1
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Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. bioRxiv 2024:2024.02.13.580169. [PMID: 38405904 PMCID: PMC10888769 DOI: 10.1101/2024.02.13.580169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. Nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). Here, we profile contributions of UHRF1 and DNMT1 to genome-wide DNA methylation inheritance and dissect specific roles for ubiquitin signaling in this process. We reveal DNA methylation maintenance at low-density CpGs is vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMD), a methylation signature observed across human cancers. Furthermore, disrupting DNMT1 UIM2 function abolishes DNA methylation maintenance. Collectively, we show DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to the development of PMDs in human cancers.
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2
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta S, Quaye C, Lynch K, Fuccillo M, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. bioRxiv 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histones occurs through multiple mechanisms including exchange with histone variants. Unlike canonical histones, variants are replication-independent and therefore accumulate in post-mitotic cells such as neurons. While recent findings link variants to neurological and neuropsychiatric disorders, few are well studied in the context of the brain. H2BE is the single H2B variant found outside germline tissues, yet its expression and effects on chromatin remained unclear. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad H2BE expression in the brain and its role in regulating chromatin structure, neuronal transcription, and mouse behavior. H2BE is enriched at promoters and enhances chromatin accessibility. We further identify a single amino acid driving these accessibility changes. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation and neuronal function underlying memory.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group
- Department of Genetics
- Epigenetics Institute
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group
- Department of Genetics
- Epigenetics Institute
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center
| | | | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Anna J. Voss
- Neuroscience Graduate Group
- Department of Genetics
- Epigenetics Institute
| | | | | | | | - Marc Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics
- Epigenetics Institute
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics
- Epigenetics Institute
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3
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Agustinus AS, David Y. Thinking outside the chromosome: epigenetic mechanisms in non-canonical chromatin species. Nat Struct Mol Biol 2024; 31:8-10. [PMID: 38253662 PMCID: PMC10964953 DOI: 10.1038/s41594-023-01200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Here we investigate the role of epigenetics in the formation, transcription regulation, maintenance and termination of several non-canonical chromatin structures. Using two examples, we demonstrate how studying non-canonical structures may reveal underlying mechanisms with implications for disease and propose intriguing epigenetic avenues for further exploration.
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Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, USA.
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4
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Banerjee R, David Y, Chan JC. Incorporating chemical structures into scientific figures. Trends Biochem Sci 2023; 48:743-745. [PMID: 37567151 PMCID: PMC10953349 DOI: 10.1016/j.tibs.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 08/13/2023]
Abstract
Of great import for biochemistry articles is the inclusion of chemical structures in figures; they are common for showing reactions, detailing protein side chains and modifications, and depicting chemical probes. In this ninth installment of the TrendsTalk Special series: Scientific figure development, two scientists share their thoughts: what aspects do you consider when generating a figure that contains chemical structures? How do you decide how to represent the chemical/residue structure(s) (i.e., level of detail, color, mechanisms, etc.)? What program(s) do you prefer for generating such figures and why? The scientists we hear from in this installment are Ruma Banerjee, primary author of ‘Gas regulation of complex II reversal via electron shunting to fumarate in the mammalian ETC’ ([1 ], see Figure 2) and Yael David, primary author of ‘Non-enzymatic covalent modifications as a new chapter in the histone code’ ([2 ], see, e.g., Figure 3), and Jennifer C. Chan, first author of ‘Nothing is yet set in (hi)stone: novel post-translational modifications regulating chromatin function’ ([3 ], see Figure 2).
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Affiliation(s)
- Ruma Banerjee
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Jennifer C Chan
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029.
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5
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Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature 2023; 619:176-183. [PMID: 37286593 PMCID: PMC10322720 DOI: 10.1038/s41586-023-06084-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/14/2023] [Indexed: 06/09/2023]
Abstract
Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.
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Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Duaa Al-Rawi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bhargavi Dameracharla
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Bailey S C L Jones
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Lorenzo Scipioni
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Jens Luebeck
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danguole Norkunaite
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Tri-institutional MD-PhD Program, New York, NY, USA
| | - Mercedes Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seongmin Choi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shira Yomtoubian
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eléonore Toufektchan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristina Keuper
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Paul S Mischel
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vivek Mittal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Maciejowski
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zuzana Storchova
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Enrico Gratton
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dan Landau
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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6
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Corless BC, Geißen R, Prescott NA, David Y, Scheinberg DA, Tan DS. Chemoenzymatic Synthesis of Novel Cytotoxic Epoxyketones Using the Eponemycin Biosynthetic Enzyme EpnF. ACS Chem Biol 2023; 18:1360-1367. [PMID: 37172287 PMCID: PMC10358350 DOI: 10.1021/acschembio.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Eponemycin is an α,β-epoxyketone natural product that inhibits the proteasome via covalent interaction of the epoxyketone warhead with catalytic N-terminal threonine residues. The epoxyketone warhead is biosynthesized from a β-ketoacid substrate by EpnF, a recently identified flavin-dependent acyl-CoA dehydrogenase-like enyzme. Herein, we report biochemical characterization of EpnF kinetics and substrate scope using a series of synthetic β-ketoacid substrates. These studies indicate that epoxide formation likely occurs prior to other tailoring reactions in the biosynthetic pathway, and have led to the identification of novel epoxyketone analogues with potent anticancer activity.
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Affiliation(s)
- Broderick C Corless
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Chemical Biology Program, Sloan Kettering Institute
| | - Raphael Geißen
- Doctoral Program, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
- Master of Biochemistry Program, Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
- Chemical Biology Program, Sloan Kettering Institute
| | - Nicholas A Prescott
- Chemical Biology Program, Sloan Kettering Institute
- Tri-Institutional PhD Program in Chemical Biology
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Chemical Biology Program, Sloan Kettering Institute
- Tri-Institutional PhD Program in Chemical Biology
| | - David A Scheinberg
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Tri-Institutional PhD Program in Chemical Biology
- Molecular Pharmacology Program, Sloan Kettering Institute
- Department of Medicine, Memorial Hospital
| | - Derek S Tan
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Chemical Biology Program, Sloan Kettering Institute
- Tri-Institutional PhD Program in Chemical Biology
- Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
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7
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Knörlein A, Xiao Y, David Y. Leveraging histone glycation for cancer diagnostics and therapeutics. Trends Cancer 2023; 9:410-420. [PMID: 36804508 PMCID: PMC10121827 DOI: 10.1016/j.trecan.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 02/22/2023]
Abstract
Cancer cells undergo metabolic reprogramming to rely mostly on aerobic glycolysis (the Warburg effect). The increased glycolytic intake enhances the intracellular levels of reactive sugars and sugar metabolites. These reactive species can covalently modify macromolecules in a process termed glycation. Histones are particularly susceptible to glycation, resulting in substantial alterations to chromatin structure, function, and transcriptional output. Growing evidence suggests a link between dysregulated metabolism of tumors and cancer proliferation through epigenetic changes. This review discusses recent advances in the understanding of histone glycation, its impact on the epigenetic landscape and cellular fate, and its role in cancer. In addition, we investigate the possibility of using histone glycation as biomarkers and targets for anticancer therapeutics.
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Affiliation(s)
- Anna Knörlein
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yang Xiao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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8
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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9
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Finkin-Groner E, Al-Kachak A, Agustinus A, Bastle R, Lepack A, Lyu Y, Maze I, David Y. Flexible and site-specific manipulation of histones in live animals. bioRxiv 2023:2023.03.19.533378. [PMID: 36993231 PMCID: PMC10055299 DOI: 10.1101/2023.03.19.533378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Recent advances in protein engineering have provided a wealth of methods that allow for the site-specific manipulation of proteins in vitro and in cells. However, the efforts to expand these toolkits for use in live animals has been limited. Here, we report a new method for the semi-synthesis of site-specifically modified and chemically defined proteins in live animals. Importantly, we illustrate the usefulness of this methodology in the context of a challenging, chromatin bound N-terminal histone tail within rodent postmitotic neurons located in ventral striatum (Nucleus Accumbens/NAc). This approach provides the field with a precise and broadly applicable methodology for manipulating histones in vivo, thereby serving as a unique template towards examining chromatin phenomena that may mediate transcriptomic and physiological plasticity within mammals.
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Affiliation(s)
| | - Amni Al-Kachak
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai, New York, NY
| | - Albert Agustinus
- Chemical Biology Program, Memorial Sloan Kettering, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
| | - Ryan Bastle
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai, New York, NY
| | - Ashley Lepack
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai, New York, NY
| | - Yang Lyu
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai, New York, NY
| | - Ian Maze
- Department of Neuroscience, Icahn School of Medicine, Mount Sinai, New York, NY
- Department of Pharmacological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY
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10
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Ray DM, Flood JR, David Y. Harnessing Split-Inteins as a Tool for the Selective Modification of Surface Receptors in Live Cells. Chembiochem 2023; 24:e202200487. [PMID: 36178424 PMCID: PMC9977608 DOI: 10.1002/cbic.202200487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/29/2022] [Indexed: 02/04/2023]
Abstract
Biochemical studies of integral membrane proteins are often hampered by low purification yields and technical limitations such as aggregation causing in vitro manipulations to be challenging. The ability of controlling proteins in live cells bypasses these limitations while broadening the scope of accessible questions owing to the proteins being in their native environment. Here we take advantage of the intein biorthogonality to mammalian systems, site specificity, fast kinetics, and auto-processing nature as an attractive option for modifying surface proteins. Using EGFR as a model, we demonstrate that the split-intein pair AvaN /NpuC can be used to efficiently and specifically modify target membrane proteins with a synthetic adduct for downstream live cell application.
