MS use in drug candidate library affinity validation and/or determination while simultaneously characterizing structure.
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Affiliation(s)
- Esther Wolf
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | | | - Maria Kutera
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Derek Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
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4
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Yang Y, Xu L, Zhang S, Yao L, Ding Y, Li W, Chen X. Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode. J Biol Chem 2024; 300:107468. [PMID: 38876301 PMCID: PMC11261779 DOI: 10.1016/j.jbc.2024.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex plays a pivotal role in chromatin regulation and transcriptional repression. In mice, methyl-CpG binding domain 3 isoform C (MBD3C) interacts specifically with the histone H3 binding protein WD repeat-containing protein 5 (WDR5) and forms the WDR5-MBD3C/Norde complex. Despite the functional significance of this interaction on embryonic stem cell gene regulation, the molecular mechanism underlying MBD3C recognition by WDR5 remains elusive. Here, we determined the crystal structure of WDR5 in complex with the peptide (residues 40-51) derived from the MBD3C protein at a resolution of 1.9 Å. Structural analysis revealed that MBD3C utilizes a unique binding mode to interact with WDR5, wherein MBD3C Arg43 and Phe47 are involved in recognizing the WDR5-interacting (WIN) site and Tyr191-related B site on the small surface of WDR5, respectively. Notably, the binding induces a ∼91° rotation of WDR5 Tyr191, generating the hydrophobic B site. Furthermore, mutation experiments combined with isothermal titration calorimetry (ITC) assays confirmed the importance of both Arg43 and Phe47 in mediating WDR5 binding affinity. By determining structures of various peptides bound to WDR5, we demonstrated that the WDR5 WIN site and B site can be concurrently recognized by WIN motif peptides containing ''Arg-Cies/Ser-Arg-Val-Phe'' consensus sequence. Overall, this study reveals the structural basis for the formation of the WDR5-MBD3C subcomplex and provides new insights into the recognition mode of WDR5 for the WIN motif. Moreover, these findings shed light on structural-based designs of WDR5-targeted anti-cancer small molecule inhibitors or peptide-mimic drugs.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Anhui University, Hefei, Anhui, China.
| | - Li Xu
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, China.
| | - Shuting Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Liangrui Yao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yuqing Ding
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Wenwen Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xuemin Chen
- School of Life Sciences, Anhui University, Hefei, Anhui, China.
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5
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Qin Y, Dong X, Lu M, Jing L, Chen Q, Guan F, Xiang Z, Huang J, Yang C, He X, Qu J, Yang Z. PARP1 interacts with WDR5 to enhance target gene recognition and facilitate tumorigenesis. Cancer Lett 2024; 593:216952. [PMID: 38750719 DOI: 10.1016/j.canlet.2024.216952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear protein that attaches negatively charged poly (ADP-ribose) (PAR) to itself and other target proteins. While its function in DNA damage repair is well established, its role in target chromatin recognition and regulation of gene expression remains to be better understood. This study showed that PARP1 interacts with SET1/MLL complexes by binding directly to WDR5. Notably, although PARP1 does not modulate WDR5 PARylation or the global level of H3K4 methylation, it exerts locus-specific effects on WDR5 binding and H3K4 methylation. Interestingly, PARP1 and WDR5 show extensive co-localization on chromatin, with WDR5 facilitating the recognition and expression of target genes regulated by PARP1. Furthermore, we demonstrated that inhibition of the WDR5 Win site impedes the interaction between PARP1 and WDR5, thereby inhibiting PARP1 from binding to target genes. Finally, the combined inhibition of the WDR5 Win site and PARP shows a profound inhibitory effect on the proliferation of cancer cells. These findings illuminate intricate mechanisms underlying chromatin recognition, gene transcription, and tumorigenesis, shedding light on previously unrecognized roles of PARP1 and WDR5 in these processes.
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Affiliation(s)
- Yali Qin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaochuan Dong
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Manman Lu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lingyun Jing
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qingchuan Chen
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fei Guan
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhengkai Xiang
- Department of Thoracic Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Jiaojuan Huang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chengxuan Yang
- Department of Galactophore, Xinxiang First People's Hospital, Xinxiang, 453000, China
| | - Ximiao He
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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6
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Cho US. The Core Complex of Yeast COMPASS and Human Mixed-Lineage Leukemia (MLL), Structure, Function, and Recognition of the Nucleosome. Subcell Biochem 2024; 104:101-117. [PMID: 38963485 DOI: 10.1007/978-3-031-58843-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Yeast COMPASS (complex of proteins associated with Set1) and human MLL (mixed-lineage leukemia) complexes are histone H3 lysine 4 methyltransferases with critical roles in gene regulation and embryonic development. Both complexes share a conserved C-terminal SET domain, responsible for catalyzing histone H3 K4 methylation on nucleosomes. Notably, their catalytic activity toward nucleosomes is enhanced and optimized with assembly of auxiliary subunits. In this review, we aim to illustrate the recent X-ray and cryo-EM structures of yeast COMPASS and human MLL1 core complexes bound to either unmodified nucleosome core particle (NCP) or H2B mono-ubiquitinated NCP (H2Bub.NCP). We further delineate how each auxiliary component of the complex contributes to the NCP and ubiquitin recognition to maximize the methyltransferase activity.
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Affiliation(s)
- Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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7
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Barsoum M, Sayadi-Boroujeni R, Stenzel AT, Bussmann P, Lüscher-Firzlaff J, Lüscher B. Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L. Sci Rep 2023; 13:22565. [PMID: 38114530 PMCID: PMC10730889 DOI: 10.1038/s41598-023-49284-x] [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: 09/15/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
The trithorax protein ASH2L is essential for organismal and tissue development. As a subunit of COMPASS/KMT2 complexes, ASH2L is necessary for methylation of histone H3 lysine 4 (H3K4). Mono- and tri-methylation at this site mark active enhancers and promoters, respectively, although the functional relevance of H3K4 methylation is only partially understood. ASH2L has a long half-life, which results in a slow decrease upon knockout. This has made it difficult to define direct consequences. To overcome this limitation, we employed a PROTAC system to rapidly degrade ASH2L and address direct effects. ASH2L loss resulted in inhibition of proliferation of mouse embryo fibroblasts. Shortly after ASH2L degradation H3K4me3 decreased with its half-life varying between promoters. Subsequently, H3K4me1 increased at promoters and decreased at some enhancers. H3K27ac and H3K27me3, histone marks closely linked to H3K4 methylation, were affected with considerable delay. In parallel, chromatin compaction increased at promoters. Of note, nascent gene transcription was not affected early but overall RNA expression was deregulated late after ASH2L loss. Together, these findings suggest that downstream effects are ordered but relatively slow, despite the rapid loss of ASH2L and inactivation of KMT2 complexes. It appears that the systems that control gene transcription are well buffered and strong effects are only beginning to unfold after considerable delay.
