1
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Karami Y, Bignon E. Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad. Comput Struct Biotechnol J 2024; 23:1387-1396. [PMID: 38596314 PMCID: PMC11001638 DOI: 10.1016/j.csbj.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Gene activity is tightly controlled by reversible chemical modifications called epigenetic marks, which are of various types and modulate gene accessibility without affecting the DNA sequence. Despite an increasing body of evidence demonstrating the role of oxidative-type modifications of histones in gene expression regulation, there remains a complete absence of structural data at the atomistic level to understand the molecular mechanisms behind their regulatory action. Owing to μs time-scale MD simulations and protein communication networks analysis, we describe the impact of histone H3 hyperoxidation (i.e., S-sulfonylation) on the nucleosome core particle dynamics. Our results reveal the atomic-scale details of the intrinsic structural networks within the canonical histone core and their perturbation by hyperoxidation of the histone H3 C110. We show that this modification involves local rearrangements of the communication networks and destabilizes the dyad, and that one modification is enough to induce a maximal structural signature. Our results suggest that cysteine hyperoxidation in the nucleosome core particle might favor its disassembly.
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Affiliation(s)
- Yasaman Karami
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France
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2
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Xu S, Chen T, Yu J, Wan L, Zhang J, Chen J, Wei W, Li X. Insights into the regulatory role of epigenetics in moyamoya disease: Current advances and future prospectives. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102281. [PMID: 39188306 PMCID: PMC11345382 DOI: 10.1016/j.omtn.2024.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Moyamoya disease (MMD) is a progressive steno-occlusive cerebrovascular disorder that predominantly affecting East Asian populations. The intricate interplay of distinct and overlapping mechanisms, including genetic associations such as the RNF213-p.R4810K variant, contributes to the steno-occlusive lesions and moyamoya vessels. However, genetic mutations alone do not fully elucidate the occurrence of MMD, suggesting a potential role for epigenetic factors. Accruing evidence has unveiled the regulatory role of epigenetic markers, including DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), in regulating pivotal cellular and molecular processes implicated in the pathogenesis of MMD by modulating endothelial cells and smooth muscle cells. The profile of these epigenetic markers in cerebral vasculatures and circulation has been determined to identify potential diagnostic biomarkers and therapeutic targets. Furthermore, in vitro studies have demonstrated the multifaceted effects of modulating specific epigenetic markers on MMD pathogenesis. These findings hold great potential for the discovery of novel therapeutic targets, translational studies, and clinical applications. In this review, we comprehensively summarize the current understanding of epigenetic mechanisms, including DNA methylation, histone modifications, and ncRNAs, in the context of MMD. Furthermore, we discuss the potential challenges and opportunities that lie ahead in this rapidly evolving field.
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Affiliation(s)
- Shuangxiang Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tongyu Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jin Yu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Lei Wan
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jianjian Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jincao Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Wei
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xiang Li
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- Sino-Italian Ascula Brain Science Joint Laboratory, Wuhan University, Wuhan 430071, China
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3
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Lin YY, Müller P, Karagianni E, Hepp N, Mueller-Planitz F, Vanderlinden W, Lipfert J. Epigenetic Histone Modifications H3K36me3 and H4K5/8/12/16ac Induce Open Polynucleosome Conformations via Different Mechanisms. J Mol Biol 2024; 436:168671. [PMID: 38908785 DOI: 10.1016/j.jmb.2024.168671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/28/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Nucleosomes are the basic compaction unit of chromatin and nucleosome structure and their higher-order assemblies regulate genome accessibility. Many post-translational modifications alter nucleosome dynamics, nucleosome-nucleosome interactions, and ultimately chromatin structure and gene expression. Here, we investigate the role of two post-translational modifications associated with actively transcribed regions, H3K36me3 and H4K5/8/12/16ac, in the contexts of tri-nucleosome arrays that provide a tractable model system for quantitative single-molecule analysis, while enabling us to probe nucleosome-nucleosome interactions. Direct visualization by AFM imaging reveals that H3K36me3 and H4K5/8/12/16ac nucleosomes adopt significantly more open and loose conformations than unmodified nucleosomes. Similarly, magnetic tweezers force spectroscopy shows a reduction in DNA outer turn wrapping and nucleosome-nucleosome interactions for the modified nucleosomes. The results suggest that for H3K36me3 the increased breathing and outer DNA turn unwrapping seen in mononucleosomes propagates to more open conformations in nucleosome arrays. In contrast, the even more open structures of H4K5/8/12/16ac nucleosome arrays do not appear to derive from the dynamics of the constituent mononucleosomes, but are driven by reduced nucleosome-nucleosome interactions, suggesting that stacking interactions can overrule DNA breathing of individual nucleosomes. We anticipate that our methodology will be broadly applicable to reveal the influence of other post-translational modifications and to observe the activity of nucleosome remodelers.
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Affiliation(s)
- Yi-Yun Lin
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Peter Müller
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Evdoxia Karagianni
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany; Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands; School of Physics and Astronomy, University of Edinburg, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
| | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands.
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4
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Nguyen MU, Iqbal J, Potgieter S, Huang W, Pfeffer J, Woo S, Zhao C, Lawlor M, Yang R, Rizly R, Halstead A, Dent S, Sáenz JB, Zheng H, Yuan ZF, Sidoli S, Ellison CE, P. Verzi M. KAT2A and KAT2B prevent double-stranded RNA accumulation and interferon signaling to maintain intestinal stem cell renewal. SCIENCE ADVANCES 2024; 10:eadl1584. [PMID: 39110797 PMCID: PMC11305398 DOI: 10.1126/sciadv.adl1584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Histone acetyltransferases KAT2A and KAT2B are paralogs highly expressed in the intestinal epithelium, but their functions are not well understood. In this study, double knockout of murine Kat2 genes in the intestinal epithelium was lethal, resulting in robust activation of interferon signaling and interferon-associated phenotypes including the loss of intestinal stem cells. Use of pharmacological agents and sterile organoid cultures indicated a cell-intrinsic double-stranded RNA trigger for interferon signaling. Acetyl-proteomics and sequencing of immunoprecipitated double-stranded RNA were used to interrogate the mechanism behind this response, which identified mitochondria-encoded double-stranded RNA as the source of intrinsic interferon signaling. Kat2a and Kat2b therefore play an essential role in regulating mitochondrial functions and maintaining intestinal health.
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Affiliation(s)
- Mai-Uyen Nguyen
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Jahangir Iqbal
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Sarah Potgieter
- Department of Animal Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Winston Huang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Julie Pfeffer
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Sean Woo
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Matthew Lawlor
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Richard Yang
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Rahma Rizly
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Angela Halstead
- Division of Gastroenterology, Departments of Medicine and Molecular Cell Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Sharon Dent
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - José B. Sáenz
- Division of Gastroenterology, Departments of Medicine and Molecular Cell Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Zuo-Fei Yuan
- St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Simone Sidoli
- Albert Einstein College of Medicine, The Bronx, NY, USA
| | - Christopher E. Ellison
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers Cancer Institute of New Jersey, Rutgers Center for Lipid Research, Division of Environmental & Population Health Biosciences, EOHSI, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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5
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Helgudóttir SS, Johnsen KB, Routhe LG, Rasmussen CLM, Thomsen MS, Moos T. Upregulation of Transferrin Receptor 1 (TfR1) but Not Glucose Transporter 1 (GLUT1) or CD98hc at the Blood-Brain Barrier in Response to Valproic Acid. Cells 2024; 13:1181. [PMID: 39056763 PMCID: PMC11275047 DOI: 10.3390/cells13141181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Transferrin receptor 1 (TfR1), glucose transporter 1 (GLUT1), and CD98hc are candidates for targeted therapy at the blood-brain barrier (BBB). Our objective was to challenge the expression of TfR1, GLUT1, and CD98hc in brain capillaries using the histone deacetylase inhibitor (HDACi) valproic acid (VPA). METHODS Primary mouse brain capillary endothelial cells (BCECs) and brain capillaries isolated from mice injected intraperitoneally with VPA were examined using RT-qPCR and ELISA. Targeting to the BBB was performed by injecting monoclonal anti-TfR1 (Ri7217)-conjugated gold nanoparticles measured using ICP-MS. RESULTS In BCECs co-cultured with glial cells, Tfrc mRNA expression was significantly higher after 6 h VPA, returning to baseline after 24 h. In vivo Glut1 mRNA expression was significantly higher in males, but not females, receiving VPA, whereas Cd98hc mRNA expression was unaffected by VPA. TfR1 increased significantly in vivo after VPA, whereas GLUT1 and CD98hc were unchanged. The uptake of anti-TfR1-conjugated nanoparticles was unaltered by VPA despite upregulated TfR expression. CONCLUSIONS VPA upregulates TfR1 in brain endothelium in vivo and in vitro. VPA does not increase GLUT1 and CD98hc proteins. The increase in TfR1 does not result in higher anti-TfR1 antibody targetability, suggesting targeting sufficiently occurs with available transferrin receptors without further contribution from accessory VPA-induced TfR1.
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Affiliation(s)
- Steinunn Sara Helgudóttir
- Neurobiology Research and Drug Delivery (NRD), Department of Health Science and Technology, Aalborg University, 9260 Gistrup, Denmark
| | - Kasper Bendix Johnsen
- Section for Biotherapeutic Engineering and Drug Targeting, Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lisa Greve Routhe
- Neurobiology Research and Drug Delivery (NRD), Department of Health Science and Technology, Aalborg University, 9260 Gistrup, Denmark
| | | | - Maj Schneider Thomsen
- Neurobiology Research and Drug Delivery (NRD), Department of Health Science and Technology, Aalborg University, 9260 Gistrup, Denmark
| | - Torben Moos
- Neurobiology Research and Drug Delivery (NRD), Department of Health Science and Technology, Aalborg University, 9260 Gistrup, Denmark
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6
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Ma W, Ding X, Xu J, Poon TCW. CHHM: a Manually Curated Catalogue of Human Histone Modifications Revealing Hotspot Regions and Unique Distribution Patterns. Int J Biol Sci 2024; 20:3760-3772. [PMID: 39113691 PMCID: PMC11302869 DOI: 10.7150/ijbs.95954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/13/2024] [Indexed: 08/10/2024] Open
Abstract
Histone modification is one of the key elements in epigenetic control and plays important roles in regulation of biological processes and disease development. Currently, records of human histone modifications with various levels of confidence in evidence are scattered in various knowledgebases and databases. In the present study, a curated catalogue of human histone modifications, CHHM, was obtained by manual retrieval, evidence assessment, and integration of modification records from 10 knowledgebases/databases and 3 complementary articles. CHHM contains 6612 nonredundant modification entries covering 31 types of modifications (including 9 types of emerging modifications) and 2 types of histone-DNA crosslinks, that were identified in 11 H1 variants, 21 H2A variants, 21 H2B variants, 9 H3 variants, and 2 H4 variants. For ease of visualization and accessibility, modification entries are presented with aligned protein sequences in an Excel file. Confidence level in evidence is provided for each entry. Acylation modifications contribute to the highest number of modification entries in CHHM. This supports that cellular metabolic status plays a very important role in epigenetic control. CHHM reveals modification hotspot regions and uneven distribution of the modification entries across the histone families. Such uneven distribution may suggest that a particular histone family is more susceptible to certain types of modifications. CHHM not only serves as an important and user-friendly resource for biomedical and clinical researches involving histone modifications and transcriptional regulation, but also provides new insights for basic researches in the mechanism of human histone modifications and epigenetic control.