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Affiliation(s)
- Devin M Ray
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Julia R Flood
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA
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11
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Pluta R, Aragón E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massagué J, David Y, Macias MJ. Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1. Nat Commun 2022; 13:7279. [PMID: 36435807 PMCID: PMC9701222 DOI: 10.1038/s41467-022-34925-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022] Open
Abstract
Forkhead box H1 (FoxH1) is an essential maternal pioneer factor during embryonic development that binds to specific GG/GT-containing DNA target sequences. Here we have determined high-resolution structures of three FoxH1 proteins (from human, frog and fish species) and four DNAs to clarify the way in which FoxH1 binds to these sites. We found that the protein-DNA interactions extend to both the minor and major DNA grooves and are thus almost twice as extensive as those of other FOX family members. Moreover, we identified two specific amino acid changes in FoxH1 that allowed the recognition of GG/GT motifs. Consistent with the pioneer factor activity of FoxH1, we found that its affinity for nucleosomal DNA is even higher than for linear DNA fragments. The structures reported herein illustrate how FoxH1 binding to distinct DNA sites provides specificity and avoids cross-regulation by other FOX proteins that also operate during the maternal-zygotic transition and select canonical forkhead sites.
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Affiliation(s)
- Radoslaw Pluta
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain
| | - Eric Aragón
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain
| | - Nicholas A. Prescott
- grid.511427.4Tri-Institutional PhD Program in Chemical Biology, New York, NY USA ,grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Lidia Ruiz
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain
| | - Rebeca A. Mees
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain
| | - Blazej Baginski
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain
| | - Julia R. Flood
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Pau Martin-Malpartida
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain
| | - Joan Massagué
- grid.51462.340000 0001 2171 9952Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Yael David
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA ,grid.5386.8000000041936877XDepartment of Pharmacology, Weill Cornell Medicine, New York, NY 10065 USA ,grid.5386.8000000041936877XDepartment of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065 USA
| | - Maria J. Macias
- grid.7722.00000 0001 1811 6966Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, 08028 Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010 Spain
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12
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Ray DM, Flood JR, David Y. Harnessing Split‐Inteins as a Tool for the Selective Modification of Surface Receptors in Live Cells. Chembiochem 2022. [DOI: 10.1002/cbic.202200654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Devin M. Ray
- Tri-Institutional PhD Program in Chemical Biology New York NY, 10065 USA
- Chemical Biology Program Memorial Sloan Kettering Cancer Center New York NY, 10065 USA
- Tri-Institutional MD-PhD Program New York NY 10065 USA
| | - Julia R. Flood
- Chemical Biology Program Memorial Sloan Kettering Cancer Center New York NY, 10065 USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology New York NY, 10065 USA
- Chemical Biology Program Memorial Sloan Kettering Cancer Center New York NY, 10065 USA
- Department of Pharmacology Weill Cornell Medical College New York NY 10065 USA
- Department of Physiology Biophysics and Systems Biology Weill Cornell Medical College New York NY, 10065 USA
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13
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Agustinus AS, Raviram R, Dameracharla B, Luebeck J, Stransky S, Scipioni L, Myers RM, Bona MD, Duran M, Weigelt B, Yomtoubian S, Toufektchan E, Mischel PS, Mittal V, Shah S, Maciejowski J, Gratton E, Ly P, Bakhoum MF, Landau D, Bafna V, Sidoli S, David Y, Bakhoum SF. Abstract 3768: Epigenetic dysregulation from chromosomal transit in micronuclei. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers, yet whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei, and subsequent micronuclear envelope rupture profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice as well as cancer and nontransformed cells. Some of the changes to histone PTMs occur due to micronuclear envelope rupture whereas others are inherited from mitotic abnormalities prior to micronucleus formation. Using orthogonal techniques, we show that micronuclei exhibit extensive differences in chromatin accessibility with a strong positional bias between promoters and distal or intergenic regions. Finally, we show that inducing CIN engenders widespread epigenetic dysregulation and that chromosomes which transit in micronuclei experience durable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, in addition to genomic copy number alterations, CIN can serve as a vehicle for epigenetic reprogramming and heterogeneity in cancer.
Citation Format: Albert S. Agustinus, Ramya Raviram, Bhargavi Dameracharla, Jens Luebeck, Stephanie Stransky, Lorenzo Scipioni, Robert M. Myers, Melody Di Bona, Mercedes Duran, Britta Weigelt, Shira Yomtoubian, Eleonore Toufektchan, Paul S. Mischel, Vivek Mittal, Sohrab Shah, John Maciejowski, Enrico Gratton, Peter Ly, Mathieu F. Bakhoum, Dan Landau, Vineet Bafna, Simone Sidoli, Yael David, Samuel F. Bakhoum. Epigenetic dysregulation from chromosomal transit in micronuclei [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3768.
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Affiliation(s)
| | | | | | - Jens Luebeck
- 3University of California San Diego, La Jolla, CA
| | | | | | | | | | | | | | | | | | - Paul S. Mischel
- 7Stanford University, School of Medicine and Stanford ChEM-H, Stanford, CA
| | | | - Sohrab Shah
- 6Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Peter Ly
- 8Department of Pathology, Dallas, TX
| | | | | | - Vineet Bafna
- 3University of California San Diego, La Jolla, CA
| | | | - Yael David
- 6Memorial Sloan Kettering Cancer Center, New York, NY
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14
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Leicher R, Osunsade A, Chua GNL, Faulkner SC, Latham AP, Watters JW, Nguyen T, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y, Liu S. Single-stranded nucleic acid binding and coacervation by linker histone H1. Nat Struct Mol Biol 2022; 29:463-471. [PMID: 35484234 DOI: 10.1038/s41594-022-00760-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/14/2022] [Indexed: 02/04/2023]
Abstract
The H1 linker histone family is the most abundant group of eukaryotic chromatin-binding proteins. However, their contribution to chromosome structure and function remains incompletely understood. Here we use single-molecule fluorescence and force microscopy to directly visualize the behavior of H1 on various nucleic acid and nucleosome substrates. We observe that H1 coalesces around single-stranded DNA generated from tension-induced DNA duplex melting. Using a droplet fusion assay controlled by optical tweezers, we find that single-stranded nucleic acids mediate the formation of gel-like H1 droplets, whereas H1-double-stranded DNA and H1-nucleosome droplets are more liquid-like. Molecular dynamics simulations reveal that multivalent and transient engagement of H1 with unpaired DNA strands drives their enhanced phase separation. Using eGFP-tagged H1, we demonstrate that inducing single-stranded DNA accumulation in cells causes an increase in H1 puncta that are able to fuse. We further show that H1 and Replication Protein A occupy separate nuclear regions, but that H1 colocalizes with the replication factor Proliferating Cell Nuclear Antigen, particularly after DNA damage. Overall, our results provide a refined perspective on the diverse roles of H1 in genome organization and maintenance, and indicate its involvement at stalled replication forks.
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Affiliation(s)
- Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Adewola Osunsade
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA.,Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sarah C Faulkner
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John W Watters
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Tuan Nguyen
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.,Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Emily C Beckwitt
- Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | - Paul G Young
- Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA. .,Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA. .,Tri-Institutional MD-PhD Program, New York, NY, USA. .,Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA. .,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA.
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA. .,Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA. .,Tri-Institutional MD-PhD Program, New York, NY, USA.
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15
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Abstract
Because of their long half-lives and highly nucleophilic tails, histones are particularly susceptible to accumulating nonenzymatic covalent modifications, such as glycation. The resulting modifications can have profound effects on cellular physiology due to the regulatory role histones play in all DNA-templated processes; however, the complexity of Maillard chemistry on proteins makes tracking and enriching for glycated proteins a challenging task. Here, we characterize glyoxal (GO) modifications on histones using quantitative proteomics and an aniline-derived GO-reactive probe. In addition, we leverage this chemistry to demonstrate that the glycation regulatory proteins DJ-1 and GLO1 reduce levels of histone GO adducts. Finally, we employ a two-round pull-down method to enrich histone H3 GO glycation and map these adducts to specific chromatin regions.