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Affiliation(s)
- Mirna Barsoum
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
| | - Roksaneh Sayadi-Boroujeni
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
- Bayer AG, Crop Science Division, R&D, Pest Control, 40789, Monheim am Rhein, Germany
| | - Alexander T Stenzel
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
- Institute of Human Genetics, Faculty of Medicine, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Philip Bussmann
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Juliane Lüscher-Firzlaff
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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8
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Ahmad S, Xu J, Feng JA, Hutchinson A, Zeng H, Ghiabi P, Dong A, Centrella PA, Clark MA, Guié MA, Guilinger JP, Keefe AD, Zhang Y, Cerruti T, Cuozzo JW, von Rechenberg M, Bolotokova A, Li Y, Loppnau P, Seitova A, Li YY, Santhakumar V, Brown PJ, Ackloo S, Halabelian L. Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning. J Med Chem 2023; 66:16051-16061. [PMID: 37996079 DOI: 10.1021/acs.jmedchem.3c01471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
WD40 repeat-containing protein 91 (WDR91) regulates early-to-late endosome conversion and plays vital roles in endosome fusion, recycling, and transport. WDR91 was recently identified as a potential host factor for viral infection. We employed DNA-encoded chemical library (DEL) selection against the WDR domain of WDR91, followed by machine learning to predict ligands from the synthetically accessible Enamine REAL database. Screening of predicted compounds identified a WDR91 selective compound 1, with a KD of 6 ± 2 μM by surface plasmon resonance. The co-crystal structure confirmed the binding of 1 to the WDR91 side pocket, in proximity to cysteine 487, which led to the discovery of covalent analogues 18 and 19. The covalent adduct formation for 18 and 19 was confirmed by intact mass liquid chromatography-mass spectrometry. The discovery of 1, 18, and 19, accompanying structure-activity relationship, and the co-crystal structures provide valuable insights for designing potent and selective chemical tools against WDR91 to evaluate its therapeutic potential.
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Affiliation(s)
- Shabbir Ahmad
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Jin Xu
- Google Research, Mountain View, California 94043, United States
| | - Jianwen A Feng
- Google Research, Mountain View, California 94043, United States
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Pegah Ghiabi
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Paolo A Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02435, United States
| | - Matthew A Clark
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02435, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02435, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02435, United States
| | - Anthony D Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02435, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02435, United States
| | - Thomas Cerruti
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - John W Cuozzo
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Moritz von Rechenberg
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Yen-Yen Li
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | | | - Peter J Brown
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S 1A8, Ontario, Canada
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9
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Guo C, Gao YY, Li ZL. Predicting leukemic transformation in myelodysplastic syndrome using a transcriptomic signature. Front Genet 2023; 14:1235315. [PMID: 37953918 PMCID: PMC10634373 DOI: 10.3389/fgene.2023.1235315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023] Open
Abstract
Background: For prediction on leukemic transformation of MDS patients, emerging model based on transcriptomic datasets, exhibited superior predictive power to traditional prognostic systems. While these models were lack of external validation by independent cohorts, and the cell origin (CD34+ sorted cells) limited their feasibility in clinical practice. Methods: Transformation associated co-expressed gene cluster was derived based on GSE58831 ('WGCNA' package, R software). Accordingly, the least absolute shrinkage and selection operator algorithm was implemented to establish a scoring system (i.e., MDS15 score), using training set (GSE58831 originated from CD34+ cells) and testing set (GSE15061 originated from unsorted cells). Results: A total of 68 gene co-expression modules were derived, and the 'brown' module was recognized to be transformation-specific (R2 = 0.23, p = 0.005, enriched in transcription regulating pathways). After 50,000-times LASSO iteration, MDS15 score was established, including the 15-gene expression signature. The predictive power (AUC and Harrison's C index) of MDS15 model was superior to that of IPSS/WPSS in both training set (AUC/C index 0.749/0.777) and testing set (AUC/C index 0.933/0.86). Conclusion: By gene co-expression analysis, the crucial gene module was discovered, and a novel prognostic system (MDS15) was established, which was validated not only by another independent cohort, but by a different cell origin.
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Affiliation(s)
| | | | - Zhen-Ling Li
- Department of Hematology, China-Japan Friendship Hospital, Beijing, China
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10
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Hao J, Huang J, Hua C, Zuo Y, Yu W, Wu X, Li L, Xue G, Wan X, Ru L, Guo Z, Han S, Deng W, Lin F, Guo W. A novel TOX3-WDR5-ABCG2 signaling axis regulates the progression of colorectal cancer by accelerating stem-like traits and chemoresistance. PLoS Biol 2023; 21:e3002256. [PMID: 37708089 PMCID: PMC10501593 DOI: 10.1371/journal.pbio.3002256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/17/2023] [Indexed: 09/16/2023] Open
Abstract
The eradication of cancer stem cells (CSCs) with drug resistance confers the probability of local tumor control after chemotherapy or targeted therapy. As the main drug resistance marker, ABCG2 is also critical for colorectal cancer (CRC) evolution, in particular cancer stem-like traits expansion. Hitherto, the knowledge about the expression regulation of ABCG2, in particular its upstream transcriptional regulatory mechanisms, remains limited in cancer, including CRC. Here, ABCG2 was found to be markedly up-regulated in CRC CSCs (cCSCs) expansion and chemo-resistant CRC tissues and closely associated with CRC recurrence. Mechanistically, TOX3 was identified as a specific transcriptional factor to drive ABCG2 expression and subsequent cCSCs expansion and chemoresistance by binding to -261 to -141 segments of the ABCG2 promoter region. Moreover, we found that TOX3 recruited WDR5 to promote tri-methylation of H3K4 at the ABCG2 promoter in cCSCs, which further confers stem-like traits and chemoresistance to CRC by co-regulating the transcription of ABCG2. In line with this observation, TOX3, WDR5, and ABCG2 showed abnormal activation in chemo-resistant tumor tissues of in situ CRC mouse model and clinical investigation further demonstrated the comprehensive assessment of TOX3, WDR5, and ABCG2 could be a more efficient strategy for survival prediction of CRC patients with recurrence or metastasis. Thus, our study found that TOX3-WDR5/ABCG2 signaling axis plays a critical role in regulating CRC stem-like traits and chemoresistance, and a combination of chemotherapy with WDR5 inhibitors may induce synthetic lethality in ABCG2-deregulated tumors.
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Affiliation(s)
- Jiaojiao Hao
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Jinsheng Huang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Chunyu Hua
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Yan Zuo
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Wendan Yu
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Xiaojun Wu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Liren Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Guoqing Xue
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Xinyu Wan
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Liyuan Ru
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Ziyue Guo
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Shilong Han
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Fei Lin
- Department of Oncology, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine; The Affiliated Nanhai Hospital of Traditional Chinese Medicine of Jinan University, Foshan, China
| | - Wei Guo
- Institute of Cancer Stem Cells & The First Affiliated Hospital, Dalian Medical University, Dalian, China
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11
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Chang JY, Neugebauer C, Schmeing S, Amrahova G, 't Hart P. Macrocyclic peptides as inhibitors of WDR5-lncRNA interactions. Chem Commun (Camb) 2023; 59:10656-10659. [PMID: 37581220 DOI: 10.1039/d3cc03221c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
WDR5 is an adaptor protein involved in the regulation of various epigenetic modifier complexes. Various inhibitors have been described but only as inhibitors of its protein-protein interactions. Here we describe peptidic macrocycles that act as inhibitors of the interaction between WDR5 and long non-coding RNAs. The findings provide a new strategy to modulate the biological function of WDR5 as an RNA binding epigenetic regulator.