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Affiliation(s)
| | | | | | - Terence Chuen Wai Poon
- Institute of Translational Medicine, Centre for Precision Medicine Research and Training, MoE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, 999078, China
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7
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Fox GC, Poncha KF, Smith BR, van der Maas LN, Robbins NN, Graham B, Dowen JM, Strahl BD, Young NL, Jain K. Histone H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation. J Biol Chem 2024; 300:107527. [PMID: 38960040 PMCID: PMC11338103 DOI: 10.1016/j.jbc.2024.107527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024] Open
Abstract
In an unmodified state, positively charged histone N-terminal tails engage nucleosomal DNA in a manner which restricts access to not only the underlying DNA but also key tail residues subject to binding and/or modification. Charge-neutralizing modifications, such as histone acetylation, serve to disrupt this DNA-tail interaction, facilitating access to such residues. We previously showed that a polyacetylation-mediated chromatin "switch" governs the read-write capability of H3K4me3 by the MLL1 methyltransferase complex. Here, we discern the relative contributions of site-specific acetylation states along the H3 tail and extend our interrogation to other chromatin modifiers. We show that the contributions of H3 tail acetylation to H3K4 methylation by MLL1 are highly variable, with H3K18 and H3K23 acetylation exhibiting robust stimulatory effects and that this extends to the related H3K4 methyltransferase complex, MLL4. We show that H3K4me1 and H3K4me3 are found preferentially co-enriched with H3 N-terminal tail proteoforms bearing dual H3K18 and H3K23 acetylation (H3{K18acK23ac}). We further show that this effect is specific to H3K4 methylation, while methyltransferases targeting other H3 tail residues (H3K9, H3K27, & H3K36), a methyltransferase targeting the nucleosome core (H3K79), and a kinase targeting a residue directly adjacent to H3K4 (H3T3) are insensitive to tail acetylation. Together, these findings indicate a unique and robust stimulation of H3K4 methylation by H3K18 and H3K23 acetylation and provide key insight into why H3K4 methylation is often associated with histone acetylation in the context of active gene expression.
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Affiliation(s)
- Geoffrey C Fox
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Karl F Poncha
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - B Rutledge Smith
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lara N van der Maas
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | - Jill M Dowen
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA.
| | - Kanishk Jain
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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8
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Patel R, Onyema A, Tang PK, Loverde SM. Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:4709-4726. [PMID: 38865599 PMCID: PMC11200259 DOI: 10.1021/acs.jcim.4c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
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Affiliation(s)
- Rutika Patel
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Augustine Onyema
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Phu K. Tang
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Sharon M. Loverde
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Physics, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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9
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Lee J, Bao X. Comparative Review on Cancer Pathology from Aberrant Histone Chaperone Activity. Int J Mol Sci 2024; 25:6403. [PMID: 38928110 PMCID: PMC11203986 DOI: 10.3390/ijms25126403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Histone chaperones are integral to chromatin dynamics, facilitating the assembly and disassembly of nucleosomes, thereby playing a crucial role in regulating gene expression and maintaining genomic stability. Moreover, they prevent aberrant histone interactions prior to chromatin assembly. Disruption in histone chaperone function may result in genomic instability, which is implicated in pathogenesis. This review aims to elucidate the role of histone chaperones in cancer pathologies and explore their potential as therapeutic targets. Histone chaperones have been found to be dysregulated in various cancers, with alterations in expression levels, mutations, or aberrant interactions leading to tumorigenesis and cancer progression. In addition, this review intends to highlight the molecular mechanisms of interactions between histone chaperones and oncogenic factors, underscoring their roles in cancer cell survival and proliferation. The dysregulation of histone chaperones is significantly correlated with cancer development, establishing them as active contributors to cancer pathology and viable targets for therapeutic intervention. This review advocates for continued research into histone chaperone-targeted therapies, which hold potential for precision medicine in oncology. Future advancements in understanding chaperone functions and interactions are anticipated to lead to novel cancer treatments, enhancing patient care and outcomes.
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Affiliation(s)
| | - Xiucong Bao
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China;
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10
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Tang Y, Cui G, Liu H, Han Y, Cai C, Feng Z, Shen H, Zeng S. Converting "cold" to "hot": epigenetics strategies to improve immune therapy effect by regulating tumor-associated immune suppressive cells. Cancer Commun (Lond) 2024; 44:601-636. [PMID: 38715348 PMCID: PMC11194457 DOI: 10.1002/cac2.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 06/26/2024] Open
Abstract
Significant developments in cancer treatment have been made since the advent of immune therapies. However, there are still some patients with malignant tumors who do not benefit from immunotherapy. Tumors without immunogenicity are called "cold" tumors which are unresponsive to immunotherapy, and the opposite are "hot" tumors. Immune suppressive cells (ISCs) refer to cells which can inhibit the immune response such as tumor-associated macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), regulatory T (Treg) cells and so on. The more ISCs infiltrated, the weaker the immunogenicity of the tumor, showing the characteristics of "cold" tumor. The dysfunction of ISCs in the tumor microenvironment (TME) may play essential roles in insensitive therapeutic reaction. Previous studies have found that epigenetic mechanisms play an important role in the regulation of ISCs. Regulating ISCs may be a new approach to transforming "cold" tumors into "hot" tumors. Here, we focused on the function of ISCs in the TME and discussed how epigenetics is involved in regulating ISCs. In addition, we summarized the mechanisms by which the epigenetic drugs convert immunotherapy-insensitive tumors into immunotherapy-sensitive tumors which would be an innovative tendency for future immunotherapy in "cold" tumor.
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Affiliation(s)
- Yijia Tang
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Guangzu Cui
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Haicong Liu
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Ying Han
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Changjing Cai
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Ziyang Feng
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Hong Shen
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
- National Clinical Resaerch Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaHunanChina
| | - Shan Zeng
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
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11
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Fox GC, Poncha KF, Smith BR, van der Maas LN, Robbins NN, Graham B, Dowen JM, Strahl BD, Young NL, Jain K. H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.590588. [PMID: 38798640 PMCID: PMC11118386 DOI: 10.1101/2024.05.13.590588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In an unmodified state, positively charged histone N-terminal tails engage nucleosomal DNA in a manner which restricts access to not only the underlying DNA, but also key tail residues subject to binding and/or modification. Charge-neutralizing modifications, such as histone acetylation, serve to disrupt this DNA-tail interaction, facilitating access to such residues. We previously showed that a polyacetylation-mediated chromatin "switch" governs the read-write capability of H3K4me3 by the MLL1 methyltransferase complex. Here, we discern the relative contributions of site-specific acetylation states along the H3 tail and extend our interrogation to other chromatin modifiers. We show that the contributions of H3 tail acetylation to H3K4 methylation by MLL1 are highly variable, with H3K18 and H3K23 acetylation exhibiting robust stimulatory effects, and that this extends to the related H3K4 methyltransferase complex, MLL4. We show that H3K4me1 and H3K4me3 are found preferentially co-enriched with H3 N-terminal tail proteoforms bearing dual H3K18 and H3K23 acetylation (H3{K18acK23ac}). We further show that this effect is specific to H3K4 methylation, while methyltransferases targeting other H3 tail residues (H3K9, H3K27, & H3K36), a methyltransferase targeting the nucleosome core (H3K79), and a kinase targeting a residue directly adjacent to H3K4 (H3T3) are insensitive to tail acetylation. Together, these findings indicate a unique and robust stimulation of H3K4 methylation by H3K18 and H3K23 acetylation and provide key insight into why H3K4 methylation is often associated with histone acetylation in the context of active gene expression.
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Affiliation(s)
- Geoffrey C. Fox
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
| | - Karl F. Poncha
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - B. Rutledge Smith
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
| | - Lara N. van der Maas
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
| | | | | | - Jill M. Dowen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
| | - Brian D. Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
| | - Nicolas L. Young
- Verna & Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Kanishk Jain
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC
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12
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Morioka S, Oishi T, Hatazawa S, Kakuta T, Ogoshi T, Umeda K, Kodera N, Kurumizaka H, Shibata M. High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes. NANO LETTERS 2024; 24:5246-5254. [PMID: 38602428 DOI: 10.1021/acs.nanolett.4c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Each nucleosome contains four types of histone proteins, each with a histone tail. These tails are essential for the epigenetic regulation of gene expression through post-translational modifications (PTMs). However, their influence on nucleosome dynamics at the single-molecule level remains undetermined. Here, we employed high-speed atomic force microscopy to visualize nucleosome dynamics in the absence of the N-terminal tail of each histone or all of the N-terminal tails. Loss of all tails stripped 6.7 base pairs of the nucleosome from the histone core, and the DNA entry-exit angle expanded by 18° from that of wild-type nucleosomes. Tail-less nucleosomes, particularly those without H2B and H3 tails, showed a 10-fold increase in dynamics, such as nucleosome sliding and DNA unwrapping/wrapping, within 0.3 s, emphasizing their role in histone-DNA interactions. Our findings illustrate that N-terminal histone tails stabilize the nucleosome structure, suggesting that histone tail PTMs modulate nucleosome dynamics.