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Affiliation(s)
- Devin M. Ray
- Tri-Institutional MD-PhD Program, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Erin Q. Jennings
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Xander Chai
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
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16
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Leicher R, Osunsade A, Chua GN, Faulkner SC, Latham AP, Watters JW, Nguyen TA, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y, Liu S. Single-stranded nucleic acid sensing and coacervation by linker histone H1. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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17
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Sheban D, Shani T, Maor R, Aguilera-Castrejon A, Mor N, Oldak B, Shmueli MD, Eisenberg-Lerner A, Bayerl J, Hebert J, Viukov S, Chen G, Kacen A, Krupalnik V, Chugaeva V, Tarazi S, Rodríguez-delaRosa A, Zerbib M, Ulman A, Masarwi S, Kupervaser M, Levin Y, Shema E, David Y, Novershtern N, Hanna JH, Merbl Y. SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity. Mol Cell 2021; 82:106-122.e9. [PMID: 34875212 DOI: 10.1016/j.molcel.2021.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, how the chromatin is organized to prohibit the reversal of the developmental program remains unclear. Specifically, the totipotency-to-pluripotency transition marks one of the most dramatic events to the chromatin, and yet, the nature of histone alterations underlying this process is incompletely characterized. Here, we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Furthermore, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress the totipotency program in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in facilitating chromatin repression and desolation of the totipotent identity.
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Affiliation(s)
- Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roey Maor
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bernardo Oldak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jakob Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Guoyun Chen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Valeriya Chugaeva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tarazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Ulman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Solaiman Masarwi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Meital Kupervaser
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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18
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David Y, Oslund RC. From Basic Biology Discovery to Translational Impact: The Boundless Roles of Chemical Biology. Chembiochem 2021; 23:e202100536. [PMID: 34730874 DOI: 10.1002/cbic.202100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As academia and industry push the boundaries of chemical biology more and more from basic science into impacting human health, we asked experts in the field what uniquely positions chemical biology as a translational science, how and when to maximize its potential, and where the field is headed. We also reflect personally on how chemical biology has impacted our careers in industry and academia.
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Affiliation(s)
- Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.,Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, 02139, USA
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19
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Shah UA, Rögnvaldsson S, Derkach A, Björkholm M, Turesson I, David Y, Hultcrantz M, Tan C, Hassoun H, Korde N, Lesokhin A, Mailankody S, Kristinsson SY, Landgren CO. Diabetes mellitus and risk of plasma cell and lymphoproliferative disorders in 94,579 cases and 368,348 matched controls. Haematologica 2021; 107:284-286. [PMID: 34474548 PMCID: PMC8719074 DOI: 10.3324/haematol.2021.278772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Urvi A Shah
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York.
| | | | - Andriy Derkach
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - Magnus Björkholm
- Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm
| | | | - Yael David
- Department of Chemical Biology, Sloan Kettering Institute, New York
| | - Malin Hultcrantz
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York
| | - Carlyn Tan
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York
| | - Hani Hassoun
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York
| | - Neha Korde
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York
| | - Alexander Lesokhin
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York
| | - Sham Mailankody
- Department of Medicine, Myeloma Service, Memorial Sloan Kettering Cancer Center, New York
| | - Sigurður Yngvi Kristinsson
- Department of Medicine, University of Iceland, Iceland; Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm
| | - C Ola Landgren
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami
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20
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Maksimovic I, David Y. Non-enzymatic Covalent Modifications as a New Chapter in the Histone Code. Trends Biochem Sci 2021; 46:718-730. [PMID: 33965314 PMCID: PMC8364488 DOI: 10.1016/j.tibs.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 12/29/2022]
Abstract
The interior of the cell abounds with reactive species that can accumulate as non-enzymatic covalent modifications (NECMs) on biological macromolecules. These adducts interfere with many cellular processes, for example, by altering proteins' surface topology, enzymatic activity, or interactomes. Here, we discuss dynamic NECMs on chromatin, which serves as the cellular blueprint. We first outline the chemistry of NECM formation and then focus on the recently identified effects of their accumulation on chromatin structure and transcriptional output. We next describe the known cellular regulatory mechanisms that prevent or reverse NECM formation. Finally, we discuss recently developed chemical biology platforms for probing and manipulating these NECMs in vitro and in vivo.
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Affiliation(s)
- Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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21
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Faulkner S, Maksimovic I, David Y. A chemical field guide to histone nonenzymatic modifications. Curr Opin Chem Biol 2021; 63:180-187. [PMID: 34157651 DOI: 10.1016/j.cbpa.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 05/03/2021] [Indexed: 12/29/2022]
Abstract
Histone nonenzymatic covalent modifications (NECMs) have recently emerged as an understudied class of posttranslational modifications that regulate chromatin structure and function. These NECMs alter the surface topology of histone proteins, their interactions with DNA and chromatin regulators, as well as compete for modification sites with enzymatic posttranslational modifications. NECM formation depends on the chemical compatibility between a reactive molecule and its target site, in addition to their relative stoichiometries. Here we survey the chemical reactions and conditions that govern the addition of NECMs onto histones as a manual to guide the identification of new physiologically relevant chemical adducts. Characterizing NECMs on chromatin is critical to attain a comprehensive understanding of this new chapter of the so-called "histone code".
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Affiliation(s)
- Sarah Faulkner
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Igor Maksimovic
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States; Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, United States
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States; Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, United States; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, United States; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, United States.
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22
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Maksimovic I, Finkin-Groner E, Fukase Y, Zheng Q, Sun S, Michino M, Huggins DJ, Myers RW, David Y. Deglycase-activity oriented screening to identify DJ-1 inhibitors. RSC Med Chem 2021; 12:1232-1238. [PMID: 34355187 DOI: 10.1039/d1md00062d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/03/2021] [Indexed: 11/21/2022] Open
Abstract
The oncoprotein and Parkinson's disease-associated enzyme DJ-1/PARK7 has emerged as a promiscuous deglycase that can remove methylglyoxal-induced glycation adducts from both proteins and nucleotides. However, dissecting its structural and enzymatic functions remains a challenge due to the lack of potent, specific, and pharmacokinetically stable inhibitors targeting its catalytic site (including Cys106). To evaluate potential drug-like leads against DJ-1, we leveraged its deglycase activity in an enzyme-coupled, fluorescence lactate-detection assay based on the recent understanding of its deglycation mechanism. In addition, we developed assays to directly evaluate DJ-1's esterase activity using both colorimetric and fluorescent substrates. The resulting optimized assay was used to evaluate a library of potential reversible and irreversible DJ-1 inhibitors. The deglycase activity-oriented screening strategy described herein establishes a new platform for the discovery of potential anti-cancer drugs.
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Affiliation(s)
- Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology New York New York 10065 USA.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center New York New York 10065 USA
| | - Efrat Finkin-Groner
- Tri-Institutional Therapeutics Discovery Institute 413 East 69th Street New York NY 10021 USA
| | - Yoshiyuki Fukase
- Tri-Institutional Therapeutics Discovery Institute 413 East 69th Street New York NY 10021 USA
| | - Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center New York New York 10065 USA
| | - Shan Sun
- Tri-Institutional Therapeutics Discovery Institute 413 East 69th Street New York NY 10021 USA
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute 413 East 69th Street New York NY 10021 USA
| | - David J Huggins
- Tri-Institutional Therapeutics Discovery Institute 413 East 69th Street New York NY 10021 USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine New York New York 10065 USA
| | - Robert W Myers
- Tri-Institutional Therapeutics Discovery Institute 413 East 69th Street New York NY 10021 USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology New York New York 10065 USA.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center New York New York 10065 USA .,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine New York New York 10065 USA.,Department of Pharmacology, Weill Cornell Medicine New York New York 10065 USA
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23
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Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol Y, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Toro LN, Zhao J, Lee CH, Hou H, Yusufova N, Meydan C, Osunsade A, David Y, Cesarman E, Melnick AM, Sidoli S, Garcia BA, Edelmann W, Macian F, Skoultchi AI. H1 histones control the epigenetic landscape by local chromatin compaction. Nature 2021; 589:293-298. [PMID: 33299182 PMCID: PMC8110206 DOI: 10.1038/s41586-020-3032-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 10/06/2020] [Indexed: 01/29/2023]
Abstract
H1 linker histones are the most abundant chromatin-binding proteins1. In vitro studies indicate that their association with chromatin determines nucleosome spacing and enables arrays of nucleosomes to fold into more compact chromatin structures. However, the in vivo roles of H1 are poorly understood2. Here we show that the local density of H1 controls the balance of repressive and active chromatin domains by promoting genomic compaction. We generated a conditional triple-H1-knockout mouse strain and depleted H1 in haematopoietic cells. H1 depletion in T cells leads to de-repression of T cell activation genes, a process that mimics normal T cell activation. Comparison of chromatin structure in normal and H1-depleted CD8+ T cells reveals that H1-mediated chromatin compaction occurs primarily in regions of the genome containing higher than average levels of H1: the chromosome conformation capture (Hi-C) B compartment and regions of the Hi-C A compartment marked by PRC2. Reduction of H1 stoichiometry leads to decreased H3K27 methylation, increased H3K36 methylation, B-to-A-compartment shifting and an increase in interaction frequency between compartments. In vitro, H1 promotes PRC2-mediated H3K27 methylation and inhibits NSD2-mediated H3K36 methylation. Mechanistically, H1 mediates these opposite effects by promoting physical compaction of the chromatin substrate. Our results establish H1 as a critical regulator of gene silencing through localized control of chromatin compaction, 3D genome organization and the epigenetic landscape.