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Affiliation(s)
- Jen-Yao Chang
- Chemical Genomics Centre of the Max Planck, Society Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Cora Neugebauer
- Chemical Genomics Centre of the Max Planck, Society Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Stefan Schmeing
- Chemical Genomics Centre of the Max Planck, Society Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Gulshan Amrahova
- Chemical Genomics Centre of the Max Planck, Society Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck, Society Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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12
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Structural insights on the KMT2-NCP interaction. Biochem Soc Trans 2023; 51:427-434. [PMID: 36695549 DOI: 10.1042/bst20221155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
The MLL/KMT2 family enzymes are frequently mutated in human cancers and congenital diseases. They deposit the majority of histone 3 lysine 4 (H3K4) mono-, di-, or tri-methylation in mammals and are tightly associated with gene activation. Structural and biochemical studies in recent years provide in-depth understanding of how the MLL1 and homologous yeast SET1 complexes interact with the nucleosome core particle (NCP) and how their activities for H3K4 methylation are regulated by the conserved core components. Here, we will discuss the recent single molecule cryo-EM studies on the MLL1 and ySET1 complexes bound on the NCP. These studies highlight the dynamic regulation of the MLL/SET1 family lysine methyltransferases with unique features as compared with other histone lysine methyltransferases. These studies provide insights for loci-specific regulation of H3K4 methylation states in cells. The mechanistic studies on the MLL1 complex have already led to the development of the MLL1 inhibitors that show efficacy in acute leukemia and metastatic breast cancers. Future studies on the MLL/SET1 family enzymes will continue to bring to light potential therapeutic opportunities.
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13
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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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14
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Yang Z, Jia Y, Wang S, Zhang Y, Fan W, Wang X, He L, Shen X, Yang X, Zhang Y, Yang H. Retinoblastoma-Binding Protein 5 Regulates H3K4 Methylation Modification to Inhibit the Proliferation of Melanoma Cells by Inactivating the Wnt/ β-Catenin and Epithelial-Mesenchymal Transition Pathways. JOURNAL OF ONCOLOGY 2023; 2023:5093941. [PMID: 36866240 PMCID: PMC9974310 DOI: 10.1155/2023/5093941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Histone 3 lysine 4 methylation (H3K4me), especially histone 3 lysine 4 trimethylation (H3K4me3), is one of the most extensively studied patterns of histone modification and plays crucial roles in many biological processes. However, as a part of H3K4 methyltransferase that participates in H3K4 methylation and transcriptional regulation, retinoblastoma-binding protein 5 (RBBP5) has not been well studied in melanoma. The present study sought to explore RBBP5-mediated H3K4 histone modification and the potential mechanisms in melanoma. RBBP5 expression in melanoma and nevi specimens was detected by immunohistochemistry. Western blotting was performed for three pairs of melanoma cancer tissues and nevi tissues. In vitro and in vivo assays were used to investigate the function of RBBP5. The molecular mechanism was determined using RT-qPCR, western blotting, ChIP assays, and Co-IP assays. Our study showed that RBBP5 was significantly downregulated in melanoma tissue and cells compared with nevi tissues and normal epithelia cells (P < 0.05). Reducing RBBP5 in human melanoma cells leads to H3K4me3 downregulation and promotes cell proliferation, migration, and invasion. On the one hand, we verified that WSB2 was an upstream gene of RBBP5-mediated H3K4 modification, which could directly bind to RBBP5 and negatively regulate its expression. On the other hand, we also confirmed that p16 (a cancer suppressor gene) was a downstream target of H3K4me3, the promoter of which can directly bind to H3K4me3. Mechanistically, our data revealed that RBBP5 inactivated the Wnt/β-catenin and epithelial-mesenchymal transition (EMT) pathways (P < 0.05), leading to melanoma suppression. Histone methylation is rising as an important factor affecting tumorigenicity and tumor progression. Our findings verified the significance of RBBP5-mediated H3K4 modification in melanoma and the potential regulatory mechanisms of melanoma proliferation and growth, suggesting that RBBP5 is a potential therapeutic target for the treatment of melanoma.
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Affiliation(s)
- Zhiqin Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
- 2Departments of Gynecology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Yue Jia
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Shaojia Wang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Yongjun Zhang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Wen Fan
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
- 3Departments of Reproduction, The Second Affiliated Hospital of Kunming Medical University, Kunming 650106, China
| | - Xin Wang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Liang He
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Xiaoyu Shen
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Xiangqun Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Yi Zhang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Hongying Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
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15
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Mitchell AV, Wu L, James Block C, Zhang M, Hackett J, Craig DB, Chen W, Zhao Y, Zhang B, Dang Y, Zhang X, Zhang S, Wang C, Gibson H, Pile LA, Kidder B, Matherly L, Yang Z, Dou Y, Wu G. FOXQ1 recruits the MLL complex to activate transcription of EMT and promote breast cancer metastasis. Nat Commun 2022; 13:6548. [PMID: 36319643 PMCID: PMC9626503 DOI: 10.1038/s41467-022-34239-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Aberrant expression of the Forkhead box transcription factor, FOXQ1, is a prevalent mechanism of epithelial-mesenchymal transition (EMT) and metastasis in multiple carcinoma types. However, it remains unknown how FOXQ1 regulates gene expression. Here, we report that FOXQ1 initiates EMT by recruiting the MLL/KMT2 histone methyltransferase complex as a transcriptional coactivator. We first establish that FOXQ1 promoter recognition precedes MLL complex assembly and histone-3 lysine-4 trimethylation within the promoter regions of critical genes in the EMT program. Mechanistically, we identify that the Forkhead box in FOXQ1 functions as a transactivation domain directly binding the MLL core complex subunit RbBP5 without interrupting FOXQ1 DNA binding activity. Moreover, genetic disruption of the FOXQ1-RbBP5 interaction or pharmacologic targeting of KMT2/MLL recruitment inhibits FOXQ1-dependent gene expression, EMT, and in vivo tumor progression. Our study suggests that targeting the FOXQ1-MLL epigenetic axis could be a promising strategy to combat triple-negative breast cancer metastatic progression.
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Affiliation(s)
- Allison V Mitchell
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Ling Wu
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - C James Block
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Mu Zhang
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Justin Hackett
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Douglas B Craig
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Wei Chen
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiaohong Zhang
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Shengping Zhang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 650 Xinsongjiang Road, Songjiang District, Shanghai, 201620, China
| | - Chuangui Wang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 650 Xinsongjiang Road, Songjiang District, Shanghai, 201620, China
| | - Heather Gibson
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Lori A Pile
- The Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Benjamin Kidder
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Larry Matherly
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA
| | - Zhe Yang
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Guojun Wu
- Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, 4100 John R, Detroit, MI, 48201, USA.
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16
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Bochyńska A, Stenzel AT, Boroujeni RS, Kuo CC, Barsoum M, Liang W, Bussmann P, Costa IG, Lüscher-Firzlaff J, Lüscher B. Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes. Nucleic Acids Res 2022; 50:7889-7905. [PMID: 35819198 PMCID: PMC9371893 DOI: 10.1093/nar/gkac591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/30/2022] [Accepted: 06/28/2022] [Indexed: 12/12/2022] Open
Abstract
Gene expression is controlled in part by post-translational modifications of core histones. Methylation of lysine 4 of histone H3 (H3K4), associated with open chromatin and gene transcription, is catalyzed by type 2 lysine methyltransferase complexes that require WDR5, RBBP5, ASH2L and DPY30 as core subunits. Ash2l is essential during embryogenesis and for maintaining adult tissues. To expand on the mechanistic understanding of Ash2l, we generated mouse embryo fibroblasts (MEFs) with conditional Ash2l alleles. Upon loss of Ash2l, methylation of H3K4 and gene expression were downregulated, which correlated with inhibition of proliferation and cell cycle progression. Moreover, we observed induction of senescence concomitant with a set of downregulated signature genes but independent of SASP. Many of the signature genes are FoxM1 responsive. Indeed, exogenous FOXM1 was sufficient to delay senescence. Thus, although the loss of Ash2l in MEFs has broad and complex consequences, a distinct set of downregulated genes promotes senescence.