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Affiliation(s)
- Shin Morioka
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takumi Oishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takahiro Kakuta
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Tomoki Ogoshi
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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13
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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14
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Yang C, Ge L, Yu X, Lazarovici P, Zheng W. Artemisinin Confers Cytoprotection toward Hydrogen Peroxide-Induced Cell Apoptosis in Retinal Pigment Epithelial Cells in Correlation with the Increased Acetylation of Histone H4 at Lysine 8. Molecules 2024; 29:1789. [PMID: 38675608 PMCID: PMC11051841 DOI: 10.3390/molecules29081789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
Increased oxidative stress is one of the critical pathologies inducing age-related macular degeneration (AMD), characterized by retinal pigment epithelial (RPE) cell damage and death. The unbalanced acetylation and deacetylation of histones have been implicated in AMD pathogenesis or hydrogen peroxide (H2O2)-induced cell damage. Therefore, strategies aimed at controlling the balance between acetylation and deacetylation may effectively protect RPE cells from oxidative damage. Artemisinin is an antimalarial lactone drug derived from Artemisia annua, with antioxidant activity known to modulate histone acetylation in the brain, but its effect on the retina is unknown. In this study, we aimed to investigate whether Artemisinin exerts a cytoprotective effect on oxidative stress-induced apoptosis in RPE cells by regulating histone acetylation. We hypothesized that Artemisinin confers cytoprotection toward H2O2-induced apoptosis in RPE cells through this mechanism. In the present study, we found that Artemisinin at a sub-clinic dosage of 20 μM inhibited the H2O2-induced cell viability decrease and B-cell lymphoma 2 (Bcl-2) protein level decrease and attenuated the H2O2-induced decrease in the histone H4 lysine (Lys) 8 acetylation [Acetyl-H4 (Lys 8)] level in the retinal RPE cell line D407. As expected, histone deacetylase inhibitor Trichostatin A at the concentration of 250 nM increased the Acetyl-H4 (Lys 8) level in D407 cells and attenuated the H2O2-induced cell viability decrease and apoptosis. Similar findings were obtained using adult RPE (ARPE)19 cells, another human RPE cell line, and primary human RPE cell cultures. In conclusion, these results confirmed our hypothesis and indicated that Artemisinin attenuated H2O2-induced apoptosis in apparent correlation with the increase in the Acetyl-H4 (Lys 8) level, which is associated with gene transcription and cell survival. By modulating histone acetylation, Artemisinin may restore the balance between acetylation and deacetylation and enhance the resistance and survival of RPE cells under oxidative stress. Our study provides novel mechanistic insights into the effect of Artemisinin on histone acetylation and apoptosis in RPE cells and supports the potential application of Artemisinin in the prevention and/or treatment of AMD.
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Affiliation(s)
- Chao Yang
- Department of Pharmaceutical Science, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China; (C.Y.); (L.G.)
| | - Lijun Ge
- Department of Pharmaceutical Science, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China; (C.Y.); (L.G.)
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiyong Yu
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China;
| | - Philip Lazarovici
- School of Pharmacy Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112002, Israel;
| | - Wenhua Zheng
- Department of Pharmaceutical Science, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China; (C.Y.); (L.G.)
- Zhuhai UM Science & Technology Research Institute, Zhuhai 519000, China
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15
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Bryant L, Sangree A, Clark K, Bhoj E. Histone 3.3-related chromatinopathy: missense variants throughout H3-3A and H3-3B cause a range of functional consequences across species. Hum Genet 2024; 143:497-510. [PMID: 36867246 DOI: 10.1007/s00439-023-02536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
There has been considerable recent interest in the role that germline variants in histone genes play in Mendelian syndromes. Specifically, missense variants in H3-3A and H3-3B, which both encode Histone 3.3, were discovered to cause a novel neurodevelopmental disorder, Bryant-Li-Bhoj syndrome. Most of the causative variants are private and scattered throughout the protein, but all seem to have either a gain-of-function or dominant negative effect on protein function. This is highly unusual and not well understood. However, there is extensive literature about the effects of Histone 3.3 mutations in model organisms. Here, we collate the previous data to provide insight into the elusive pathogenesis of missense variants in Histone 3.3.
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Affiliation(s)
- Laura Bryant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Annabel Sangree
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Clark
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth Bhoj
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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16
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Blum K, Bowirrat A, Baron D, Elman I, Makale MT, Cadet JL, Thanos PK, Hanna C, Ahmed R, Gondre-Lewis MC, Dennen CA, Braverman ER, Soni D, Carney P, Khalsa J, Modestino EJ, Barh D, Bagchi D, Badgaiyan RD, McLaughlin T, Cortese R, Ceccanti M, Murphy KT, Gupta A, Makale MT, Sunder K, Gold MS. Identification of stress-induced epigenetic methylation onto dopamine D2 gene and neurological and behavioral consequences. GENE & PROTEIN IN DISEASE 2024; 3:10.36922/gpd.1966. [PMID: 38766604 PMCID: PMC11100097 DOI: 10.36922/gpd.1966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The D2 dopamine receptor (DRD2) gene has garnered substantial attention as one of the most extensively studied genes across various neuropsychiatric disorders. Since its initial association with severe alcoholism in 1990, particularly through the identification of the DRD2 Taq A1 allele, numerous international investigations have been conducted to elucidate its role in different conditions. As of February 22, 2024, there are 5485 articles focusing on the DRD2 gene listed in PUBMED. There have been 120 meta-analyses with mixed results. In our opinion, the primary cause of negative reports regarding the association of various DRD2 gene polymorphisms is the inadequate screening of controls, not adequately eliminating many hidden reward deficiency syndrome behaviors. Moreover, pleiotropic effects of DRD2 variants have been identified in neuropsychologic, neurophysiologic, stress response, social stress defeat, maternal deprivation, and gambling disorder, with epigenetic DNA methylation and histone post-translational negative methylation identified as discussed in this article. There are 70 articles listed in PUBMED for DNA methylation and 20 articles listed for histone methylation as of October 19, 2022. For this commentary, we did not denote DNA and/or histone methylation; instead, we provided a brief summary based on behavioral effects. Based on the fact that Blum and Noble characterized the DRD2 Taq A1 allele as a generalized reward gene and not necessarily specific alcoholism, it now behooves the field to find ways to either use effector moieties to edit the neuroepigenetic insults or possibly harness the idea of potentially removing negative mRNA-reduced expression by inducing "dopamine homeostasis."
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Affiliation(s)
- Kenneth Blum
- Department of Molecular Biology, Adelson School of Medicine, Ariel University, Ariel, Israel
- Division of Addiction Research & Education, Center for Sports, Exercise & Mental Health, Western University of the Health Sciences, Pomona, CA, United States of America
- Institute of Psychology, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Psychiatry, University of Vermont, Burlington, VT 05405, United States of America
- Department of Psychiatry, Wright University Boonshoft School of Medicine, Dayton, OH, United States of America
- Division of Nutrigenomics, The Kenneth Blum Behavioral Neurogenetic Institute, Austin, TX United States of America
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
- Department of Nutrigenomic Research, Victory Nutrition International, Inc., Bonita Springs, FL, United States of America
- Division of Personalized Neuromodulation Research, Sunder Foundation, Palm Springs, CA, United States of America
| | - Abdalla Bowirrat
- Department of Molecular Biology, Adelson School of Medicine, Ariel University, Ariel, Israel
| | - David Baron
- Division of Addiction Research & Education, Center for Sports, Exercise & Mental Health, Western University of the Health Sciences, Pomona, CA, United States of America
| | - Igor Elman
- Division of Personalized Neuromodulation Research, Sunder Foundation, Palm Springs, CA, United States of America
- Cambridge Health Alliance, Harvard Medical School, Cambridge, MA, United States of America
| | - Milan T. Makale
- Department of Radiation Medicine and Applied Sciences, UC San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States of America
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD., United States of America
| | - Panayotis K. Thanos
- Behavioral Neuropharmacology and Neuroimaging Laboratory on Addictions, Clinical Research Institute on Addictions, Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biosciences, State University of New York at Buffalo, Buffalo, NY, United States of America; Department of Psychology, State University of New York at Buffalo, Buffalo, NY., United States of America
| | - Colin Hanna
- Behavioral Neuropharmacology and Neuroimaging Laboratory on Addictions, Clinical Research Institute on Addictions, Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biosciences, State University of New York at Buffalo, Buffalo, NY, United States of America; Department of Psychology, State University of New York at Buffalo, Buffalo, NY., United States of America
| | - Rania Ahmed
- Behavioral Neuropharmacology and Neuroimaging Laboratory on Addictions, Clinical Research Institute on Addictions, Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biosciences, State University of New York at Buffalo, Buffalo, NY, United States of America; Department of Psychology, State University of New York at Buffalo, Buffalo, NY., United States of America
| | - Marjorie C. Gondre-Lewis
- Department of Anatomy, Howard University College of Medicine, and Developmental Neuropsychopharmacology Laboratory, Howard University College of Medicine, Washington D.C., United States of America
| | - Catherine A. Dennen
- Department of Family Medicine, Jefferson Health Northeast, Philadelphia, PA, United States of America
| | - Eric R. Braverman
- Division of Nutrigenomics, The Kenneth Blum Behavioral Neurogenetic Institute, Austin, TX United States of America
| | - Diwanshu Soni
- Division of Addiction Research & Education, Center for Sports, Exercise & Mental Health, Western University of the Health Sciences, Pomona, CA, United States of America
| | - Paul Carney
- Division Pediatric Neurology, University of Missouri, School of Medicine, Columbia, MO., United States of America
| | - Jag Khalsa
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, School of Medicine and Health Sciences, Washington, DC, United States of America
| | - Edward J. Modestino
- Department of Psychology, Curry College, Milton, MA., United States of America
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debasis Bagchi
- Department of Pharmaceutical Sciences, Texas Southern University College of Pharmacy and Health Sciences, Houston, TX, United States of America
| | - Rajendra D. Badgaiyan
- Department of Psychiatry, Case Western Reserve University School of Medicine, Cleveland OH., 44106, USA and Department of Psychiatry, Mt. Sinai School of Medicine, New York, NY, United States of America
| | - Thomas McLaughlin
- Division of Nutrigenomics, The Kenneth Blum Behavioral Neurogenetic Institute, Austin, TX United States of America
| | - Rene Cortese
- Department of Child Health – Child Health Research Institute, & Department of Obstetrics, Gynecology and Women’s Health School of Medicine, University of Missouri, MO, United States of America
| | - Mauro Ceccanti
- Alcohol Addiction Program, Latium Region Referral Center, Sapienza University of Rome, Roma, Italy
| | - Kevin T. Murphy
- Division of Personalized Neuromodulation and Patient Care, PeakLogic, LLC, Del Mar, CA, United States of America
| | - Ashim Gupta
- Future Biologics, Lawrenceville, Georgia, 30043, United States of America
| | - Miles T. Makale
- Department of Psychology, UC San Diego, 3855 Health Sciences Drive, La Jolla, CA 92093-0819, United States of America
| | - Keerthy Sunder
- Division of Personalized Neuromodulation Research, Sunder Foundation, Palm Springs, CA, United States of America
- Department of Psychiatry, UC Riverside School of Medicine, Riverside, CA, United States of America
| | - Mark S. Gold
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States of America
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17
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Shah A, Choudhary A, Jain M, Perumal S, Patel V, Parmar G, Patel A. Discovery of novel anticancer flavonoids as potential HDAC2 inhibitors: virtual screening approach based on molecular docking, DFT and molecular dynamics simulations studies. 3 Biotech 2024; 14:83. [PMID: 38375511 PMCID: PMC10874358 DOI: 10.1007/s13205-023-03912-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/30/2023] [Indexed: 02/21/2024] Open
Abstract
Virtual screening of a library of 329 flavonoids obtained from the NPACT database was performed to find out potential novel HDAC2 inhibitors. Eleven out of 329 selected flavonoids were screened based on molecular docking studies, as they have higher binding affinities than the standard drugs vorinostat and panobinostat. All screened compounds occupying the catalytic site of HDAC2 showed important molecular interaction with Zn2+ and other important amino acids in the binding pocket. The screened compounds were validated using ADMET filtration and bioactivity prediction from which we obtained six compounds, NPACT00270, NPACT00676, NPACT00700, NPACT001008, NPACT001054, and NPACT001407, which were analyzed using DFT studies. DFT studies were performed for all six screened flavonoids. In DFT studies, three flavonoids, NPACT00700, NPACT001008, and NPACT001407, were found to be better based on HOMO-LUMO and molecular electrostatic potential (MEP) analyses. Furthermore, MD simulations were performed for 100 ns for the three compounds. In the MD analysis, NPACT001407 was found to be more stable in the active site of HDAC2 as zinc formed a coordination bond with ASP181, HIS183, ASP269, and GLY305, along with two hydroxyl groups of the ligand. Our findings reveal that these flavonoids can interact as ligands with the active site of HDAC2. Because of the absence of a hydroxamate group in flavonoids, there are no possibilities for the formation of isocyanate. This suggests that the major drawback of current HDACs inhibitors may be solved. Further experimental validation is needed to understand the selectivity of flavonoids as HDAC2 inhibitors. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03912-5.