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Affiliation(s)
| | - Sean E Healton
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Cary N Weiss
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yair Botbol
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Laxmi N Mishra
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Dhruv S Sidhwani
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Tommy J Wilson
- Department of Neurology, Columbia University College of Physicians and Surgeons, Columbia University Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - Hugo B Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maxim I Maron
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Karin A Skalina
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Laura Norwood Toro
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jie Zhao
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea
| | - Harry Hou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nevin Yusufova
- Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Adewola Osunsade
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
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24
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Yusufova NZ, Teater M, Kloetgen A, Soshnev A, Osunade A, Chin C, Doane A, Staudt L, Scott D, Kelleher N, Tsirigos A, Imielinski M, David Y, Allis D, Cesarman E, Melnick A. Abstract PO-10: Histone 1 deficiency drives lymphoma through disruption of 3D chromatin architecture. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Linker histone H1 binds to nucleosomes and causes chromatin compaction, yet little is known about their biologic function. Somatic missense mutations in histone 1 genes (HIST1H1B-E) occur in ~30% of follicular lymphomas and DLBCL, with significant mutual co-occurrence among these alleles, most frequently involving H1C and H1E. Examining whole exomes in 547 DLBCL patients, we found significant enrichment for H1 gene SNVs and copy number loss in the MCD class of ABC-DLBCLs as compared to other subtypes. Next we performed a genetic driver analysis in 101 DLBCLs with matched germline control to identify mutations significantly enriched over background somatic variation. We find that lymphoma-associated H1 alleles H1C and H1E are true genetic driver mutations in lymphomas. Lymphoma H1 mutations affect the H1 globular domain or C-terminus. We found that the globular domain mutants fail to bind to chromatin whereas C-ter mutants fail to compact chromatin as shown by atomic force microscopy, in vitro assembled nucleosome arrays, and FRAP assays in live cells. Hence both types of mutation confer loss of function. Constitutive H1C/E knockout mice are healthy and have no overt phenotype. However, immunization with T cell-dependent antigen caused significant GC hyperplasia (p=0.013) and disruption of polarity due to expansion in the number of centrocytes. Notably, H1C/EDKO GC B-cells readily outcompeted WT GC B-cells in mixed chimera experiments, indicating that they have superior fitness (p=0.0086). We performed RNA-seq in H1C/EDKO GC B-cells, which revealed an aberrant gene derepression signature. Strikingly, these same genes are upregulated during induced pluripotency (iPS cell) reprogramming and are normally silenced during early development by the PRC2 complex (p <0.05 to 1e-05). Indeed, histone mass spectrometry showed reduced H3K27me3 (p=0.0003) and increased H3K36me2 (p =0.001) in H1C/EDKO GC B cells. This prompted us to characterize the epigenome of purified H1C/EDKO vs WT GC B cells using Hi-C, ATAC-seq, and ChIP-seq for multiple histone marks. H1 deficiency causes profound architectural remodeling of the genome characterized by large-scale yet focal compartment shifts from compartment B to compartment A. The degree of decompaction results in distinct epigenetic states, primarily due to gain of H3K36me2 and/or loss of repressive H3K27me3. Strikingly, the H1C/EDKO primitive stem cell gene expression signature was highly significantly enriched (NES 1.24, FDR<0.001) in the RNA-seq profiles of independent cohorts of DLBCL patients with H1C and H1E mutations. We crossed H1C+/-H1E+/- mice with VavP-Bcl2 transgenic mice and observed significant acceleration of lymphomagenesis (p=0.0001). Consistent with acquisition of stem cell characteristics, H1C+/-H1E+/-;VavP-Bcl2 but not VavP-Bcl2 primary lymphoma cells manifested lymphoma-initiating functionality after secondary transplantation into recipient animals.
Citation Format: Nevin Z. Yusufova, Matt Teater, Andreas Kloetgen, Alexey Soshnev, Adewola Osunade, Christopher Chin, Ashley Doane, Louis Staudt, David Scott, Neil Kelleher, Aristotelis Tsirigos, Marcin Imielinski, Yael David, David Allis, Ethel Cesarman, Ari Melnick. Histone 1 deficiency drives lymphoma through disruption of 3D chromatin architecture [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-10.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Scott
- 6British Columbia Cancer Agency, Vancouver, BC, Canada,
| | | | | | | | - Yael David
- 4Memorial Sloan Kettering Cancer Center, New York, NY,
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25
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Abstract
Protein arginine deiminase 4 (PAD4) facilitates the post-translational citrullination of the core histones H3 and H4. While the precise epigenetic function of this modification has not been resolved, it has been shown to associate with general chromatin decompaction and compete with arginine methylation. Recently, we found that histones are subjected to methylglyoxal (MGO)-induced glycation on nucleophilic side chains, particularly arginines, under metabolic stress conditions. These non-enzymatic adducts change chromatin architecture and the epigenetic landscape by competing with enzymatic modifications, as well as changing the overall biophysical properties of the fiber. Here, we report that PAD4 antagonizes histone MGO-glycation by protecting the reactive arginine sites, as well as by converting already-glycated arginine residues into citrulline. Moreover, we show that similar to the deglycase DJ-1, PAD4 is overexpressed and histone citrullination is upregulated in breast cancer tumors, suggesting an additional mechanistic link to PAD4's oncogenic properties.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Adewola Osunsade
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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26
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Abstract
Reactive cellular metabolites can modify macromolecules and form adducts known as nonenzymatic covalent modifications (NECMs). The dissection of the mechanisms, regulation, and consequences of NECMs, such as glycation, has been challenging due to the complex and often ambiguous nature of the adducts formed. Specific chemical tools are required to directly track the formation of these modifications on key targets in order to uncover their underlying physiological importance. Here, we present the novel chemoenzymatic synthesis of an active azido-modified ribose analog, 5-azidoribose (5-AR), as well as the synthesis of an inactive control derivative, 1-azidoribose (1-AR), and their application toward understanding protein ribose-glycation in vitro and in cellulo. With these new probes we found that, similar to methylglyoxal (MGO) glycation, ribose glycation specifically accumulates on histones. In addition to fluorescent labeling, we demonstrate the utility of the probe in enriching modified targets, which were identified by label-free quantitative proteomics and high-resolution MS/MS workflows. Finally, we establish that the known oncoprotein and hexose deglycase, fructosamine 3-kinase (FN3K), recognizes and facilitates the removal of 5-AR glycation adducts in live cells, supporting the dynamic regulation of ribose glycation as well as validating the probe as a new platform to monitor FN3K activity. Altogether, we demonstrate this probe's utilities to uncover ribose-glycation and deglycation events as well as track FN3K activity toward establishing its potential as a new cancer vulnerability.
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Affiliation(s)
- Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Marissa N Trujillo
- Department of Pharmaocology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - James J Galligan
- Department of Pharmaocology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, New York, New York 10065, United States
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York 10065, United States
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27
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Zheng Q, Maksimovic I, Upad A, David Y. Non-enzymatic covalent modifications: a new link between metabolism and epigenetics. Protein Cell 2020; 11:401-416. [PMID: 32356279 PMCID: PMC7251012 DOI: 10.1007/s13238-020-00722-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenetic modifications, including those on DNA and histones, have been shown to regulate cellular metabolism by controlling expression of enzymes involved in the corresponding metabolic pathways. In turn, metabolic flux influences epigenetic regulation by affecting the biosynthetic balance of enzyme cofactors or donors for certain chromatin modifications. Recently, non-enzymatic covalent modifications (NECMs) by chemically reactive metabolites have been reported to manipulate chromatin architecture and gene transcription through multiple mechanisms. Here, we summarize these recent advances in the identification and characterization of NECMs on nucleic acids, histones, and transcription factors, providing an additional mechanistic link between metabolism and epigenetics.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Igor Maksimovic
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Akhil Upad
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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28
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Ducournau F, Arianni M, Awwad S, Baur EM, Beaulieu JY, Bouloudhnine M, Caloia M, Chagar K, Chen Z, Chin AY, Chow EC, Cobb T, David Y, Delgado PJ, Woon Man Fok M, French R, Golubev I, Haugstvedt JR, Ichihara S, Jorquera RA, Koo SCJJ, Lee JY, Lee YK, Lee YJ, Liu B, Kaleli T, Mantovani GR, Mathoulin C, Messina JC, Muccioli C, Nazerani S, Ng CY, Obdeijn MC, Van Overstraeten L, Prasetyono TOH, Ross M, Shih JT, Smith N, Suarez R FA, Chan PT, Tiemdjo H, Wahegaonkar A, Wells MC, Wong WY, Wu F, Yang XF, Yanni D, Yao J, Liverneaux PA. COVID-19: Initial experience of an international group of hand surgeons. Hand Surg Rehabil 2020; 39:159-166. [PMID: 32278932 PMCID: PMC7194873 DOI: 10.1016/j.hansur.2020.04.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 12/29/2022]
Abstract
The emergence of the COVID-19 pandemic has severely affected medical treatment protocols throughout the world. While the pandemic does not affect hand surgeons at first glance, they have a role to play. The purpose of this study was to describe the different measures that have been put in place in response to the COVID-19 pandemic by hand surgeons throughout the world. The survey comprised 47 surgeons working in 34 countries who responded to an online questionnaire. We found that the protocols varied in terms of visitors, health professionals in the operating room, patient waiting areas, wards and emergency rooms. Based on these preliminary findings, an international consensus on hand surgery practices for the current viral pandemic, and future ones, needs to be built rapidly.