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Affiliation(s)
- Agnieszka Bochyńska
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Alexander T Stenzel
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Roksaneh Sayadi Boroujeni
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Chao-Chung Kuo
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany.,Interdisciplinary Center for Clinical Research (IZKF), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Mirna Barsoum
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Weili Liang
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Philip Bussmann
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Juliane Lüscher-Firzlaff
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany
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17
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Poreba E, Lesniewicz K, Durzynska J. Histone-lysine N-methyltransferase 2 (KMT2) complexes - a new perspective. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108443. [PMID: 36154872 DOI: 10.1016/j.mrrev.2022.108443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/25/2022] [Accepted: 09/19/2022] [Indexed: 01/01/2023]
Abstract
Histone H3 Lys4 (H3K4) methylation is catalyzed by the Histone-Lysine N-Methyltransferase 2 (KMT2) protein family, and its members are required for gene expression control. In vertebrates, the KMT2s function in large multisubunit complexes known as COMPASS or COMPASS-like complexes (COMplex of Proteins ASsociated with Set1). The activity of these complexes is critical for proper development, and mutation-induced defects in their functioning have frequently been found in human cancers. Moreover, inherited or de novo mutations in KMT2 genes are among the etiological factors in neurodevelopmental disorders such as Kabuki and Kleefstra syndromes. The canonical role of KMT2s is to catalyze H3K4 methylation, which results in a permissive chromatin environment that drives gene expression. However, current findings described in this review demonstrate that these enzymes can regulate processes that are not dependent on methylation: noncatalytic functions of KMT2s include DNA damage response, cell division, and metabolic activities. Moreover, these enzymes may also methylate non-histone substrates and play a methylation-dependent function in the DNA damage response. In this review, we present an overview of the new, noncanonical activities of KMT2 complexes in a variety of cellular processes. These discoveries may have crucial implications for understanding the functions of these methyltransferases in developmental processes, disease, and epigenome-targeting therapeutic strategies in the future.
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Affiliation(s)
- Elzbieta Poreba
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Julia Durzynska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
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18
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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19
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Albert L, Nagpal J, Steinchen W, Zhang L, Werel L, Djokovic N, Ruzic D, Hoffarth M, Xu J, Kaspareit J, Abendroth F, Royant A, Bange G, Nikolic K, Ryu S, Dou Y, Essen LO, Vázquez O. Bistable Photoswitch Allows in Vivo Control of Hematopoiesis. ACS CENTRAL SCIENCE 2022; 8:57-66. [PMID: 35106373 PMCID: PMC8796299 DOI: 10.1021/acscentsci.1c00434] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 05/09/2023]
Abstract
Optical control has enabled functional modulation in cell culture with unparalleled spatiotemporal resolution. However, current tools for in vivo manipulation are scarce. Here, we design and implement a genuine on-off optochemical probe capable of achieving hematopoietic control in zebrafish. Our photopharmacological approach first developed conformationally strained visible light photoswitches (CS-VIPs) as inhibitors of the histone methyltransferase MLL1 (KMT2A). In blood homeostasis MLL1 plays a crucial yet controversial role. CS-VIP 8 optimally fulfils the requirements of a true bistable functional system in vivo under visible-light irradiation, and with unprecedented stability. These properties are exemplified via hematopoiesis photoinhibition with a single isomer in zebrafish. The present interdisciplinary study uncovers the mechanism of action of CS-VIPs. Upon WDR5 binding, CS-VIP 8 causes MLL1 release with concomitant allosteric rearrangements in the WDR5/RbBP5 interface. Since our tool provides on-demand reversible control without genetic intervention or continuous irradiation, it will foster hematopathology and epigenetic investigations. Furthermore, our workflow will enable exquisite photocontrol over other targets inhibited by macrocycles.
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Affiliation(s)
- Lea Albert
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Jatin Nagpal
- APC Microbiome
Ireland, University College Cork, Cork, Ireland
| | - Wieland Steinchen
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
| | - Lei Zhang
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Laura Werel
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Nemanja Djokovic
- Department
of Pharmaceutical Chemistry, University
of Belgrade, 11000 Belgrade, Serbia
| | - Dusan Ruzic
- Department
of Pharmaceutical Chemistry, University
of Belgrade, 11000 Belgrade, Serbia
| | - Malte Hoffarth
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Jing Xu
- Department
of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Johanna Kaspareit
- University
Medical Center, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
| | - Frank Abendroth
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
| | - Antoine Royant
- Univ.
Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
- European
Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Gert Bange
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
| | - Katarina Nikolic
- Department
of Pharmaceutical Chemistry, University
of Belgrade, 11000 Belgrade, Serbia
| | - Soojin Ryu
- University
Medical Center, Johannes Gutenberg University Mainz, 55122 Mainz, Germany
- College
of Medicine and Health, University of Exeter, Exeter EX4 4PY, U.K.
- Living
Systems Institute, University of Exeter, Exeter EX4 QD, U.K.
| | - Yali Dou
- Norris
Comprehensive Cancer Center, University
of Southern California, Los Angeles, California 90007, United States
| | - Lars-Oliver Essen
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
| | - Olalla Vázquez
- Department
of Chemistry, University of Marburg, 35037 Marburg, Germany
- Center
for Synthetic Microbiology (SYNMIKRO), University
of Marburg, 35037 Marburg, Germany
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20
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Chen X, Xu J, Wang X, Long G, You Q, Guo X. Targeting WD Repeat-Containing Protein 5 (WDR5): A Medicinal Chemistry Perspective. J Med Chem 2021; 64:10537-10556. [PMID: 34283608 DOI: 10.1021/acs.jmedchem.1c00037] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
WD repeat-containing protein 5 (WDR5) is a member of the WD40 protein family, and it is widely involved in various biological activities and not limited to epigenetic regulation in vivo. WDR5 is also involved in the initiation and development of many diseases and plays a key role in these diseases. Since WDR5 was discovered, it has been suggested as a potential disease treatment target, and a large number of inhibitors targeting WDR5 have been discovered. In this review, we discussed the development of inhibitors targeting WDR5 over the years, and the biological mechanisms of these inhibitors based on previous mechanistic studies were explored. Finally, we describe the development potential of inhibitors targeting WDR5 and prospects for further applications.
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Affiliation(s)
- Xin Chen
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Junjie Xu
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xianghan Wang
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Guanlu Long
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaoke Guo
- Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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21
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Chen W, Chen X, Li D, Wang X, Long G, Jiang Z, You Q, Guo X. Discovery of a potent MLL1 and WDR5 protein-protein interaction inhibitor with in vivo antitumor activity. Eur J Med Chem 2021; 223:113677. [PMID: 34225179 DOI: 10.1016/j.ejmech.2021.113677] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 10/21/2022]
Abstract
MLL1-WDR5 interaction is essential for the formation of MLL core complex and its H3K4 methyltransferase activity. Disrupting MLL1-WDR5 interaction has been proposed as a potential therapeutic approach in the treatment of leukemia. A "toolkit" of well-characterized chemical probe will allow exploring animal studies. Based on a specific MLL1-WDR5 PPI inhibitor (DDO-2117), which was previously reported by our group, we conducted a bioisosterism approach by click chemistry to discover novel phenyltriazole scaffold MLL1-WDR5 interaction blockers. Here, our efforts resulted in the best inhibitor 24 (DDO-2093) with high binding affinity (Kd = 11.6 nM) and with improved drug-like properties. Both in vitro and in vivo assays revealed 24 could efficiently block the MLL1-WDR5 interaction. Furthermore, 24 significantly suppressed tumor growth in the MV4-11 xenograft mouse model and showed a favorable safety profile. We propose 24 as a chemical probe that is suitable for in vivo pharmacodynamic and biological studies of MLL1-WDR5 interaction.