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Affiliation(s)
- Ashish Shah
- Department of Pharmacy, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat India
| | - Aarti Choudhary
- Department of Pharmacy, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat India
| | - Manav Jain
- Division of Clinical Pharmacology, Department of Pediatrics, University of Utah, Salt Lake City, UT USA
| | - Sathiaseelan Perumal
- Department of Chemistry, Bishop Heber College, Tiruchirappalli, Tamil Nadu India
| | - Vaishali Patel
- Department of Pharmaceutics, Laxminarayan Dev College of Pharmacy, Bharuch, Gujarat India
| | - Ghanshyam Parmar
- Department of Pharmacy, Sumandeep Vidyapeeth Deemed to be University, Vadodara, Gujarat India
| | - Ashish Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Anand, Gujarat India
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18
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Teichmann T, Malacarne P, Zehr S, Günther S, Pflüger-Müller B, Warwick T, Brandes RP. NCoR1 limits angiogenic capacity by altering Notch signaling. J Mol Cell Cardiol 2024; 188:65-78. [PMID: 38359551 DOI: 10.1016/j.yjmcc.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024]
Abstract
Corepressors negatively regulate gene expression by chromatin compaction. Targeted regulation of gene expression could provide a means to control endothelial cell phenotype. We hypothesize that by targeting corepressor proteins, endothelial angiogenic function can be improved. To study this, the expression and function of nuclear corepressors in human umbilical vein endothelial cells (HUVEC) and in murine organ culture was studied. RNA-seq revealed that nuclear receptor corepressor 1 (NCoR1), silencing mediator of retinoid and thyroid hormone receptors (SMRT) and repressor element-1 silencing transcription factor (REST) are the highest expressed corepressors in HUVECs. Knockout and knockdown strategies demonstrated that the depletion of NCoR1 increased the angiogenic capacity of endothelial cells, whereas depletion of SMRT or REST did not. Interestingly, the effect was VEGF signaling independent. NCoR1 depletion significantly upregulated angiogenesis-associated genes, especially tip cell genes, including ESM1, DLL4 and NOTCH4, as observed by RNA- and ATAC-seq. Confrontation assays comparing cells with and without NCoR1-deficiency revealed that loss of NCoR1 promotes a tip-cell position during spheroid sprouting. Moreover, a proximity ligation assay identified NCoR1 as a direct binding partner of the Notch-signaling-related transcription factor RBPJk. Luciferase assays showed that siRNA-mediated knockdown of NCOR1 promotes RBPJk activity. Furthermore, NCoR1 depletion prompts upregulation of several elements in the Notch signaling cascade. Downregulation of NOTCH4, but not NOTCH1, prevented the positive effect of NCOR1 knockdown on spheroid outgrowth. Collectively, these data indicate that decreasing NCOR1 expression is an attractive approach to promote angiogenic function.
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Affiliation(s)
- Tom Teichmann
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Pedro Malacarne
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Simonida Zehr
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart- and Lung Research (MPI-HLR), Bad Nauheim 61231, Germany
| | - Beatrice Pflüger-Müller
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany.
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main 60590, Germany; German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany.
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19
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Van Moortel L, Verhee A, Thommis J, Houtman R, Melchers D, Delhaye L, Van Leene C, Hellemans M, Gevaert K, Eyckerman S, De Bosscher K. Selective Modulation of the Human Glucocorticoid Receptor Compromises GR Chromatin Occupancy and Recruitment of p300/CBP and the Mediator Complex. Mol Cell Proteomics 2024; 23:100741. [PMID: 38387774 PMCID: PMC10957501 DOI: 10.1016/j.mcpro.2024.100741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
Exogenous glucocorticoids are frequently used to treat inflammatory disorders and as adjuncts for the treatment of solid cancers. However, their use is associated with severe side effects and therapy resistance. Novel glucocorticoid receptor (GR) ligands with a patient-validated reduced side effect profile have not yet reached the clinic. GR is a member of the nuclear receptor family of transcription factors and heavily relies on interactions with coregulator proteins for its transcriptional activity. To elucidate the role of the GR interactome in the differential transcriptional activity of GR following treatment with the selective GR agonist and modulator dagrocorat compared to classic (ant)agonists, we generated comprehensive interactome maps by high-confidence proximity proteomics in lung epithelial carcinoma cells. We found that dagrocorat and the antagonist RU486 both reduced GR interaction with CREB-binding protein/p300 and the mediator complex compared to the full GR agonist dexamethasone. Chromatin immunoprecipitation assays revealed that these changes in GR interactome were accompanied by reduced GR chromatin occupancy with dagrocorat and RU486. Our data offer new insights into the role of differential coregulator recruitment in shaping ligand-specific GR-mediated transcriptional responses.
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Affiliation(s)
- Laura Van Moortel
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annick Verhee
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jonathan Thommis
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | | | - Louis Delhaye
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Chloé Van Leene
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Madeleine Hellemans
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB-UGent Inflammation Research Center, VIB Institute, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Karolien De Bosscher
- VIB-UGent Center for Medical Biotechnology, VIB Institute, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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20
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Klimczak S, Śliwińska A. Epigenetic regulation of inflammation in insulin resistance. Semin Cell Dev Biol 2024; 154:185-192. [PMID: 36109307 DOI: 10.1016/j.semcdb.2022.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022]
Abstract
Epigenetics focuses on the study of changes in gene expression based on modifications that do not interfere with the DNA sequence, such as DNA methylation, post-translational histone modification, and non-coding RNA. Epigenetic changes regulate the expression of many genes, including inflammatory ones. Chronic inflammation is often accompanied by insulin resistance (IR), which is characteristic of inter alia type 2 diabetes. Recently, it has been reported that altered epigenetic signature in the promoter regions of inflammatory genes may contribute to the development of IR. Therefore, the aim of this review is to present the current state of knowledge regarding the epigenetic regulation of inflammation in IR. It includes original papers published from 2014 to 2022. It appears that hypomethylation of the SOCS3 gene increases the risk of IR, while the alteration of H3K4me in the NF-kB promoter promotes changes in inflammatory phenotype. Finally, in hyperglycemic states associated with IR, altered levels of H3K4/K9m3 and H3K9/K14ac result in increased expression of the inflammatory cytokine IL-6. In addition, numerous miRNAs have been identified that may become a target in the fight against diseases related to inflammation and IR. Future studies should examine the epigenetic modifications of IR inflammatory markers associated with environmental factors.
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Affiliation(s)
- S Klimczak
- Department of Nucleic Acid Biochemistry, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland; AllerGen, Center of Personalized Medicine, 97-300 Piotrkow Trybunalski, Poland.
| | - A Śliwińska
- Department of Nucleic Acid Biochemistry, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland.
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21
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Nosella ML, Kim TH, Huang SK, Harkness RW, Goncalves M, Pan A, Tereshchenko M, Vahidi S, Rubinstein JL, Lee HO, Forman-Kay JD, Kay LE. Poly(ADP-ribosyl)ation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates. Mol Cell 2024; 84:429-446.e17. [PMID: 38215753 DOI: 10.1016/j.molcel.2023.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Nucleosomes, the basic structural units of chromatin, hinder recruitment and activity of various DNA repair proteins, necessitating modifications that enhance DNA accessibility. Poly(ADP-ribosyl)ation (PARylation) of proteins near damage sites is an essential initiation step in several DNA-repair pathways; however, its effects on nucleosome structural dynamics and organization are unclear. Using NMR, cryoelectron microscopy (cryo-EM), and biochemical assays, we show that PARylation enhances motions of the histone H3 tail and DNA, leaving the configuration of the core intact while also stimulating nuclease digestion and ligation of nicked nucleosomal DNA by LIG3. PARylation disrupted interactions between nucleosomes, preventing self-association. Addition of LIG3 and XRCC1 to PARylated nucleosomes generated condensates that selectively partition DNA repair-associated proteins in a PAR- and phosphorylation-dependent manner in vitro. Our results establish that PARylation influences nucleosomes across different length scales, extending from the atom-level motions of histone tails to the mesoscale formation of condensates with selective compositions.