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Affiliation(s)
- F Ducournau
- Icube CNRS 7357, department of hand surgery, hôpital de Hautepierre, university hospital of Strasbourg, FMTS, university of Strasbourg, 1, avenue Molière, 67200 Strasbourg cedex, France
| | - M Arianni
- Department of Surgery, RSUD Pasar Minggu Hospital, Jl. TB Simatupang No.1, RT.1/RW.5, Ragunan, Kec. Ps. Minggu, Kota Jakarta Selatan, Daerah Khusus Ibukota Jakarta 12550, Indonesia
| | - S Awwad
- National Guard Hospital Medina, Ad Dar, Medina, Saudi Arabia
| | - E-M Baur
- Practice of Plastic and Hand Surgery, James-Loeb-Straße 13, 82418 Murnau am Staffelsee, Germany
| | - J-Y Beaulieu
- Hôpitaux universitaire de Genève, département de chirurgie, rue Gabrielle-Perret-Gentil 4, 1205 Genève, Switzerland
| | - M Bouloudhnine
- Les Cliniques El Manar, 2092 rue Habib Echatti, Tunis, Tunisia
| | - M Caloia
- Department of Orthopaedic Surgery, Facultad de Ciencias Biomedicas, Universidad Austral, Hospital Universitario Austral, Pilar, Buenos Aires, Argentina
| | - K Chagar
- Pôle de chirurgie orthopédique, hôpital Militaire d'Instruction Mohamed V, Hay Riad, Rabat, Morocco
| | - Z Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 328 Qi'an Ave, Xinzhou, Wuhan, Hubei, China
| | - A Y Chin
- Department of Hand and Reconstructive Microsurgery, Singapore General Hospital, Academia Building, Outram Rd, Singapour 169608, Singapore
| | - E C Chow
- Department of Orthopaedics and Traumatology, United Christian Hospital, 130 Hip Wo St, Kwun Tong, Hong Kong
| | - T Cobb
- Orthopedic Specialists, P.C., 4622 Progress Drive Suite C, Davenport, IA 52807, USA
| | - Y David
- Hand surgery unit and microsurgery, Hospital Kaplan medical center, Derech Pasternak, Rehovot, Israel
| | - P J Delgado
- Hand Surgery and Microsurgery Department, University Hospital HM Monteprincipe, CEU San Pablo University, Calle de Julián Romea 23, 28003 Madrid, Spain
| | - M Woon Man Fok
- Department of Orthopaedics and Traumatology 5/F, Professorial Block, Queen Mary Hospital, The University of Hong Kong, Queen Mary Hospital Main Block, Pok Fu Lam Rd, Pok Fu Lam, Hong Kong
| | - R French
- The Specialist Referral Clinic, 555W 12th Ave #121, Vancouver, BC V5Z 3X7, Canada
| | - I Golubev
- N. Priorov Research Institute of Trauma Surgery and Orthopaedics, 10 Moscow Ulitsa Priorova, Russia
| | - J R Haugstvedt
- Division of Handsurgery, Department of Orthopedics, Østfold Hospital, Per Gynts vei 78, 1535 Moss, Norway
| | - S Ichihara
- Department of Hand Surgery, Juntendo University Urayasu Hospital, 2 Chome-1-1 Tomioka, Urayasu, Chiba 279-0021, Japan
| | - R A Jorquera
- Department of Hand Surgery and Microsurgery, Clínica Indisa, Andrés Bello University, Av. Sta. María 1810, Santiago, Providencia, Región Metropolitana, Chile
| | - S C J J Koo
- Department of Orthoapedics and Traumatology, Alice Ho Miu Ling Nethersole Hospital, 11 Chuen On Road, Tai Po, NT, Hong Kong
| | - J Y Lee
- Department of Orthopedic Surgery, The Catholic University of Korea, Eunpyeong St. Mary's Hospital, 1021 Tongil-ro, Eunpyeong-gu, 03312 Seoul, Korea
| | - Y K Lee
- Department of Orthopedic Surgery, Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, 567 Baekje-daero, Geumam 1(il)-dong, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Y J Lee
- Department of Orthopaedic Surgery, Kyungpook National University Hospital, 130 Dongdeok-ro, Jung-gu, Daegu 41944, Republic of Korea
| | - B Liu
- Department of Hand Surgery, Beijing Ji Shui Tan Hospital, the 4th Clinical College of Peking University, 31 Xinjiekou E Rd, Beijing Xicheng District, China
| | - T Kaleli
- Uludag University, Faculty of Medicine, Department of Orthopaedics, Hand Surgery Clinic, Özlüce, Görükle Kampüsü, 16059 Nilüfer/Bursa, Turkey
| | - G R Mantovani
- Department of Hand Surgery, Sao Paolo Hand center, Ben Portuguesa Hospital, R. Maestro Cardim 769, Bela Vista, São Paulo, SP, 01323-001, Brazil
| | - C Mathoulin
- International Wrist Center, clinique Bizet, Institut de la main, 23, rue Georges-Bizet, 75116 Paris, France
| | - J C Messina
- Gaetano Pini- CTO Orthopaedic Institute, First Orthopaedic Clinic University of Milan, Piazza Cardinale Andrea Ferrari 1, 20122 Milano MI, Italy
| | - C Muccioli
- Icube CNRS 7357, department of hand surgery, hôpital de Hautepierre, university hospital of Strasbourg, FMTS, university of Strasbourg, 1, avenue Molière, 67200 Strasbourg cedex, France
| | - S Nazerani
- Department of Hand and Reconstructive Microsurgery, Mehr General Hospital, W Zartosht St, District 6, Tehran, Tehran Province, IR, Iran
| | - C Y Ng
- Upper Limb Unit, Wrightington Hospital, Appley Bridge, Wigan, UK
| | - M C Obdeijn
- Department of Plastic, Reconstructive and Hand surgery, Amsterdam University Medical Centers, AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - L Van Overstraeten
- Hôpital Erasme, ULB, route de Lennik 808, 1070 Bruxelles, Belgium; Hand and foot surgery unit, Rue Pierre Caille 9, 7500 Tournai, Belgium
| | - T O H Prasetyono
- Division of Plastic Surgery, Department of Surgery, Cipto Mangunkusumo Hospital/Faculty of Medicine Universitas Indonesia, Jl. Pangeran Diponegoro No.71, RW.5, Kenari, Kec. Senen, Kota Jakarta Pusat, Daerah Khusus Ibukota Jakarta 10430, Indonesia
| | - M Ross
- Brisbane Hand and Upper Limb Research Institute, Brisbane Private Hospital, 259 Wickham Terrace, Brisbane City QLD 4000, Australia
| | - J T Shih
- Department of Orthopaedic Surgery, Armed Forces Taoyuan General Hospital, No. 168, Zhongxing Road, Longtan District, Taoyuan City, Taiwan
| | - N Smith
- Southern Highlands Private Hospital, St Jude Specialist Centre, 21 St Jude St, Bowral NSW 2576, Australia
| | - F A Suarez R
- Universidad Militar Nueva Granada, Bogota, Colombia/Private clinic Centro de Cirugia Minimamente Invasiva CECIMIN, 76, Autopista Nte. #104, Bogotá, Colombia
| | - P-T Chan
- Department of Orthopaedics and Traumatology, Tuen Mun Hospital, Block H, Tsing Chung Koon Rd, Tuen Mun, Hong Kong
| | - H Tiemdjo
- Centre de chirurgie de la main et des paralysies de Douala, Bonamoussadi, Douala, Cameroon
| | - A Wahegaonkar
- Dept of Upper Limb, Hand and Microvascular Reconstructive Surgery, Brachial Plexus and Peripheral Nerve Surgery, Sancheti Institute for Orthopaedics and Rehabilitation, Jehangir Hospital, 32, Sasoon Road Opposite Railway Station, Central Excise Colony, Sangamvadi, Pune, Maharashtra 411001, India; The Hand Surgery Clinics, 81/A/11 Giridarshan Society, Behind NEXA Showroom, Baner Road, Pune, Maharashtra 411007, India
| | - M C Wells
- Orthopaedic hand surgeon, Mediclinic Panorama, Panorama, Rothschild Blvd, Panorama, Cape Town, 7500, South Africa
| | - W-Y Wong
- Department of Orthopaedics and Traumatology, the Chinese University of Hong Kong, Central Ave, Hong Kong
| | - F Wu
- Dept of Orthopaedics, University Hospitals Birmingham, Bordesley Green East, Bordesley Green E, Birmingham B9 5SS, UK
| | - X F Yang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiang'an District, Wuhan, Hubei, China
| | - D Yanni
- KIMS Hospital, Newnham Ct Way, Weavering, Maidstone ME14 5FT, Kent, UK
| | - J Yao
- Robert A. Chase Hand and Upper Limb Center, Stanford University Medical Center, 450 Broadway, Redwood City, CA 94063, USA
| | - P A Liverneaux
- Icube CNRS 7357, department of hand surgery, hôpital de Hautepierre, university hospital of Strasbourg, FMTS, university of Strasbourg, 1, avenue Molière, 67200 Strasbourg cedex, France.