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Affiliation(s)
- Weilin Chen
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Xin Chen
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Dongdong Li
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Xianghan Wang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Guanlu Long
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengyu Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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22
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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23
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Li X, Song Y. Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins. J Hematol Oncol 2021; 14:56. [PMID: 33823889 PMCID: PMC8022399 DOI: 10.1186/s13045-021-01057-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia 1 (MLL1, also known as MLL or KMT2A) is an important transcription factor and histone-H3 lysine-4 (H3K4) methyltransferase. It is a master regulator for transcription of important genes (e.g., Hox genes) for embryonic development and hematopoiesis. However, it is largely dispensable in matured cells. Dysregulation of MLL1 leads to overexpression of certain Hox genes and eventually leukemia initiation. Chromosome translocations involving MLL1 cause ~ 75% of acute leukemia in infants and 5–10% in children and adults with a poor prognosis. Targeted therapeutics against oncogenic fusion MLL1 (onco-MLL1) are therefore needed. Onco-MLL1 consists of the N-terminal DNA-interacting domains of MLL1 fused with one of > 70 fusion partners, among which transcription cofactors AF4, AF9 and its paralog ENL, and ELL are the most frequent. Wild-type (WT)- and onco-MLL1 involve numerous protein–protein interactions (PPI), which play critical roles in regulating gene expression in normal physiology and leukemia. Moreover, WT-MLL1 has been found to be essential for MLL1-rearranged (MLL1-r) leukemia. Rigorous studies of such PPIs have been performed and much progress has been achieved in understanding their structures, structure–function relationships and the mechanisms for activating gene transcription as well as leukemic transformation. Inhibition of several critical PPIs by peptides, peptidomimetic or small-molecule compounds has been explored as a therapeutic approach for MLL1-r leukemia. This review summarizes the biological functions, biochemistry, structure and inhibition of the critical PPIs involving MLL1 and its fusion partner proteins. In addition, challenges and perspectives of drug discovery targeting these PPIs for the treatment of MLL1-r leukemia are discussed.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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24
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Guarnaccia AD, Rose KL, Wang J, Zhao B, Popay TM, Wang CE, Guerrazzi K, Hill S, Woodley CM, Hansen TJ, Lorey SL, Shaw JG, Payne WG, Weissmiller AM, Olejniczak ET, Fesik SW, Liu Q, Tansey WP. Impact of WIN site inhibitor on the WDR5 interactome. Cell Rep 2021; 34:108636. [PMID: 33472061 PMCID: PMC7871196 DOI: 10.1016/j.celrep.2020.108636] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/17/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
The chromatin-associated protein WDR5 is a promising pharmacological target in cancer, with most drug discovery efforts directed against an arginine-binding cavity in WDR5 called the WIN site. Despite a clear expectation that WIN site inhibitors will alter the repertoire of WDR5 interaction partners, their impact on the WDR5 interactome remains unknown. Here, we use quantitative proteomics to delineate how the WDR5 interactome is changed by WIN site inhibition. We show that the WIN site inhibitor alters the interaction of WDR5 with dozens of proteins, including those linked to phosphatidylinositol 3-kinase (PI3K) signaling. As proof of concept, we demonstrate that the master kinase PDPK1 is a bona fide high-affinity WIN site binding protein that engages WDR5 to modulate transcription of genes expressed in the G2 phase of the cell cycle. This dataset expands our understanding of WDR5 and serves as a resource for deciphering the action of WIN site inhibitors.
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Affiliation(s)
- Alissa D Guarnaccia
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristie L Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tessa M Popay
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Christina E Wang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kiana Guerrazzi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Salisha Hill
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chase M Woodley
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tyler J Hansen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - J Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - William G Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Edward T Olejniczak
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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25
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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26
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Ye X, Chen G, Jin J, Zhang B, Wang Y, Cai Z, Ye F. The Development of Inhibitors Targeting the Mixed Lineage Leukemia 1 (MLL1)-WD Repeat Domain 5 Protein (WDR5) Protein- Protein Interaction. Curr Med Chem 2020; 27:5530-5542. [PMID: 31132972 DOI: 10.2174/0929867326666190528080514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Mixed Lineage Leukemia 1 (MLL1), an important member of Histone Methyltransferases (HMT) family, is capable of catalyzing mono-, di-, and trimethylation of Histone 3 lysine 4 (H3K4). The optimal catalytic activity of MLL1 requires the formation of a core complex consisting of MLL1, WDR5, RbBP5, and ASH2L. The Protein-Protein Interaction (PPI) between WDR5 and MLL1 plays an important role in abnormal gene expression during tumorigenesis, and disturbing this interaction may have a potential for the treatment of leukemia harboring MLL1 fusion proteins. In this review, we will summarize recent progress in the development of inhibitors targeting MLL1- WDR5 interaction.
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Affiliation(s)
- Xiaoqing Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gang Chen
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Jia Jin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Binzhong Zhang
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yinda Wang
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Zhenhai Cai
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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27
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Huang D, Chen X, Chen X, Qu Y, Wang Y, Yang Y, Cheng Y. WDR5 Promotes Proliferation and Correlates with Poor Prognosis in Oesophageal Squamous Cell Carcinoma. Onco Targets Ther 2020; 13:10525-10534. [PMID: 33116631 PMCID: PMC7573303 DOI: 10.2147/ott.s234773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Background The WD40 protein family member WD repeat domain 5 (WDR5) plays significant roles in the tumorigenesis and development of multiple organ tumours. However, the correlation between WDR5 expression and oesophageal squamous cell carcinoma (ESCC) has not been elucidated. Methods WDR5 mRNA expression data were acquired from The Cancer Genome Atlas (TCGA) database, and the expression and prognostic potential of WDR5 were assessed by immunohistochemistry (IHC) and Western blot. The cell counting kit-8 (CCK-8), colony formation assay and cell cycle evaluation were performed to verify the WDR5 function in vitro. The xenograft model was used to verify WDR5 function in vivo. Results The mRNA and protein expression levels of WDR5 were significantly upregulated in ESCC tissues compared with expression in adjacent normal tissues. Kaplan-Meier analysis showed that high WDR5 expression in ESCC patients was associated with poor overall survival (P=0.004). Multivariate analysis revealed that WDR5 overexpression emerged as an independent predictor of poor overall survival (P=0.013) in ESCC. The in vitro and in vivo experiments revealed that downregulation of WDR5 expression blocked cell proliferation of ESCC. Mechanistically, we found that WDR5 may influence ESCC proliferation by targeting the PI3K/AKT/mTOR signalling pathway. Conclusion Our data demonstrate that overexpression of WDR5 was associated with poor prognosis in patients with ESCC and that WDR5 may act as a potential novel prognostic biomarker for ESCC.
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Affiliation(s)
- Di Huang
- Department of Radiation Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Xue Chen
- Department of Radiation Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Xuan Chen
- Department of Radiation Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Yan Qu
- Department of Radiation Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Yuanyuan Wang
- Department of Oncology, People's Hospital of Linyi County, Dezhou, Shandong 251500, People's Republic of China
| | - Yafei Yang
- Department of Hepatobiliary Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, People's Republic of China
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28
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Sugeedha J, Gautam J, Tyagi S. SET1/MLL family of proteins: functions beyond histone methylation. Epigenetics 2020; 16:469-487. [PMID: 32795105 PMCID: PMC8078731 DOI: 10.1080/15592294.2020.1809873] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The SET1 family of enzymes are well known for their involvement in the histone 3 lysine 4 (H3K4) methylation, a conserved trait of euchromatin associated with transcriptional activation. These methyltransferases are distinct, and involved in various biological functions in the cell. Impairment in the function of SET1 family members leads to a number of abnormalities such as skeletal and neurological defects, leukaemogenesis and even lethality. Tremendous progress has been made in understanding the unique biological roles and the mechanism of SET1 enzymes in context with H3K4 methylation/canonical functions. However, in recent years, several studies have indicated the novel role of SET1 family proteins, other than H3K4 methylation, which are equally important for cellular functions. In this review, we focus on these non-canonical function of SET1 family members.