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Affiliation(s)
- Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Tae Hun Kim
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuya Kate Huang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert W Harkness
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Monica Goncalves
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alisia Pan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Lewis E Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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22
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Wang X, Martínez-Fernández L, Zhang Y, Wu P, Kohler B, Improta R, Chen J. Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation. J Am Chem Soc 2024; 146:1839-1848. [PMID: 38194423 DOI: 10.1021/jacs.3c04567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Peicong Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via De Amicis 95, Napoli I-80145, Italy
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, Shanxi, China
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23
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Olichwier A, Sowka A, Balatskyi VV, Gan AM, Dziewulska A, Dobrzyn P. SCD1-related epigenetic modifications affect hormone-sensitive lipase (Lipe) gene expression in cardiomyocytes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119608. [PMID: 37852324 DOI: 10.1016/j.bbamcr.2023.119608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Stearoyl-CoA desaturase 1 (SCD1) is an enzyme that is involved in the regulation of lipolysis in the heart. SCD1 also affects epigenetic mechanisms, such as DNA and histone modifications, in various tissues. Both epigenetic modifications and changes in lipid metabolism are involved in the heart's response to hypoxia. The present study tested the hypothesis that SCD1 and epigenetic modifications interact to control lipolysis in cardiomyocytes under normoxic and hypoxic conditions. We found that the inhibition of SCD1 activity and loss of SCD1 expression reduced global DNA methylation levels, DNA methyltransferase (DNMT) activity, and DNMT1 expression in HL-1 cardiomyocytes and the mouse heart. We also found that the inhibition of adipose triglyceride lipase is involved in the control of global DNA methylation levels in cardiomyocytes in an SCD1-independent manner. Additionally, SCD1 inhibition reduced expression of the hormone-sensitive lipase (Lipe) gene through an increase in methylation of the Lipe gene promoter. Under hypoxic conditions, SCD1 inhibition abolished hypoxia-inducible transcription factor 1α, likely through decreases in histone deacetylase, protein kinase A, and abhydrolase domain containing 5 protein levels, leading to the attenuation of DNA hypomethylation by DNMT1. Hypoxia led to demethylation of the Lipe promoter in cardiomyocytes with SCD1 inhibition, which increased Lipe expression. These results indicate that SCD1 is involved in the control of epigenetic mechanisms in the heart and may affect Lipe expression through changes in methylation in its promoter region. Therefore, SCD1 may be considered a key player in the epigenetic response to normoxia and hypoxia in cardiomyocytes.
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Affiliation(s)
- Adam Olichwier
- Laboratory of Molecular Medical Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Adrian Sowka
- Laboratory of Molecular Medical Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Volodymyr V Balatskyi
- Laboratory of Molecular Medical Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Ana-Maria Gan
- Laboratory of Molecular Medical Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Anna Dziewulska
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Pawel Dobrzyn
- Laboratory of Molecular Medical Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland.
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24
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El Hadad J, Schreiner P, Vavricka SR, Greuter T. The Genetics of Inflammatory Bowel Disease. Mol Diagn Ther 2024; 28:27-35. [PMID: 37847439 PMCID: PMC10787003 DOI: 10.1007/s40291-023-00678-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/18/2023]
Abstract
The genetic background of inflammatory bowel disease, both Crohn's disease and ulcerative colitis, has been known for more than 2 decades. In the last 20 years, genome-wide association studies have dramatically increased our knowledge on the genetics of inflammatory bowel disease with more than 200 risk genes having been identified. Paralleling this increasing knowledge, the armamentarium of inflammatory bowel disease medications has been growing constantly. With more available therapeutic options, treatment decisions become more complex, with still many patients experiencing a debilitating disease course and a loss of response to treatment over time. With a better understanding of the disease, more effective personalized treatment strategies are looming on the horizon. Genotyping has long been considered a strategy for treatment decisions, such as the detection of thiopurine S-methyltransferase and nudix hydrolase 15 polymorphisms before the initiation of azathioprine. However, although many risk genes have been identified in inflammatory bowel disease, a substantial impact of genetic risk assessment on therapeutic strategies and disease outcome is still missing. In this review, we discuss the genetic background of inflammatory bowel disease, with a particular focus on the latest advances in the field and their potential impact on management decisions.
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Affiliation(s)
- Jasmina El Hadad
- Department of Internal Medicine, Triemli Hospital, Zurich, Switzerland
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Philipp Schreiner
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Stephan R Vavricka
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
- Center for Gastroenterology and Hepatology, Zurich, Switzerland
| | - Thomas Greuter
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland.
- Division of Gastroenterology and Hepatology, University Hospital Lausanne-CHUV, Lausanne, Switzerland.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, GZO Zurich Regional Health Center, Spitalstrasse 66, 8620, Wetzikon, Switzerland.
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25
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Liu J, Fan H, Liang X, Chen Y. Polycomb repressor complex: Its function in human cancer and therapeutic target strategy. Biomed Pharmacother 2023; 169:115897. [PMID: 37981459 DOI: 10.1016/j.biopha.2023.115897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
The Polycomb Repressor Complex (PRC) plays a pivotal role in gene regulation during development and disease, with dysregulation contributing significantly to various human cancers. The intricate interplay between PRC and cellular signaling pathways sheds light on cancer complexity. PRC presents promising therapeutic opportunities, with inhibitors undergoing rigorous evaluation in preclinical and clinical studies. In this review, we emphasize the critical role of PRC complex in gene regulation, particularly PcG proteins mediated chromatin compaction through phase separation. We also highlight the pathological implications of PRC complex dysregulation in various tumors, elucidating underlying mechanisms driving cancer progression. The burgeoning field of therapeutic strategies targeting PRC complexes, notably EZH2 inhibitors, has advanced significantly. However, we explore the need for combination therapies to enhance PRC targeted treatments efficacy, providing a glimpse into the future of cancer therapeutics.
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Affiliation(s)
- Jingrong Liu
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Xinmiao Liang
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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26
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Park S, Athreya A, Carrizo GE, Benning NA, Mitchener MM, Bhanu NV, Garcia BA, Zhang B, Muir TW, Pearce EL, Ha T. Electrostatic encoding of genome organization principles within single native nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570828. [PMID: 38106048 PMCID: PMC10723453 DOI: 10.1101/2023.12.08.570828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The eukaryotic genome, first packed into nucleosomes of about 150 bp around the histone core, is organized into euchromatin and heterochromatin, corresponding to the A and B compartments, respectively. Here, we asked if individual nucleosomes in vivo know where to go. That is, do mono-nucleosomes by themselves contain A/B compartment information, associated with transcription activity, in their biophysical properties? We purified native mono-nucleosomes to high monodispersity and used physiological concentrations of biological polyamines to determine their condensability. The chromosomal regions known to partition into A compartments have low condensability and vice versa. In silico chromatin polymer simulations using condensability as the only input showed that biophysical information needed to form compartments is all contained in single native nucleosomes and no other factors are needed. Condensability is also strongly anticorrelated with gene expression, and especially so near the promoter region and in a cell type dependent manner. Therefore, individual nucleosomes in the promoter know whether the gene is on or off, and that information is contained in their biophysical properties. Comparison with genetic and epigenetic features suggest that nucleosome condensability is a very meaningful axis onto which to project the high dimensional cellular chromatin state. Analysis of condensability using various condensing agents including those that are protein-based suggests that genome organization principle encoded into individual nucleosomes is electrostatic in nature. Polyamine depletion in mouse T cells, by either knocking out ornithine decarboxylase (ODC) or inhibiting ODC, results in hyperpolarized condensability, suggesting that when cells cannot rely on polyamines to translate biophysical properties of nucleosomes to control gene expression and 3D genome organization, they accentuate condensability contrast, which may explain dysfunction known to occur with polyamine deficiency.
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Affiliation(s)
- Sangwoo Park
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Advait Athreya
- Computational and Systems Biology Program, MIT, Cambridge, MA, 02139, USA
| | - Gustavo Ezequiel Carrizo
- Department of Oncology, The Bloomberg–Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nils A. Benning
- Department of Biology, Johns Hopkins University. Baltimore, MD 21218, USA
| | | | - Natarajan V. Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine St. Louis, St. Louis, MO 63110, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine St. Louis, St. Louis, MO 63110, USA
| | - Bin Zhang
- Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Erika L. Pearce
- Department of Oncology, The Bloomberg–Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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27
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Khan P, Singha P, Nag Chaudhuri R. RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes. Mol Cell Biol 2023; 43:596-610. [PMID: 37937370 PMCID: PMC10761024 DOI: 10.1080/10985549.2023.2270912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.
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Affiliation(s)
- Preeti Khan
- Department of Biotechnology, St Xavier’s College, Kolkata, India
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28
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Jana A, Bellver-Sanchis A, Griñán-Ferré C, Banerjee DR. Repurposing of Raltitrexed as an Effective G9a/EHMT2 Inhibitor and Promising Anti-Alzheimer's Agent. ACS Med Chem Lett 2023; 14:1531-1536. [PMID: 37974951 PMCID: PMC10641905 DOI: 10.1021/acsmedchemlett.3c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
Herein, we report for the first time the G9a/EHMT2 inhibition and anti-Alzheimer's activities of the drug raltitrexed. G9a is a lysine methyltransferase that mainly dimethylates the H3K9 of chromatin, which triggers the repression of genes epigenetically, leading to various diseased conditions, including Alzheimer's disease (AD). First, we demonstrate that raltitrexed inhibits G9a at 120 nM. Moreover, raltitrexed lowers the total H3K9me2/H3K9 levels in AD transgenic C. elegans CL2006 worms, indicating that raltitrexed targets G9a directly. As toxicity is the bottleneck in G9a drug discovery, we conducted detailed in silico toxicity (TOPKAT) analyses of raltitrexed and measured the food consumption by C. elegans, demonstrating that raltitrexed's toxicity/function range is safe for the worm's growth. Moreover, we demonstrate that raltitrexed enhances the locomotive function of worms dose-dependently. Finally, we show that raltitrexed reduced the Aβ aggregates in worms up to 47%, highlighting the potential of raltitrexed in AD treatment.
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Affiliation(s)
- Abhisek Jana
- Department
of Chemistry, National Institute of Technology
Durgapur, M G Avenue, Durgapur-713209 , West Bengal, India
| | - Aina Bellver-Sanchis
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, Universitat de Barcelona (NeuroUB), Av. Joan XXIII 27−31, 08028 Barcelona, Spain
| | - Christian Griñán-Ferré
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, Universitat de Barcelona (NeuroUB), Av. Joan XXIII 27−31, 08028 Barcelona, Spain
- Centro
de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Deb Ranjan Banerjee
- Department
of Chemistry, National Institute of Technology
Durgapur, M G Avenue, Durgapur-713209 , West Bengal, India
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29
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Elathram N, Ackermann BE, Clark ET, Dunn SR, Debelouchina GT. Phosphorylated HP1α-Nucleosome Interactions in Phase Separated Environments. J Am Chem Soc 2023; 145:23994-24004. [PMID: 37870432 PMCID: PMC10636758 DOI: 10.1021/jacs.3c06481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
In the nucleus, transcriptionally silent genes are sequestered into heterochromatin compartments comprising nucleosomes decorated with histone H3 Lys9 trimethylation and a protein called HP1α. This protein can form liquid-liquid droplets in vitro and potentially organize heterochromatin through a phase separation mechanism that is promoted by phosphorylation. Elucidating the molecular interactions that drive HP1α phase separation and its consequences on nucleosome structure and dynamics has been challenging due to the viscous and heterogeneous nature of such assemblies. Here, we tackle this problem by a combination of solution and solid-state NMR spectroscopy, which allows us to dissect the interactions of phosphorylated HP1α with nucleosomes in the context of phase separation. Our experiments indicate that phosphorylated human HP1α does not cause any major rearrangements to the nucleosome core, in contrast to the yeast homologue Swi6. Instead, HP1α interacts specifically with the methylated H3 tails and slows the dynamics of the H4 tails. Our results shed light on how phosphorylated HP1α proteins may regulate the heterochromatin landscape, while our approach provides an atomic resolution view of a heterogeneous and dynamic biological system regulated by a complex network of interactions and post-translational modifications.