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29
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Rosinsky P, Netzer N, David Y, Kosashvili Y, Been E, Oron A. Fifth metacarpal instability and its effect on hamatometacarpal arthritis patterns–a cadaver study. Hand Surgery and Rehabilitation 2020; 39:48-52. [DOI: 10.1016/j.hansur.2019.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
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30
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Zheng Q, Maksimovic I, Upad A, Guber D, David Y. Synthesis of an Alkynyl Methylglyoxal Probe to Investigate Nonenzymatic Histone Glycation. J Org Chem 2020; 85:1691-1697. [PMID: 31875401 DOI: 10.1021/acs.joc.9b02504] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methylglyoxal (MGO) is a reactive dicarbonyl metabolite that modifies histones in vivo and induces changes in chromatin structure and function. Here we report the synthesis and application of a chemical probe for investigating MGO-glycation. A two-step synthesis of a Cu-click compatible alkynyl oxoaldehyde probe (AlkMGO) via sequential Dess-Martin and Riley oxidations is presented. This synthesis elevates the accessibility and utility of an important tool for tracking, enriching, and studying MGO-glycation to aid in understanding its underlying biochemical functions.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - Igor Maksimovic
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Tri-Institutional Ph.D. Program in Chemical Biology , New York , New York 10065 , United States
| | - Akhil Upad
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States
| | - David Guber
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Department of Chemistry , City University of New York, Hunter College , New York , New York 10065 , United States
| | - Yael David
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Tri-Institutional Ph.D. Program in Chemical Biology , New York , New York 10065 , United States.,Department of Pharmacology , Weill Cornell Medicine , New York , New York 10065 , United States.,Department of Physiology, Biophysics and Systems Biology , Weill Cornell Medicine , New York , New York 10065 , United States
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31
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Prescott NA, Bram Y, Schwartz RE, David Y. Targeting Hepatitis B Virus Covalently Closed Circular DNA and Hepatitis B Virus X Protein: Recent Advances and New Approaches. ACS Infect Dis 2019; 5:1657-1667. [PMID: 31525994 DOI: 10.1021/acsinfecdis.9b00249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chronic Hepatitis B virus (HBV) infection remains a worldwide concern and public health problem. Two key aspects of the HBV life cycle are essential for viral replication and thus the development of chronic infections: the establishment of the viral minichromosome, covalently closed circular (ccc) DNA, within the nucleus of infected hepatocytes and the expression of the regulatory Hepatitis B virus X protein (HBx). Interestingly, nuclear HBx redirects host epigenetic machinery to activate cccDNA transcription. In this Perspective, we provide an overview of recent advances in understanding the regulation of cccDNA and the mechanistic and functional roles of HBx. We also describe the progress toward targeting both cccDNA and HBx for therapeutic purposes. Finally, we outline standing questions in the field and propose complementary chemical biology approaches to address them.
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Affiliation(s)
- Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Robert E. Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
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32
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Abstract
Cells are continuously subjected to an array of reactive/toxic chemical species which are produced both endogenously through metabolic pathways and taken up exogenously by diet and exposure to drugs or toxins. As a result, proteins often undergo non-enzymatic covalent modifications (NECMs) by these species, which can alter protein structure, function, stability, and binding partner affinity. NECMs accumulate over time and are linked to various diseases such as Alzheimer's disease, cancer, and diabetes. In the cellular proteome, histones have some of the longest half-lives, making them prime targets for NECMs. In addition, histones have emerged as key regulators of transcription, a function that is primarily controlled by modification of their tails. These modifications are usually installed or removed enzymatically, but recent evidence suggests that some may also occur non-enzymatically. Despite the vast knowledge detailing the relationship between histone modifications and gene regulation, NECMs on histones remain poorly explored. A major reason for this difference stems from the fact that, unlike their enzymatically installed counterparts, NECMs are difficult to both control and test in vivo. Here, we review advances in our understanding of the effect non-enzymatic covalent modifications (NECMs) have on the epigenetic landscape, cellular fate, and their implications in disease. Cumulatively, this illustrates how the epigenetic code is directly toxified by chemicals and detoxified by corresponding eraser enzymes.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas A. Prescott
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Igor Maksimovic
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Yael David
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY
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Zheng Q, Omans ND, Leicher R, Osunsade A, Agustinus AS, Finkin-Groner E, D'Ambrosio H, Liu B, Chandarlapaty S, Liu S, David Y. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nat Commun 2019; 10:1289. [PMID: 30894531 PMCID: PMC6426841 DOI: 10.1038/s41467-019-09192-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Cellular proteins continuously undergo non-enzymatic covalent modifications (NECMs) that accumulate under normal physiological conditions and are stimulated by changes in the cellular microenvironment. Glycation, the hallmark of diabetes, is a prevalent NECM associated with an array of pathologies. Histone proteins are particularly susceptible to NECMs due to their long half-lives and nucleophilic disordered tails that undergo extensive regulatory modifications; however, histone NECMs remain poorly understood. Here we perform a detailed analysis of histone glycation in vitro and in vivo and find it has global ramifications on histone enzymatic PTMs, the assembly and stability of nucleosomes, and chromatin architecture. Importantly, we identify a physiologic regulation mechanism, the enzyme DJ-1, which functions as a potent histone deglycase. Finally, we detect intense histone glycation and DJ-1 overexpression in breast cancer tumors. Collectively, our results suggest an additional mechanism for cellular metabolic damage through epigenetic perturbation, with implications in pathogenesis.
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Affiliation(s)
- Qingfei Zheng
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Nathaniel D Omans
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - Rachel Leicher
- Laboratory of Nanoscale Biophysics and Biochemistry, Rockefeller University, New York, NY, 10065, USA
- Tri-institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Adewola Osunsade
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
| | - Albert S Agustinus
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Efrat Finkin-Groner
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hannah D'Ambrosio
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bo Liu
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, Rockefeller University, New York, NY, 10065, USA
| | - Yael David
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA.
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Osunsade A, Prescott NA, Hebert JM, Ray DM, Jmeian Y, Lorenz IC, David Y. A Robust Method for the Purification and Characterization of Recombinant Human Histone H1 Variants. Biochemistry 2019; 58:171-176. [PMID: 30585724 PMCID: PMC6541009 DOI: 10.1021/acs.biochem.8b01060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Higher order compaction of the eukaryotic genome is key to the regulation of all DNA-templated processes, including transcription. This tightly controlled process involves the formation of mononucleosomes, the fundamental unit of chromatin, packaged into higher order architectures in an H1 linker histone-dependent process. While much work has been done to delineate the precise mechanism of this event in vitro and in vivo, major gaps still exist, primarily due to a lack of molecular tools. Specifically, there has never been a successful purification and biochemical characterization of all human H1 variants. Here we present a robust method to purify H1 and illustrate its utility in the purification of all somatic variants and one germline variant. In addition, we performed a first ever side-by-side biochemical comparison, which revealed a gradient of nucleosome binding affinities and compaction capabilities. These data provide new insight into H1 redundancy and lay the groundwork for the mechanistic investigation of disease-driving mutations.
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Affiliation(s)
- Adewola Osunsade
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
| | - Jakob M. Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
| | - Devin M. Ray
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
- Tri-Institutional MD-PhD Program, New York, NY
| | - Yazen Jmeian
- Tri-Institutional Therapeutics Discovery Institute, New York, NY
| | - Ivo C. Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, NY
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY
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Abstract
Chromosomes present one of most challenging of all substrates for biochemical study. This is because genomic DNA is physically associated with an astonishing collection of nuclear factors, which serve to not only store the nucleic acid in a stable form, but also grant access to the information it encodes when needed. Understanding this complex molecular choreography is central to the field of epigenetics. One of the great challenges in this area is to move beyond correlative type information, which is now in abundant supply, to the point where we can truly connect the dots at the molecular level. Establishing such causal relationships requires precise manipulation of the covalent structure of chromatin. Tools for this purpose are currently in short supply, creating an opportunity that, as we will argue in this Perspective, is well suited to the sensibilities of the chemist.