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Affiliation(s)
- Jeyapal Sugeedha
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Jyoti Gautam
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
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29
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Insights on the regulation of the MLL/SET1 family histone methyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194561. [PMID: 32304759 DOI: 10.1016/j.bbagrm.2020.194561] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/07/2020] [Accepted: 04/09/2020] [Indexed: 01/09/2023]
Abstract
In eukaryotes, histone H3K4 methylation by the MLL/SET1 family histone methyltransferases is enriched at transcription regulatory elements including gene promoters and enhancers. The level of H3K4 methylation is highly correlated with transcription activation and is one of the most frequently used histone post-translational modifications to predict transcriptional outcome. Recently, it has been shown that rearrangement of the cellular landscape of H3K4 mono-methylation at distal enhancers precedes cell fate transition and is used for identification of novel regulatory elements for development and disease progression. Similarly, broad H3K4 tri-methylation regions have also been used to predict intrinsic tumor suppression properties of regulator regions in a variety of cellular models. Understanding the regulation for how H3K4 methylation is deposited and regulated is of paramount importance. In this review, we will discuss new findings on how the MLL/SET1 family enzymes are regulated on chromatin and their potential functional and regulatory implications. This article is part of a Special Issue entitled: The MLL family of proteins in normal development and disease edited by Thomas A Milne.
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30
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Chacón Simon S, Wang F, Thomas LR, Phan J, Zhao B, Olejniczak ET, Macdonald JD, Shaw JG, Schlund C, Payne W, Creighton J, Stauffer SR, Waterson AG, Tansey WP, Fesik SW. Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2020; 63:4315-4333. [PMID: 32223236 DOI: 10.1021/acs.jmedchem.0c00224] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The frequent deregulation of MYC and its elevated expression via multiple mechanisms drives cells to a tumorigenic state. Indeed, MYC is overexpressed in up to ∼50% of human cancers and is considered a highly validated anticancer target. Recently, we discovered that WD repeat-containing protein 5 (WDR5) binds to MYC and is a critical cofactor required for the recruitment of MYC to its target genes and reported the first small molecule inhibitors of the WDR5-MYC interaction using structure-based design. These compounds display high binding affinity, but have poor physicochemical properties and are hence not suitable for in vivo studies. Herein, we conducted an NMR-based fragment screening to identify additional chemical matter and, using a structure-based approach, we merged a fragment hit with the previously reported sulfonamide series. Compounds in this series can disrupt the WDR5-MYC interaction in cells, and as a consequence, we observed a reduction of MYC localization to chromatin.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Shaun R Stauffer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Alex G Waterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | | | - Stephen W Fesik
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
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31
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Worden EJ, Zhang X, Wolberger C. Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome. eLife 2020; 9:53199. [PMID: 31922488 PMCID: PMC7039682 DOI: 10.7554/elife.53199] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/10/2020] [Indexed: 12/27/2022] Open
Abstract
Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxxxRR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation.
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Affiliation(s)
- Evan J Worden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Xiangbin Zhang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
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32
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Yang Y, Joshi M, Takahashi YH, Ning Z, Qu Q, Brunzelle JS, Skiniotis G, Figeys D, Shilatifard A, Couture JF. A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS. Nucleic Acids Res 2020; 48:421-431. [PMID: 31724694 PMCID: PMC7145517 DOI: 10.1093/nar/gkz1037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/28/2022] Open
Abstract
COMPlex ASsociating with SET1 (COMPASS) is a histone H3 Lys-4 methyltransferase that typically marks the promoter region of actively transcribed genes. COMPASS is a multi-subunit complex in which the catalytic unit, SET1, is required for H3K4 methylation. An important subunit known to regulate SET1 methyltransferase activity is the CxxC zinc finger protein 1 (Cfp1). Cfp1 binds to COMPASS and is critical to maintain high level of H3K4me3 in cells but the mechanisms underlying its stimulatory activity is poorly understood. In this study, we show that Cfp1 only modestly activates COMPASS methyltransferase activity in vitro. Binding of Cfp1 to COMPASS is in part mediated by a new type of monovalent zinc finger (ZnF). This ZnF interacts with the COMPASS's subunits RbBP5 and disruption of this interaction blunts its methyltransferase activity in cells and in vivo. Collectively, our studies reveal that a novel form of ZnF on Cfp1 enables its integration into COMPASS and contributes to epigenetic signaling.
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Affiliation(s)
- Yidai Yang
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Monika Joshi
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Yoh-hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Zhibin Ning
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Qianhui Qu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Figeys
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
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33
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Macdonald JD, Simon SC, Han C, Wang F, Shaw JG, Howes JE, Sai J, Yuh JP, Camper D, Alicie BM, Alvarado J, Nikhar S, Payne W, Aho ER, Bauer JA, Zhao B, Phan J, Thomas LR, Rossanese OW, Tansey WP, Waterson AG, Stauffer SR, Fesik SW. Discovery and Optimization of Salicylic Acid-Derived Sulfonamide Inhibitors of the WD Repeat-Containing Protein 5-MYC Protein-Protein Interaction. J Med Chem 2019; 62:11232-11259. [PMID: 31724864 PMCID: PMC6933084 DOI: 10.1021/acs.jmedchem.9b01411] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The treatment of tumors driven by overexpression or amplification of MYC oncogenes remains a significant challenge in drug discovery. Here, we present a new strategy toward the inhibition of MYC via the disruption of the protein-protein interaction between MYC and its chromatin cofactor WD Repeat-Containing Protein 5. Blocking the association of these proteins is hypothesized to disrupt the localization of MYC to chromatin, thus disrupting the ability of MYC to sustain tumorigenesis. Utilizing a high-throughput screening campaign and subsequent structure-guided design, we identify small-molecule inhibitors of this interaction with potent in vitro binding affinity and report structurally related negative controls that can be used to study the effect of this disruption. Our work suggests that disruption of this protein-protein interaction may provide a path toward an effective approach for the treatment of multiple tumors and anticipate that the molecules disclosed can be used as starting points for future efforts toward compounds with improved drug-like properties.
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Affiliation(s)
- Jonathan D. Macdonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Selena Chacón Simon
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Changho Han
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Feng Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - J. Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Jennifer E. Howes
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Joannes P. Yuh
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Demarco Camper
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Bethany M. Alicie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Joseph Alvarado
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Sameer Nikhar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - William Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Erin R. Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Joshua A. Bauer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Lance R. Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Olivia W. Rossanese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Alex G. Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
| | - Shaun R. Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
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34
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Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nat Commun 2019; 10:5540. [PMID: 31804488 PMCID: PMC6895043 DOI: 10.1038/s41467-019-13550-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity. MLL family histone methyltransferases deposit histone H3 Lys4 mono-/di-/tri-methylation and regulate gene expression in mammals. Here the authors report the single-particle cryo-EM structure of the NCP-bound human MLL1 core complex, shedding light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.
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Affiliation(s)
- Sang Ho Park
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Young-Tae Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Wei Zheng
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Biao Zhang
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Liang Sha
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Sojin An
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yang Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yali Dou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA. .,Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.