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Affiliation(s)
- Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Evan T. Clark
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shelby R. Dunn
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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30
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Gemeinhardt TM, Regy RM, Mendiola AJ, Ledterman HJ, Henrickson A, Phan TM, Kim YC, Demeler B, Kim CA, Mittal J, Francis NJ. How a disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564264. [PMID: 37961422 PMCID: PMC10634872 DOI: 10.1101/2023.10.26.564264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The Polycomb Group (PcG) complex PRC1 represses transcription, forms condensates in cells, and modifies chromatin architecture. These processes are connected through the essential, polymerizing Sterile Alpha Motif (SAM) present in the PRC1 subunit Polyhomeotic (Ph). In vitro, Ph SAM drives formation of short oligomers and phase separation with DNA or chromatin in the context of a Ph truncation ("mini-Ph"). Oligomer length is controlled by the long disordered linker (L) that connects the SAM to the rest of Ph--replacing Drosophila PhL with the evolutionarily diverged human PHC3L strongly increases oligomerization. How the linker controls SAM polymerization, and how polymerization and the linker affect condensate formation are not know. We analyzed PhL and PHC3L using biochemical assays and molecular dynamics (MD) simulations. PHC3L promotes mini-Ph phase separation and makes it relatively independent of DNA. In MD simulations, basic amino acids in PHC3L form contacts with acidic amino acids in the SAM. Engineering the SAM to make analogous charge-based contacts with PhL increased polymerization and phase separation, partially recapitulating the effects of the PHC3L. Ph to PHC3 linker swaps and SAM surface mutations alter Ph condensate formation in cells, and Ph function in Drosophila imaginal discs. Thus, SAM-driven phase separation and polymerization are conserved between flies and mammals, but the underlying mechanisms have diverged through changes to the disordered linker.
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Affiliation(s)
- Tim M Gemeinhardt
- Montreal Clinical Research Institute (IRCM), Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Roshan M Regy
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Andrea J Mendiola
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ, USA
| | - Heather J Ledterman
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ, USA
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, The University of Lethbridge, Lethbridge, AB, Canada
| | - Tien M Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, The University of Lethbridge, Lethbridge, AB, Canada
- Department of Chemistry, University of Montana, Missoula, MT, United States
| | - Chongwoo A Kim
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, AZ, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Chemistry, Texas A&M University, College Station, TX, USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Nicole J Francis
- Montreal Clinical Research Institute (IRCM), Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC, Canada
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31
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Baby S, Shinde SD, Kulkarni N, Sahu B. Lysine-Specific Demethylase 1 (LSD1) Inhibitors: Peptides as an Emerging Class of Therapeutics. ACS Chem Biol 2023; 18:2144-2155. [PMID: 37812385 DOI: 10.1021/acschembio.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aberrant expression of the epigenetic regulator lysine-specific demethylase 1 (LSD1) has been associated with the incidence of many diseases, particularly cancer, and it has evolved as a promising epigenetic target over the years for treatment. The advent of LSD1 inhibitor-based clinical utility began with tranylcypromine, and it is now considered an inevitable scaffold in the search for other irreversible novel LSD1 inhibitors (IMG-7289 or bomedemstat, ORY1001 or iadademstat, ORY-2001 or vafidemstat, GSK2879552, and INCB059872). Moreover, numerous reversible inhibitors for LSD1 have been reported in the literature, including clinical candidates CC-90011 (pulrodemstat) and SP-2577 (seclidemstat). There is parallel mining for peptide-based LSD1 inhibitors, which exploits the opportunities in the LSD1 substrate binding pocket. This Review highlights the research progress on reversible and irreversible peptide/peptide-derived LSD1 inhibitors. For the first time, we comprehensively organized the peptide-based LSD1 inhibitors from the design strategy. Peptide inhibitors of LSD1 are classified as H3 peptide and SNAIL1 peptide derivatives, along with miscellaneous peptides that include naturally occurring LSD1 inhibitors.
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Affiliation(s)
- Stephin Baby
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Neeraj Kulkarni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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32
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Wang T, Ye Z, Li Z, Jing D, Fan G, Liu M, Zhuo Q, Ji S, Yu X, Xu X, Qin Y. Lactate-induced protein lactylation: A bridge between epigenetics and metabolic reprogramming in cancer. Cell Prolif 2023; 56:e13478. [PMID: 37060186 PMCID: PMC10542650 DOI: 10.1111/cpr.13478] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/25/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Lactate is not only an endpoint of glycolysis but is gradually being discovered to play the role of a universal metabolic fuel for energy via the 'lactate shuttle' moving between cells and transmitting signals. The glycolytic-dependent metabolism found in tumours and fast-growing cells has made lactate a pivotal player in energy metabolism reprogramming, which enables cells to obtain abundant energy in a short time. Moreover, lactate can provide favourable conditions for tumorigenesis by shaping the acidic tumour microenvironment, recruiting immune cells, etc. and the recently discovered lactate-induced lactylation moves even further on pro-tumorigenesis mechanisms of lactate production, circulation and utilization. As with other epigenetic modifications, lactylation can modify histone proteins to alter the spatial configuration of chromatin, affect DNA accessibility and regulate the expression of corresponding genes. What's more, the degree of lactylation is inseparable from the spatialized lactate concentration, which builds a bridge between epigenetics and metabolic reprogramming. Here, we review the important role of lactate in energy reprogramming, summarize the latest finding of lactylation in tumorigenesis and try to explore therapeutic strategies in oncotherapy that can kill two birds with one stone.
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Affiliation(s)
- Ting Wang
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Zeng Ye
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Zheng Li
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - De‐sheng Jing
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Gui‐xiong Fan
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Meng‐qi Liu
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Qi‐feng Zhuo
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Shun‐rong Ji
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Xian‐jun Yu
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Xiao‐wu Xu
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
| | - Yi Qin
- Department of Pancreatic SurgeryFudan University Shanghai Cancer CenterShanghaiChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Pancreatic Cancer InstituteShanghaiChina
- Pancreatic Cancer InstituteFudan UniversityShanghaiChina
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33
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Lin X, Zong C, Zhang Z, Fang W, Xu P. Progresses in biomarkers for cancer immunotherapy. MedComm (Beijing) 2023; 4:e387. [PMID: 37799808 PMCID: PMC10547938 DOI: 10.1002/mco2.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023] Open
Abstract
Currently, checkpoint inhibitor-based immunotherapy has emerged as prevailing treatment modality for diverse cancers. However, immunotherapy as a first-line therapy has not consistently yielded durable responses. Moreover, the risk of immune-related adverse events increases with combination regimens. Thus, the development of predictive biomarkers is needed to optimize individuals benefit, minimize risk of toxicities, and guide combination approaches. The greatest focus has been on tumor programmed cell death-ligand 1 (PD-L1), microsatellite instability (MSI), and tumor mutational burden (TMB). However, there remains a subject of debate due to thresholds variability and significant heterogeneity. Major unmet challenges in immunotherapy are the discovery and validation of predictive biomarkers. Here, we show the status of tumor PD-L1, MSI, TMB, and emerging data on novel biomarker strategies with oncogenic signaling and epigenetic regulation. Considering the exploration of peripheral and intestinal immunity has served as noninvasive alternative in predicting immunotherapy, this review also summarizes current data in systemic immunity, encompassing solute PD-L1 and TMB, circulating tumor DNA and infiltrating lymphocytes, routine emerging inflammatory markers and cytokines, as well as gut microbiota. This review provides up-to-date information on the evolving field of currently available biomarkers in predicting immunotherapy. Future exploration of novel biomarkers is warranted.
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Affiliation(s)
- Xuwen Lin
- Department of Pulmonary and Critical Care MedicinePeking University Shenzhen HospitalShenzhenGuangdong ProvinceChina
- Department of Internal MedicineShantou University Medical CollegeShantouGuangdong ProvinceChina
| | - Chenyu Zong
- Department of Pulmonary and Critical Care MedicinePeking University Shenzhen HospitalShenzhenGuangdong ProvinceChina
- Department of Internal MedicineZunyi Medical UniversityZunyiGuizhou ProvinceChina
| | - Zhihan Zhang
- Department of Pulmonary and Critical Care MedicinePeking University Shenzhen HospitalShenzhenGuangdong ProvinceChina
| | - Weiyi Fang
- Cancer Research InstituteSchool of Basic Medical ScienceSouthern Medical UniversityGuangzhouGuangdong ProvinceChina
- Cancer CenterIntegrated Hospital of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdong ProvinceChina
| | - Ping Xu
- Department of Pulmonary and Critical Care MedicinePeking University Shenzhen HospitalShenzhenGuangdong ProvinceChina
- Department of Internal MedicineZunyi Medical UniversityZunyiGuizhou ProvinceChina
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34
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Arechaga-Ocampo E. Epigenetics as a determinant of radiation response in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:145-190. [PMID: 38359968 DOI: 10.1016/bs.ircmb.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Radiation therapy is a cornerstone of modern cancer treatment. Treatment is based on depositing focal radiation to the tumor to inhibit cell growth, proliferation and metastasis, and to promote the death of cancer cells. In addition, radiation also affects non-tumor cells in the tumor microenvironmental (TME). Radiation resistance of the tumor cells is the most common cause of treatment failure, allowing survival of cancer cell and subsequent tumor growing. Molecular radioresistance comprises genetic and epigenetic characteristics inherent in cancer cells, or characteristics acquired after exposure to radiation. Furthermore, cancer stem cells (CSCs) and non-tumor cells into the TME as stromal and immune cells have a role in promoting and maintaining radioresistant tumor phenotypes. Different regulatory molecules and pathways distinctive of radiation resistance include DNA repair, survival signaling and cell death pathways. Epigenetic mechanisms are one of the most relevant events that occur after radiotherapy to regulate the expression and function of key genes and proteins in the differential radiation-response. This article reviews recent data on the main molecular mechanisms and signaling pathways related to the biological response to radiotherapy in cancer; highlighting the epigenetic control exerted by DNA methylation, histone marks, chromatin remodeling and m6A RNA methylation on gene expression and activation of signaling pathways related to radiation therapy response.
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Affiliation(s)
- Elena Arechaga-Ocampo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City, Mexico.