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Affiliation(s)
- Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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Altun M, Walter TS, Kramer HB, Herr P, Iphöfer A, Boström J, David Y, Komsany A, Ternette N, Navon A, Stuart DI, Ren J, Kessler BM. The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages. PLoS One 2015; 10:e0115344. [PMID: 25590432 PMCID: PMC4295869 DOI: 10.1371/journal.pone.0115344] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/21/2014] [Indexed: 01/10/2023] Open
Abstract
Ovarian tumor domain containing proteases cleave ubiquitin (Ub) and ubiquitin-like polypeptides from proteins. Here we report the crystal structure of human otubain 2 (OTUB2) in complex with a ubiquitin-based covalent inhibitor, Ub-Br2. The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs) bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs. In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains. N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.
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Affiliation(s)
- Mikael Altun
- Target Discovery Institute, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7FZ, United Kingdom
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden
| | - Thomas S. Walter
- Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Holger B. Kramer
- Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford, OX1 3DQ, United Kingdom
| | - Patrick Herr
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden
| | - Alexander Iphöfer
- Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Johan Boström
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden
| | - Yael David
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alia Komsany
- Target Discovery Institute, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7FZ, United Kingdom
| | - Nicola Ternette
- Target Discovery Institute, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7FZ, United Kingdom
| | - Ami Navon
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - David I. Stuart
- Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, United Kingdom
- * E-mail: (BMK); (JR)
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7FZ, United Kingdom
- * E-mail: (BMK); (JR)
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Berko D, Herkon O, Braunstein I, Isakov E, David Y, Ziv T, Navon A, Stanhill A. Inherent asymmetry in the 26S proteasome is defined by the ubiquitin receptor RPN13. J Biol Chem 2014; 289:5609-18. [PMID: 24429290 DOI: 10.1074/jbc.m113.509380] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The 26S double-capped proteasome is assembled in a hierarchic event that is orchestrated by dedicated set of chaperons. To date, all stoichiometric subunits are considered to be present in equal ratios, thus providing symmetry to the double-capped complex. Here, we show that although the vast majority (if not all) of the double-capped 26S proteasomes, both 19S complexes, contain the ubiquitin receptor Rpn10/S5a, only one of these 19S particles contains the additional ubiquitin receptor Rpn13, thereby defining asymmetry in the 26S proteasome. These results were validated in yeast and mammals, utilizing biochemical and unbiased AQUA-MS methodologies. Thus, the double-capped 26S proteasomes are asymmetric in their polyubiquitin binding capacity. Our data point to a potential new role for ubiquitin receptors as directionality factors that may participate in the prevention of simultaneous substrates translocation into the 20S from both 19S caps.
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Affiliation(s)
- Dikla Berko
- From the Department of Biochemistry, The Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Yuan L, Wu Q, Jiang Y, Li T, Yin F, David Y, Ge Y. Incorporating Trade-Off in Knowledge Modeling of Parotid Dose Sparing in Head and Neck IMRT. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.1893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Pomerantz Y, Elbaz J, Ben-Eliezer I, Reizel Y, David Y, Galiani D, Nevo N, Navon A, Dekel N. From ubiquitin-proteasomal degradation to CDK1 inactivation: requirements for the first polar body extrusion in mouse oocytes. FASEB J 2012; 26:4495-505. [PMID: 22859367 DOI: 10.1096/fj.12-209866] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Completion of the first meiotic division, manifested by extrusion of the first polar body (PBI), depends on proteasomal degradation of cyclin B1 and securin and the subsequent respective CDK1 inactivation and chromosome segregation. We aimed at identifying the polyubiquitin signal that mediates proteasomal action and at a better characterization of the role of CDK1 inactivation at this stage of meiosis. Microinjections of mutated ubiquitin proteins into mouse oocytes revealed that interference with lysine-11 polyubiquitin chains abrogated chromosome segregation and reduced PBI extrusion by 63% as compared to WT ubiquitin-injected controls. Inactivation of CDK1 in oocytes arrested at first metaphase by a proteasome inhibitor fully rescued PBI extrusion. However, removal of CDK1 inhibition failed to allow progression to the second metaphase, rather, inducing PBI reengulfment in 62% of the oocytes. Inhibition of either PLK1 or MEK1/2 during the first anaphase changed spindle dimensions. The PLK1 inhibitor also blocked PBI emission and prevented RhoA translocation. Our results identified lysine-11 rather than the canonic lysine-48 ubiquitin chains as the degradation signal in oocytes resuming meiosis, further disclosing that CDK1 inactivation is necessary and sufficient for PBI emission. This information significantly contributes to our understanding of faulty chromosome segregation that may lead to aneuploidy.
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Affiliation(s)
- Yael Pomerantz
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel
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David Y, Ternette N, Edelmann MJ, Ziv T, Gayer B, Sertchook R, Dadon Y, Kessler BM, Navon A. E3 ligases determine ubiquitination site and conjugate type by enforcing specificity on E2 enzymes. J Biol Chem 2011; 286:44104-44115. [PMID: 21965653 DOI: 10.1074/jbc.m111.234559] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-conjugating enzymes (E2s) have a dominant role in determining which of the seven lysine residues of ubiquitin is used for polyubiquitination. Here we show that tethering of a substrate to an E2 enzyme in the absence of an E3 ubiquitin ligase is sufficient to promote its ubiquitination, whereas the type of the ubiquitin conjugates and the identity of the target lysine on the substrate are promiscuous. In contrast, when an E3 enzyme is introduced, a clear decision between mono- and polyubiquitination is made, and the conjugation type as well as the identity of the target lysine residue on the substrate becomes highly specific. These features of the E3 can be further regulated by auxiliary factors as exemplified by MDMX (Murine Double Minute X). In fact, we show that this interactor reconfigures MDM2-dependent ubiquitination of p53. Based on several model systems, we propose that although interaction with an E2 is sufficient to promote substrate ubiquitination the E3 molds the reaction into a specific, physiologically relevant protein modification.
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Affiliation(s)
- Yael David
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nicola Ternette
- The Henry Wellcome Building for Molecular Physiology, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Mariola J Edelmann
- The Henry Wellcome Building for Molecular Physiology, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Tamar Ziv
- Smoler Proteomics Center, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Batya Gayer
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sertchook
- Faculty of Biochemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yakir Dadon
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Benedikt M Kessler
- The Henry Wellcome Building for Molecular Physiology, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ami Navon
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.
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Shimshon L, Michaeli A, Hadar R, Nutt SL, David Y, Navon A, Waisman A, Tirosh B. SUMOylation of Blimp-1 promotes its proteasomal degradation. FEBS Lett 2011; 585:2405-9. [PMID: 21722636 DOI: 10.1016/j.febslet.2011.06.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 06/13/2011] [Accepted: 06/15/2011] [Indexed: 11/28/2022]
Abstract
B lymphocyte induced maturation protein-1 (Blimp-1) is a transcription repressor of the Krueppel-like family. Blimp-1 plays important roles in developmental processes, such as of germ cells and hair follicle stem cells. In B lymphocytes Blimp-1 orchestrates the terminal differentiation into plasma cells. We discovered that Blimp-1 undergoes SUMOylation by SUMO-1. This SUMOylation is modulated by the SUMO protease SENP1. While Blimp-1 is relatively stable in 293T cells, a fusion with SUMO1 rendered it to rapid proteasomal degradation. Increase in SENP1 activity stabilized Blimp-1, while a decrease promoted its degradation. Our data indicate that SUMOylation of Blimp-1 regulates its intracellular stability.
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Affiliation(s)
- Livnat Shimshon
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University, Jerusalem, Israel
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Mungrue K, Nixon C, David Y, Dookwah D, Durga S, Greene K, Mohammed H. Trinidadian women's knowledge, perceptions, and preferences regarding cesarean section: How do they make choices? Int J Womens Health 2010; 2:387-91. [PMID: 21151686 PMCID: PMC2990908 DOI: 10.2147/ijwh.s12857] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objectives The objective of this study is to determine the awareness of perception and attitude toward cesarean section (CS) in a high-user setting. Design and methods A cross-sectional design using multistage sampling methods was used to select participants from antenatal and postnatal clinics in a primary health care setting in north Trinidad. A multi-item structured questionnaire was designed and administered by in-depth interviews. Sociodemographic data and data about history of previous pregnancies and outcomes and about knowledge and perceptions of CSs were collected from women aged 16 years and older. Results Of the women who were eligible for entry into the study, 368 participated. However, participants chose not to respond to some questions. The majority of women (46.2%) were found to have very little information from which to make informed decisions about selecting CS as the preferred choice of delivery. Their preference was significantly associated with the perception of safety (maternal or fetal death, P = 0.001), difficulty (complications to mother and baby, P = 0.001), and pain (P = 0.001). Notwithstanding, persons who received information from health care professionals (odds ratio [OR], 1.9; confidence interval, 1.50–2.33) were more likely to have high or adequate levels of information about CSs. Data were analyzed using SPSS software, and ORs were calculated using logistic regression. Conclusion The majority of women attending antenatal and postnatal clinics in north Trinidad were not sufficiently knowledgeable about CS to enable them to make informed choices. In addition, the information obtained was from an unreliable source, emphasizing the need for information on CS to form a component of a structured antenatal education program.