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35
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Arrowsmith CH, Schapira M. Targeting non-bromodomain chromatin readers. Nat Struct Mol Biol 2019; 26:863-869. [DOI: 10.1038/s41594-019-0290-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
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36
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Kaustov L, Lemak A, Wu H, Faini M, Fan L, Fang X, Zeng H, Duan S, Allali-Hassani A, Li F, Wei Y, Vedadi M, Aebersold R, Wang Y, Houliston S, Arrowsmith CH. The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions. Nucleic Acids Res 2019; 47:9433-9447. [PMID: 31400120 PMCID: PMC6755125 DOI: 10.1093/nar/gkz697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/14/2022] Open
Abstract
Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with additional conserved proteins, but the structural basis for subunit assembly and the mechanism of regulation is not well understood. We used a hybrid methods approach to study the assembly and biochemical function of the minimally active MLL1 complex (MLL1, WDR5 and RbBP5). A combination of small angle X-ray scattering, cross-linking mass spectrometry, nuclear magnetic resonance spectroscopy and computational modeling were used to generate a dynamic ensemble model in which subunits are assembled via multiple weak interaction sites. We identified a new interaction site between the MLL1 SET domain and the WD40 β-propeller domain of RbBP5, and demonstrate the susceptibility of the catalytic function of the complex to disruption of individual interaction sites.
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Affiliation(s)
- Lilia Kaustov
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
- Department of Anesthesia, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Marco Faini
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Lixin Fan
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Xianyang Fang
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Yong Wei
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
- Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Yunxing Wang
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
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37
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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38
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Architecture and subunit arrangement of the complete Saccharomyces cerevisiae COMPASS complex. Sci Rep 2018; 8:17405. [PMID: 30479350 PMCID: PMC6258710 DOI: 10.1038/s41598-018-35609-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/17/2018] [Indexed: 01/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4) is catalyzed by the multi-component COMPASS or COMPASS-like complex, which is highly conserved from yeast to human, and plays essential roles in gene expression and transcription, cell cycle progression, and DNA repair. Here we present a cryo-EM map of the complete S. cerevisiae COMPASS complex. Through tag or Fab labeling strategy combined with cryo-EM 3D reconstruction and cross-linking and mass spectrometry (XL-MS) analysis, we uncovered new information on the subunit arrangement: Cps50, Cps35, and Cps30 were determined to group together to form the face region in the head of the complex, and Cps40 and the N-terminal portion of Set1 reside on the top of the head. Our map reveals the location of the active center and a canyon in the back of the head. Together, our study provides the first snapshot of the complete architecture of yeast COMPASS and a picture of its subunit interaction network, which could facilitate our understanding of the COMPASS machinery and its functionality.
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39
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Perla V, Nadimi M, Reddy R, Hankins GR, Nimmakayala P, Harris RT, Valluri J, Sirbu C, Reddy UK. Effect of ghost pepper on cell proliferation, apoptosis, senescence and global proteomic profile in human renal adenocarcinoma cells. PLoS One 2018; 13:e0206183. [PMID: 30379886 PMCID: PMC6209291 DOI: 10.1371/journal.pone.0206183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/07/2018] [Indexed: 12/19/2022] Open
Abstract
Chili peppers are an important constituent of many foods and contain medicinally valuable compounds, such as capsaicin and dihydrocapsaicin. As various dietary botanicals have anticancer properties, this study was aimed to examine the effect of Ghost pepper (Bhut Jolokia), one of the hottest chili peppers in the world, on cell proliferation, apoptosis, senescence and the global proteomic profile in human renal cell adenocarcinoma in vitro. 769-P human renal adenocarcinoma cells were cultured on RPMI-1640 media supplemented with fetal bovine serum (10%) and antibiotic-antimycotic solution (1%). Treatment stock solutions were prepared in ethanol. Cell proliferation was tested with phenol red-free media with capsaicin (0-400 μM), dihydrocapsaicin (0-400 μM), capsaicin + dihydrocapsaicin (5:1), and dry Ghost peppers (0-3 g L-1) for 24, 48 and 72 h. Polycaspase and senescence associated-beta-galactosidase (SA-beta-gal) activities were tested with capsaicin (400 μM), dihydrocapsaicin (400 μM), capsaicin (400 μM) + dihydrocapsaicin (80 μM), and ghost pepper (3 g L-1) treatments. Global proteomic profile of cells in control and ghost pepper treatment (3 g L-1) was analyzed after 6 h by a shotgun proteomic approach using tandem mass spectrometry. At 24 h after treatment (24 HAT), relative to control, cell proportion with capsaicin (400 μM), dihydrocapsaicin (400 μM), capsaicin (400 μM) + dihydrocapsaicin (80 μM), and ghost pepper (3 g L-1) treatments was reduced to 36%, 18%, 33% and 20%, respectively, and further reduced at 48 and 72 HAT. All treatments triggered an early polycaspase response. SA-beta-gal activity was normal or suppressed with all treatments. About 68,220 protein isoforms were identified by shotgun proteomic approach. Among these, about 8.2% were significantly affected by ghost pepper. Ghost pepper regulated various proteins involved in intrinsic and extrinsic apoptotic pathways, Ras, Rb/E2F, p53, TGF-beta, WNT-beta catenin, and calcium induced cell death pathways. Ghost pepper also induced changes in proteins related to methylation, acetylation, genome stability, cell cycle check points, carbohydrate, protein and other metabolism and cellular mechanisms. Ghost pepper exhibited antiproliferation activity by inducing apoptosis through a complex network of proteins in human renal cell adenocarcinoma in vitro.
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Affiliation(s)
- Venu Perla
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Marjan Nadimi
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Rishi Reddy
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Gerald R. Hankins
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Padma Nimmakayala
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Robert T. Harris
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Jagan Valluri
- Department of Biological Sciences, One John Marshall Drive, Marshall University, Huntington, West Virginia, United States of America
| | - Cristian Sirbu
- Center for Cancer Research, Charleston Area Medical Center, SE, Charleston, West Virginia, United States of America
| | - Umesh K. Reddy
- Gus R. Douglass Land-Grant Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
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40
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Haddad JF, Yang Y, Takahashi YH, Joshi M, Chaudhary N, Woodfin AR, Benyoucef A, Yeung S, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation. Structure 2018; 26:1594-1603.e4. [PMID: 30270175 DOI: 10.1016/j.str.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/28/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Dpy-30 is a regulatory subunit controlling the histone methyltransferase activity of the KMT2 enzymes in vivo. Paradoxically, in vitro methyltransferase assays revealed that Dpy-30 only modestly participates in the positive heterotypic allosteric regulation of these methyltransferases. Detailed genome-wide, molecular and structural studies reveal that an extensive network of interactions taking place at the interface between Dpy-30 and Ash2L are critical for the correct placement, genome-wide, of H3K4me2 and H3K4me3 but marginally contribute to the methyltransferase activity of KMT2 enzymes in vitro. Moreover, we show that H3K4me2 peaks persisting following the loss of Dpy-30 are found in regions of highly transcribed genes, highlighting an interplay between Complex of Proteins Associated with SET1 (COMPASS) kinetics and the cycling of RNA polymerase to control H3K4 methylation. Overall, our data suggest that Dpy-30 couples its modest positive heterotypic allosteric regulation of KMT2 methyltransferase activity with its ability to help the positioning of SET1/COMPASS to control epigenetic signaling.
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Affiliation(s)
- John Faissal Haddad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yidai Yang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Nidhi Chaudhary
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Aissa Benyoucef
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada.