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35
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Moleri P, Wilkins BJ. Unnatural Amino Acid Crosslinking for Increased Spatiotemporal Resolution of Chromatin Dynamics. Int J Mol Sci 2023; 24:12879. [PMID: 37629060 PMCID: PMC10454095 DOI: 10.3390/ijms241612879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The utilization of an expanded genetic code and in vivo unnatural amino acid crosslinking has grown significantly in the past decade, proving to be a reliable system for the examination of protein-protein interactions. Perhaps the most utilized amino acid crosslinker, p-benzoyl-(l)-phenylalanine (pBPA), has delivered a vast compendium of structural and mechanistic data, placing it firmly in the upper echelons of protein analytical techniques. pBPA contains a benzophenone group that is activated with low energy radiation (~365 nm), initiating a diradical state that can lead to hydrogen abstraction and radical recombination in the form of a covalent bond to a neighboring protein. Importantly, the expanded genetic code system provides for site-specific encoding of the crosslinker, yielding spatial control for protein surface mapping capabilities. Paired with UV-activation, this process offers a practical means for spatiotemporal understanding of protein-protein dynamics in the living cell. The chromatin field has benefitted particularly well from this technique, providing detailed mapping and mechanistic insight for numerous chromatin-related pathways. We provide here a brief history of unnatural amino acid crosslinking in chromatin studies and outlooks into future applications of the system for increased spatiotemporal resolution in chromatin related research.
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Affiliation(s)
| | - Bryan J. Wilkins
- Department of Chemistry and Biochemistry, Manhattan College, 4513 Manhattan College Parkway, Riverdale, NY 10471, USA
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36
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Mohamed Abdoul-Latif F, Ainane A, Houmed Aboubaker I, Mohamed J, Ainane T. Exploring the Potent Anticancer Activity of Essential Oils and Their Bioactive Compounds: Mechanisms and Prospects for Future Cancer Therapy. Pharmaceuticals (Basel) 2023; 16:1086. [PMID: 37631000 PMCID: PMC10458506 DOI: 10.3390/ph16081086] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide, affecting millions of people each year. Fortunately, the last decades have been marked by considerable advances in the field of cancer therapy. Researchers have discovered many natural substances, some of which are isolated from plants that have promising anti-tumor activity. Among these, essential oils (EOs) and their constituents have been widely studied and shown potent anticancer activities, both in vitro and in vivo. However, despite the promising results, the precise mechanisms of action of EOs and their bioactive compounds are still poorly understood. Further research is needed to better understand these mechanisms, as well as their effectiveness and safety in use. Furthermore, the use of EOs as anticancer drugs is complex, as it requires absolute pharmacodynamic specificity and selectivity, as well as an appropriate formulation for effective administration. In this study, we present a synthesis of recent work on the mechanisms of anticancer action of EOs and their bioactive compounds, examining the results of various in vitro and in vivo studies. We also review future research prospects in this exciting field, as well as potential implications for the development of new cancer drugs.
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Affiliation(s)
- Fatouma Mohamed Abdoul-Latif
- Medicinal Research Institute, Center for Studies and Research of Djibouti, IRM-CERD, Route de l’Aéroport, Haramous, Djibouti City P.O. Box 486, Djibouti;
| | - Ayoub Ainane
- Superior School of Technology of Khenifra, University of Sultan Moulay Slimane, P.O. Box 170, Khenifra 54000, Morocco; (A.A.); (T.A.)
| | | | - Jalludin Mohamed
- Medicinal Research Institute, Center for Studies and Research of Djibouti, IRM-CERD, Route de l’Aéroport, Haramous, Djibouti City P.O. Box 486, Djibouti;
| | - Tarik Ainane
- Superior School of Technology of Khenifra, University of Sultan Moulay Slimane, P.O. Box 170, Khenifra 54000, Morocco; (A.A.); (T.A.)
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37
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Coleman OD, Macdonald J, Thomson B, Ward JA, Stubbs CJ, McAllister TE, Clark S, Amin S, Cao Y, Abboud MI, Zhang Y, Sanganee H, Huber KVM, Claridge TDW, Kawamura A. Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function. Chem Sci 2023; 14:7136-7146. [PMID: 37416723 PMCID: PMC10321576 DOI: 10.1039/d2sc05944d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/15/2023] [Indexed: 07/08/2023] Open
Abstract
Plant homeodomain fingers (PHD-fingers) are a family of reader domains that can recruit epigenetic proteins to specific histone modification sites. Many PHD-fingers recognise methylated lysines on histone tails and play crucial roles in transcriptional regulation, with their dysregulation linked to various human diseases. Despite their biological importance, chemical inhibitors for targeting PHD-fingers are very limited. Here we report a potent and selective de novo cyclic peptide inhibitor (OC9) targeting the Nε-trimethyllysine-binding PHD-fingers of the KDM7 histone demethylases, developed using mRNA display. OC9 disrupts PHD-finger interaction with histone H3K4me3 by engaging the Nε-methyllysine-binding aromatic cage through a valine, revealing a new non-lysine recognition motif for the PHD-fingers that does not require cation-π interaction. PHD-finger inhibition by OC9 impacted JmjC-domain mediated demethylase activity at H3K9me2, leading to inhibition of KDM7B (PHF8) but stimulation of KDM7A (KIAA1718), representing a new approach for selective allosteric modulation of demethylase activity. Chemoproteomic analysis showed selective engagement of OC9 with KDM7s in T cell lymphoblastic lymphoma SUP T1 cells. Our results highlight the utility of mRNA-display derived cyclic peptides for targeting challenging epigenetic reader proteins to probe their biology, and the broader potential of this approach for targeting protein-protein interactions.
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Affiliation(s)
- Oliver D Coleman
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Jessica Macdonald
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Ben Thomson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Jennifer A Ward
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Christopher J Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Tom E McAllister
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
| | - Shane Clark
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Siddique Amin
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
| | - Yimang Cao
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Martine I Abboud
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Yijia Zhang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Hitesh Sanganee
- Emerging Innovations Unit, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Kilian V M Huber
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
| | - Tim D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Akane Kawamura
- School of Natural and Environmental Sciences - Chemistry, Newcastle University Newcastle NE1 7RU UK
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford Roosevelt Drive Old Road Campus Oxford OX3 7BN UK
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38
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Hong ZZ, Yu RR, Zhang X, Webb AM, Burge NL, Poirier MG, Ottesen JJ. Development of Convergent Hybrid Phase Ligation for Efficient and Convenient Total Synthesis of Proteins. Pept Sci (Hoboken) 2023; 115:e24323. [PMID: 37692919 PMCID: PMC10488053 DOI: 10.1002/pep2.24323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 09/12/2023]
Abstract
Simple and efficient total synthesis of homogeneous and chemically modified protein samples remains a significant challenge. Here, we report development of a convergent hybrid phase native chemical ligation (CHP-NCL) strategy for facile preparation of proteins. In this strategy, proteins are split into ~100-residue blocks, and each block is assembled on solid support from synthetically accessible peptide fragments before ligated together into full-length protein in solution. With the new method, we increase the yield of CENP-A synthesis by 2.5-fold compared to the previous hybrid phase ligation approach. We further extend the new strategy to the total chemical synthesis of 212-residue linker histone H1.2 in unmodified, phosphorylated, and citrullinated forms, each from eight peptide segments with only one single purification. We demonstrate that fully synthetic H1.2 replicates the binding interactions of linker histones to intact mononucleosomes, as a proxy for the essential function of linker histones in the formation and regulation of higher order chromatin structure.
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Affiliation(s)
- Ziyong Z. Hong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Ruixuan R. Yu
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Xiaoyu Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Allison M. Webb
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Nathaniel L. Burge
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Michael G. Poirier
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
- Department of Physics, Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Jennifer J. Ottesen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
- Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, Ohio, 43210
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39
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Gómez de Cedrón M, Moreno Palomares R, Ramírez de Molina A. Metabolo-epigenetic interplay provides targeted nutritional interventions in chronic diseases and ageing. Front Oncol 2023; 13:1169168. [PMID: 37404756 PMCID: PMC10315663 DOI: 10.3389/fonc.2023.1169168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023] Open
Abstract
Epigenetic modifications are chemical modifications that affect gene expression without altering DNA sequences. In particular, epigenetic chemical modifications can occur on histone proteins -mainly acetylation, methylation-, and on DNA and RNA molecules -mainly methylation-. Additional mechanisms, such as RNA-mediated regulation of gene expression and determinants of the genomic architecture can also affect gene expression. Importantly, depending on the cellular context and environment, epigenetic processes can drive developmental programs as well as functional plasticity. However, misbalanced epigenetic regulation can result in disease, particularly in the context of metabolic diseases, cancer, and ageing. Non-communicable chronic diseases (NCCD) and ageing share common features including altered metabolism, systemic meta-inflammation, dysfunctional immune system responses, and oxidative stress, among others. In this scenario, unbalanced diets, such as high sugar and high saturated fatty acids consumption, together with sedentary habits, are risk factors implicated in the development of NCCD and premature ageing. The nutritional and metabolic status of individuals interact with epigenetics at different levels. Thus, it is crucial to understand how we can modulate epigenetic marks through both lifestyle habits and targeted clinical interventions -including fasting mimicking diets, nutraceuticals, and bioactive compounds- which will contribute to restore the metabolic homeostasis in NCCD. Here, we first describe key metabolites from cellular metabolic pathways used as substrates to "write" the epigenetic marks; and cofactors that modulate the activity of the epigenetic enzymes; then, we briefly show how metabolic and epigenetic imbalances may result in disease; and, finally, we show several examples of nutritional interventions - diet based interventions, bioactive compounds, and nutraceuticals- and exercise to counteract epigenetic alterations.