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Affiliation(s)
- K Mungrue
- Faculty of Medical Sciences, Department of Paraclinical Sciences, Public Health & Primary Care Unit, The University of the West Indies, St Augustine, Trinidad and Tobago.
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Uche-Nwachi EO, Odekunle A, Jacinto S, Burnett M, Clapperton M, David Y, Durga S, Greene K, Jarvis J, Nixon C, Seereeram R, Poon-King C, Singh R. Anaemia in pregnancy: associations with parity, abortions and child spacing in primary healthcare clinic attendees in Trinidad and Tobago. Afr Health Sci 2010; 10:66-70. [PMID: 20811527 PMCID: PMC2895803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVE To determine the prevalence of anaemia in antenatal clinic attendees; to investigate the effects of parity, age, gravidity, previous abortions, child spacing and other factors on the prevalence of anaemia in pregnancy. METHODS This was a retrospective and cross-sectional study. Antenatal records of 2287 pregnant women attending 40 public healthcare centres from January 2000 to December 2005 in Trinidad and Tobago were used. Data pertaining to the investigated variables were recorded. The national prevalence of anaemia was calculated and chi-square tests, odds ratios and logistic regression were used to assess the relationship between anaemia and each variable. RESULTS The prevalence of anaemia was 15.3% (95% CI 13.4%, 16.6%). No significant difference in the prevalence of anaemia was found among the different clinics or counties. At the first haemoglobin reading, age was inversely related to the presence of anaemia, whereas gestational age at first visit was directly related. At the final haemoglobin reading, parity, gravidity, and previous spontaneous abortions were directly related to the prevalence of anaemia, while the number of visits was inversely related. Age was inversely associated to the severity of anaemia while gravidity was directly related. CONCLUSION The prevalence of anaemia decreased by 18.7% from 1967. Despite this positive indication, women under 24 years and those commencing antenatal care after the first trimester are still at a higher risk for developing anaemia. Early commencement of antenatal care and close monitoring of the risk groups identified should be strongly advocated.
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Affiliation(s)
- E O Uche-Nwachi
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Abstract
The ubiquitin-proteasome pathway plays a crucial role in many cellular processes by degrading substrates tagged by polyubiquitin chains, linked mostly through lysine 48 of ubiquitin. Although polymerization of ubiquitin via its six other lysine residues exists in vivo as part of various physiological pathways, the molecular mechanisms that determine the type of polyubiquitin chains remained largely unknown. We undertook a systematic, in vitro, approach to evaluate the role of E2 enzymes in determining the topology of polyubiquitin. Because this study was performed in the absence of an E3 enzyme, our data indicate that the E2 enzymes are capable of directing the ubiquitination process to distinct subsets of ubiquitin lysines, depending on the specific E2 utilized. Moreover, our findings are in complete agreement with prior analyses of lysine preference assigned to certain E2s in the context of E3 (in vitro and in vivo). Finally, our findings support the rising notion that the functional unit of E2 is a dimer. To our knowledge, this is the first systematic indication for the involvement of E2 enzymes in specifying polyubiquitin chain assembly.
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Affiliation(s)
- Yael David
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
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Shahar A, Reuveny S, David Y, Budu C, Shainberg A. Cerebral neurons, skeletal myoblasts, and cardiac muscle cells cultured on macroporous beads. Biotechnol Bioeng 2009; 43:826-31. [PMID: 18615806 DOI: 10.1002/bit.260430817] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Biodegradable macroporous spherical microcarriers (MCs) offer a suitable substrate for adhesion, growth, and differentiation of cerebral neurons, skeletal myoblasts, and cardiac cells. The cavernous structure of these gelatin beads supplies a large surface and a tridimensional habitat for cell propagation. Within hours from their seeding, all three cell types became firmly attached to the MCs, forming cell-MC aggregates, which remained floating in the medium. Neuronal aggregates were composed mainly of single or groups of perikarya, and their sprouted nerve processes formed a ramified network. In skeletal muscle aggregates, fusion of myoblasts into myotubes occurred within 5 days. The myotubes, arranged in bundles having the same orientation, became striated and the whole aggregate, or parts of it, contracted spontaneously. Cardiac cells divided in the aggregate to form one or more layers of flat cells, which exhibited single microvilli. The cells were interconnected at uneven intervals and the whole aggregate contracted actively. Morphological and biochemical analysis of sampled aggregates ensured that cells reached the proper stage of maturation and could be used for either physiological and pharmacological studies or implantation into injured or dystrophic tissue.
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Affiliation(s)
- A Shahar
- Department of Virology, Israel Institute for Biological Research, Ness-Ziona 70450, Israel
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Abstract
Appropriate deployment of technological innovation contributes to improvement in the quality of healthcare delivered, the containment of cost, and access to the healthcare system. Hospitals have been allocating a significant portion of their resources to procuring and managing capital assets; they are continuously faced with demands for new medical equipment and are asked to manage existing inventory for which they are not well prepared. To objectively manage their investment, hospitals are developing medical technology management programs that need pertinent information and planning methodology for integrating new equipment into existing operations as well as for optimizing costs of ownership of all equipment. Clinical engineers can identify technological solutions based on the matching of new medical equipment with hospital's objectives. They can review their institution's overall technological position, determine strengths and weaknesses, develop equipment-selection criteria, supervise installations, train users and monitor post procurement performance to assure meeting of goals. This program, together with cost accounting analysis, will objectively guide the capital assets decision-making process. Cost accounting analysis is a multivariate function that includes determining the amount, based upon a strategic plan and financial resources, of funding to be allocated annually for medical equipment acquisition and replacement. Often this function works closely with clinical engineering to establish equipment useful life and prioritization of acquisition, upgrade, and replacement of inventory within budget confines and without conducting time consuming, individual financial capital project evaluations.
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Affiliation(s)
- Y David
- Biomedical Engineering 1-3650, Texas Children's Hospital, 6621 Fannin, Houston, TX 77030, USA
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47
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David Y. The Center for Telemedicine Law. Telemed J 1999; 1:401-2. [PMID: 10165344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Y David
- Center for Telemedicine Law, Washington, D.C., USA
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49
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Abstract
When brain death in children occurs, commonly the scalp feels cold despite a normal core temperature. This phenomenon might reflect absent cerebral blood flow and metabolic activity. The authors, therefore, measured rectal-scalp temperature differences in critically ill comatose children to test the hypothesis that a particular temperature difference may correlate with clinical brain death. In a prospective cohort study set in a pediatric intensive care unit, rectal-scalp, rectal-abdomen, and rectal-mastoid temperatures in critically ill comatose children older than 18 months of age were measured before and during brain death evaluations. Twelve children were enrolled. Clinical criteria for brain death were met by seven patients, and five patients survived. All of the seven children who died had rectal-scalp temperature differences greater than 4 degrees C (mean = 6.7, range = 6.0-7.4) at the time of clinical brain death. No survivor had a rectal-scalp temperature difference of 4 degrees C at any time (mean = 3.4, range = 2.9-3.9). Rectal-scalp temperature differences of those who died and those who survived were significantly different at the P < 0.005 level. Rectal-abdomen and rectal-mastoid temperature differences did not correlate with clinical brain death or rectal-scalp temperature difference. In this preliminary study a rectal-scalp temperature difference of greater than 4 degrees C correlates with clinical criteria for brain death in children.
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Affiliation(s)
- G Miller
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston 77030, USA
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50
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Goddard-Finegold J, Louis PT, Rodriguez DL, David Y, Contant CF, Rolfe P. Correlation of near infrared spectroscopy cerebral blood flow estimations and microsphere quantitations in newborn piglets. Biol Neonate 1998; 74:376-84. [PMID: 9742267 DOI: 10.1159/000014056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We compared cerebral blood flow (CBF) estimated using transmission mode near infrared spectroscopy (NIRS) and a modification of the Fick principle with CBF quantitations by radioactive microspheres (MSs) in newborn piglets. Thirteen piglets were studied during steady state, ischemia, and during two reflow periods. NIRS and MS flows were not significantly different during any measurement period. NIRS flows were compared to total brain blood flows and to regional brain blood flows quantitated with MSs and correlated best with temporal cortical flows. Linear regression analysis of the NIRS flows plotted against MS-quantitated temporal cortical flows showed r = 0.71. Thus, CBFs obtained with NIRS were not significantly different from, showed the same directional changes, and correlated acceptably with flows quantitated by MSs.
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Affiliation(s)
- J Goddard-Finegold
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.
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