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41
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Qu Q, Takahashi YH, Yang Y, Hu H, Zhang Y, Brunzelle JS, Couture JF, Shilatifard A, Skiniotis G. Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex. Cell 2018; 174:1117-1126.e12. [PMID: 30100186 PMCID: PMC6108936 DOI: 10.1016/j.cell.2018.07.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 11/25/2022]
Abstract
The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics. The Cps50 C-terminal tail weaves within the complex to provide a central scaffold for assembly. The SET domain, snugly positioned at the junction of the Y-shaped complex, is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). The mobile SET-I motif of the SET domain is engaged by Cps30, explaining its key role in COMPASS catalytic activity toward higher H3K4 methylation states.
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Affiliation(s)
- Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yidai Yang
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON K1H 8M5, Canada
| | - Hongli Hu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Jean-Francois Couture
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON K1H 8M5, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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42
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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: 62] [Impact Index Per Article: 10.3] [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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43
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Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat Chem Biol 2018; 14:895-900. [PMID: 30013062 PMCID: PMC6103845 DOI: 10.1038/s41589-018-0099-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 06/07/2018] [Indexed: 11/16/2022]
Abstract
Rapidly determining the biological effect of perturbing a site within a potential drug target could guide drug discovery efforts but it remains challenging. Here, we describe a facile target validation approach that exploits monobodies, small synthetic binding proteins that can be fully functionally expressed in cells. We developed a potent and selective monobody to WDR5, a core component of the Mixed Lineage Leukemia (MLL) methyltransferase complex. The monobody bound to the MLL-interaction site of WDR5, the same site for small molecule inhibitors whose efficacy has been demonstrated in cells but not in animals. As a genetically encoded reagent, the monobody inhibited proliferation of an MLL-AF9 cell line in vitro, suppressed its leukemogenesis and conferred survival benefit in an in vivo mouse leukemia model. The capacity of this approach to readily bridge biochemical, structural, cellular characterization and tests in animal models may accelerate discovery and validation of druggable sites.
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Affiliation(s)
- Ankit Gupta
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shirley Lee
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Steven T Tsai
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kohei Kurosawa
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Michael S Werner
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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44
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Mittal A, Hobor F, Zhang Y, Martin SR, Gamblin SJ, Ramos A, Wilson JR. The structure of the RbBP5 β-propeller domain reveals a surface with potential nucleic acid binding sites. Nucleic Acids Res 2018; 46:3802-3812. [PMID: 29897600 PMCID: PMC6283417 DOI: 10.1093/nar/gky199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 03/03/2018] [Accepted: 03/07/2018] [Indexed: 12/26/2022] Open
Abstract
The multi-protein complex WRAD, formed by WDR5, RbBP5, Ash2L and Dpy30, binds to the MLL SET domain to stabilize the catalytically active conformation required for histone H3K4 methylation. In addition, the WRAD complex contributes to the targeting of the activated complex to specific sites on chromatin. RbBP5 is central to MLL catalytic activation, by making critical contacts with the other members of the complex. Interestingly its only major structural domain, a canonical WD40 repeat β-propeller, is not implicated in this function. Here, we present the structure of the RbBP5 β-propeller domain revealing a distinct, feature rich surface, dominated by clusters of Arginine residues. Our nuclear magnetic resonance binding data supports the hypothesis that in addition to the role of RbBP5 in catalytic activation, its β-propeller domain is a platform for the recruitment of the MLL complexes to chromatin targets through its direct interaction with nucleic acids.
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Affiliation(s)
| | - Fruzsina Hobor
- Institute of Structural and Molecular Biology, University College London, London WC1E 6XA, UK
| | - Ying Zhang
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, London WC1E 6XA, UK
| | - Jon R Wilson
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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45
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Ding B, Cao Z, Hong R, Li H, Zuo X, Luo L, Li Y, Huang W, Li W, Zhang K, Zhang Y. WDR5 in porcine preimplantation embryos: expression, regulation of epigenetic modifications and requirement for early development†. Biol Reprod 2018; 96:758-771. [PMID: 28379447 DOI: 10.1093/biolre/iox020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/29/2017] [Indexed: 11/12/2022] Open
Abstract
WD repeat-containing protein 5 (WDR5), a member of conserved WD40 protein family, is an essential component of the mixed lineage leukemia (MLL) complexes, which are crucial for numerous key biological processes including methylation of histone H3 lysine 4 (H3K4), self-renewal of embryonic stem cells, and formation of induced pluripotent stem cells. The expression pattern and functional role of WDR5 during porcine preimplantation embryonic development, however, remain unknown. Our results showed that the transcripts and protein of WDR5 exhibited stage-specific expression pattern in porcine early embryos. Moreover, blastocyst rate and total cell number per blastocyst were reduced by RNAi-mediated silencing of WDR5 or pharmacological inhibition of WDR5. Knockdown of WDR5 also disturbed the expression of several pluripotency genes. Interestingly, tri-methylation of H3K4 (H3K4me3) level was dramatically increased by WDR5 depletion. Further analysis revealed that loss of MLL3 phenocopied WDR5 knockdown, triggering increased H3K4me3 level. Simultaneously, WDR5 depletion significantly decreased the levels of histone H4 lysine 16 acetylation (H4K16ac) and its writer males absent on the first (MOF). Last but not least, WDR5 knockdown induced DNA damage and DNA repair defects during porcine preimplantation development. Taken together, results of described studies establish that WDR5 plays a significant role in porcine preimplantation embryos probably through regulating key epigenetic modifications and genome integrity.
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Affiliation(s)
- Biao Ding
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Key Laboratory of Embryo Development and Reproduction Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui, China
| | - Zubing Cao
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Renyun Hong
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Hui Li
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaoyuan Zuo
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Lei Luo
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Yunsheng Li
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Weiping Huang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Wenyong Li
- Key Laboratory of Embryo Development and Reproduction Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yunhai Zhang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
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46
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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47
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Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF. Molecular basis for the methylation specificity of ATXR5 for histone H3. Nucleic Acids Res 2017; 45:6375-6387. [PMID: 28383693 PMCID: PMC5499861 DOI: 10.1093/nar/gkx224] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 03/23/2017] [Indexed: 12/30/2022] Open
Abstract
In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.
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Affiliation(s)
- Elisa Bergamin
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Sabina Sarvan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Josée Malette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Vanessa Mongeon
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Scott D Michaels
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Alexandre Blais
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5J 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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48
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Schapira M, Tyers M, Torrent M, Arrowsmith CH. WD40 repeat domain proteins: a novel target class? Nat Rev Drug Discov 2017; 16:773-786. [PMID: 29026209 PMCID: PMC5975957 DOI: 10.1038/nrd.2017.179] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antagonism of protein-protein interactions (PPIs) with small molecules is becoming more feasible as a therapeutic approach. Successful PPI inhibitors tend to target proteins containing deep peptide-binding grooves or pockets rather than the more common large, flat protein interaction surfaces. Here, we review one of the most abundant PPI domains in the human proteome, the WD40 repeat (WDR) domain, which has a central peptide-binding pocket and is a member of the β-propeller domain-containing protein family. Recently, two WDR domain-containing proteins, WDR5 and EED, as well as other β-propeller domains have been successfully targeted by potent, specific, cell-active, drug-like chemical probes. Could WDR domains be a novel target class for drug discovery? Although the research is at an early stage and therefore not clinically validated, cautious optimism is justified, as WDR domain-containing proteins are involved in multiple disease-associated pathways. The druggability and structural diversity of WDR domain binding pockets suggest that understanding how to target this prevalent domain class will open up areas of disease biology that have so far resisted drug discovery efforts.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mount Sinai Hospital, The Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Maricel Torrent
- Discovery Research, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
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49
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Abstract
![]()
Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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50
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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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