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Affiliation(s)
- Marta Gómez de Cedrón
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- Cell Metabolism Unit, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
| | - Rocío Moreno Palomares
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- FORCHRONIC S.L, Avda. Industria, Madrid, Spain
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Stein RA, Riber L. Epigenetic effects of short-chain fatty acids from the large intestine on host cells. MICROLIFE 2023; 4:uqad032. [PMID: 37441522 PMCID: PMC10335734 DOI: 10.1093/femsml/uqad032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
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Affiliation(s)
- Richard A Stein
- Corresponding author. Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA. Tel: +1-917-684-9438; E-mail: ;
| | - Leise Riber
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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Ozden B, Boopathi R, Barlas AB, Lone IN, Bednar J, Petosa C, Kale S, Hamiche A, Angelov D, Dimitrov S, Karaca E. Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox. J Chem Inf Model 2023. [PMID: 37307148 DOI: 10.1021/acs.jcim.2c01520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pioneer transcription factors (PTFs) have the remarkable ability to directly bind to chromatin to stimulate vital cellular processes. In this work, we dissect the universal binding mode of Sox PTF by combining extensive molecular simulations and physiochemistry approaches, along with DNA footprinting techniques. As a result, we show that when Sox consensus DNA is located at the solvent-facing DNA strand, Sox binds to the compact nucleosome without imposing any significant conformational changes. We also reveal that the base-specific Sox:DNA interactions (base reading) and Sox-induced DNA changes (shape reading) are concurrently required for sequence-specific nucleosomal DNA recognition. Among three different nucleosome positions located on the positive DNA arm, a sequence-specific reading mechanism is solely satisfied at the superhelical location 2 (SHL2). While SHL2 acts transparently for solvent-facing Sox binding, among the other two positions, SHL4 permits only shape reading. The final position, SHL0 (dyad), on the other hand, allows no reading mechanism. These findings demonstrate that Sox-based nucleosome recognition is essentially guided by intrinsic nucleosome properties, permitting varying degrees of DNA recognition.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Ramachandran Boopathi
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble 38000, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
- Laboratoire de Biologie et de Modélisation de la Cellule (LBMC), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, 46 Allée d'Italie, Lyon 69007, France
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Imtiaz N Lone
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Jan Bednar
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble 38000, France
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, Illkirch Cedex 67404, France
| | - Dimitar Angelov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Laboratoire de Biologie et de Modélisation de la Cellule (LBMC), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, 46 Allée d'Italie, Lyon 69007, France
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble 38000, France
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
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Xie Z, Zhou Z, Yang S, Zhang S, Shao B. Epigenetic regulation and therapeutic targets in the tumor microenvironment. MOLECULAR BIOMEDICINE 2023; 4:17. [PMID: 37273004 DOI: 10.1186/s43556-023-00126-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/02/2023] [Indexed: 06/06/2023] Open
Abstract
The tumor microenvironment (TME) is crucial to neoplastic processes, fostering proliferation, angiogenesis and metastasis. Epigenetic regulations, primarily including DNA and RNA methylation, histone modification and non-coding RNA, have been generally recognized as an essential feature of tumor malignancy, exceedingly contributing to the dysregulation of the core gene expression in neoplastic cells, bringing about the evasion of immunosurveillance by influencing the immune cells in TME. Recently, compelling evidence have highlighted that clinical therapeutic approaches based on epigenetic machinery modulate carcinogenesis through targeting TME components, including normalizing cells' phenotype, suppressing cells' neovascularization and repressing the immunosuppressive components in TME. Therefore, TME components have been nominated as a promising target for epigenetic drugs in clinical cancer management. This review focuses on the mechanisms of epigenetic modifications occurring to the pivotal TME components including the stroma, immune and myeloid cells in various tumors reported in the last five years, concludes the tight correlation between TME reprogramming and tumor progression and immunosuppression, summarizes the current advances in cancer clinical treatments and potential therapeutic targets with reference to epigenetic drugs. Finally, we summarize some of the restrictions in the field of cancer research at the moment, further discuss several interesting epigenetic gene targets with potential strategies to boost antitumor immunity.
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Affiliation(s)
- Zhuojun Xie
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, South Renmin Road, Sichuan, 610041, Chengdu, China
| | - Zirui Zhou
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, South Renmin Road, Sichuan, 610041, Chengdu, China
| | - Shuxian Yang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, South Renmin Road, Sichuan, 610041, Chengdu, China
| | - Shiwen Zhang
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, South Renmin Road, Sichuan, 610041, Chengdu, China.
| | - Bin Shao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, South Renmin Road, Sichuan, 610041, Chengdu, China.
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Affandi T, Haas A, Ohm AM, Wright GM, Black JC, Reyland ME. PKCδ regulates chromatin remodeling and DNA repair through SIRT6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.541991. [PMID: 37292592 PMCID: PMC10245827 DOI: 10.1101/2023.05.24.541991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein kinase C delta (PKCδ) is a ubiquitous kinase whose function is defined in part by localization to specific cellular compartments. Nuclear PKCδ is both necessary and sufficient for IR-induced apoptosis, while inhibition of PKCδ activity provides radioprotection in vivo. How nuclear PKCδ regulates DNA-damage induced cell death is poorly understood. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double stranded break (DSB) repair through a mechanism that requires SIRT6. Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via non-homologous end joining (NHEJ) and homologous recombination (HR) as evidenced by more rapid formation of NHEJ (DNA-PK) and HR (Rad51) DNA damage foci, increased expression of repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis revealed that PKCδ depletion increases chromatin associated H3K36me2, and reduces ribosylation of KDM2A and chromatin bound KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased expression of SIRT6, and depletion of SIRT6 reverses the changes in chromatin accessibility, histone modification and NHEJ and HR DNA repair seen with PKCδ-depletion. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6-dependent changes in chromatin accessibility to increase DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ.
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Affiliation(s)
- Trisiani Affandi
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ami Haas
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angela M. Ohm
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gregory M. Wright
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joshua C. Black
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary E. Reyland
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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Gaire S, Fabian RL, Adhikari R, Tuma PL, Pegg IL, Sarkar A. Micromechanical Study of Hyperacetylated Nucleosomes Using Single Molecule Transverse Magnetic Tweezers. Int J Mol Sci 2023; 24:ijms24076188. [PMID: 37047156 PMCID: PMC10094661 DOI: 10.3390/ijms24076188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Nucleosomes are stable complexes of DNA and histone proteins that are essential for the proper functioning of the genome. These structures must be unwrapped and disassembled for processes such as gene expression, replication, and repair. Histone post-translational modifications (PTMs) are known to play a significant role in regulating the structural changes of nucleosomes. However, the underlying mechanisms by which these modifications function remain unclear. In this study, we report the results of single molecule micromanipulation experiments on DNA–protein complexes composed of hyperacetylated histone proteins using transverse magnetic tweezers. The experiments were conducted by pre-extending λ-DNA with a force less than 4 pN before introducing hyperacetylated histones into the sample chamber. The DNA shortened as the histones formed complexes with it and the nucleosome arrays were then exposed to increasing tension, resulting in quantized changes in the DNA’s extension with step sizes of (integral multiples of) ~50 nm. We also compared results of experiments using PTM histones and native histones with data collected for both types of histones for the same force ranges (2–80 pN) and loading rates. Our data show that hyperacetylated nucleosomes require an unbinding force of around ~2.5 pN, which is similar to that required for native histones. Moreover, we identified clear differences between the step-size distributions of native and hyperacetylated histones and found that in contrast to tethers reconstituted with native histones, the majority of nucleosomes in tethers compacted with hyperacetylated histones underwent disassembly at forces significantly lower than 6 pN.
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Huynh MT, Sengupta B, Krajewski WA, Lee TH. Effects of Histone H2B Ubiquitylations and H3K79me 3 on Transcription Elongation. ACS Chem Biol 2023; 18:537-548. [PMID: 36857155 PMCID: PMC10023449 DOI: 10.1021/acschembio.2c00887] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Post-translational modifications of histone proteins often mediate gene regulation by altering the global and local stability of the nucleosome, the basic gene-packing unit of eukaryotes. We employed semisynthetic approaches to introduce histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3K79 trimethylation (H3K79me3). With these modified histones, we investigated their effects on the kinetics of transcription elongation by RNA polymerase II (Pol II) using single-molecule FRET. Pol II pauses at several locations within the nucleosome for a few seconds to minutes, which governs the overall transcription efficiency. We found that H2B ubiquitylations suppress pauses and shorten the pause durations near the nucleosome entry while H3K79me3 shortens the pause durations and increases the rate of RNA elongation near the center of the nucleosome. We also found that H2BK34ub facilitates partial rewrapping of the nucleosome upon Pol II passage. These observations suggest that H2B ubiquitylations promote transcription elongation and help maintain the chromatin structure by inducing and stabilizing nucleosome intermediates and that H3K79me3 facilitates Pol II progression possibly by destabilizing the local structure of the nucleosome. Our results provide the mechanisms of how these modifications coupled by a network of regulatory proteins facilitate transcription in two different regions of the nucleosome and help maintain the chromatin structure during active transcription.
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Affiliation(s)
- Mai T. Huynh
- Department of Chemistry, The Pennsylvania State University, State College, PA 16801, USA
| | - Bhaswati Sengupta
- Department of Chemistry, The Pennsylvania State University, State College, PA 16801, USA
| | - Wladyslaw A. Krajewski
- N. K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russia
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, State College, PA 16801, USA
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Abiraami TV, Sanyal RP, Misra HS, Saini A. Genome-wide analysis of bromodomain gene family in Arabidopsis and rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1120012. [PMID: 36968369 PMCID: PMC10030601 DOI: 10.3389/fpls.2023.1120012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The bromodomain-containing proteins (BRD-proteins) belongs to family of 'epigenetic mark readers', integral to epigenetic regulation. The BRD-members contain a conserved 'bromodomain' (BRD/BRD-fold: interacts with acetylated-lysine in histones), and several additional domains, making them structurally/functionally diverse. Like animals, plants also contain multiple Brd-homologs, however the extent of their diversity and impact of molecular events (genomic duplications, alternative splicing, AS) therein, is relatively less explored. The present genome-wide analysis of Brd-gene families of Arabidopsis thaliana and Oryza sativa showed extensive diversity in structure of genes/proteins, regulatory elements, expression pattern, domains/motifs, and the bromodomain (w.r.t. length, sequence, location) among the Brd-members. Orthology analysis identified thirteen ortholog groups (OGs), three paralog groups (PGs) and four singleton members (STs). While more than 40% Brd-genes were affected by genomic duplication events in both plants, AS-events affected 60% A. thaliana and 41% O. sativa genes. These molecular events affected various regions (promoters, untranslated regions, exons) of different Brd-members with potential impact on expression and/or structure-function characteristics. RNA-Seq data analysis indicated differences in tissue-specificity and stress response of Brd-members. Analysis by RT-qPCR revealed differential abundance and salt stress response of duplicate A. thaliana and O. sativa Brd-genes. Further analysis of AtBrd gene, AtBrdPG1b showed salinity-induced modulation of splicing pattern. Bromodomain (BRD)-region based phylogenetic analysis placed the A. thaliana and O. sativa homologs into clusters/sub-clusters, mostly consistent with ortholog/paralog groups. The bromodomain-region displayed several conserved signatures in key BRD-fold elements (α-helices, loops), along with variations (1-20 sites) and indels among the BRD-duplicates. Homology modeling and superposition identified structural variations in BRD-folds of divergent and duplicate BRD-members, which might affect their interaction with the chromatin histones, and associated functions. The study also showed contribution of various duplication events in Brd-gene family expansion among diverse plants, including several monocot and dicot plant species.
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Affiliation(s)
- T. V. Abiraami
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Ravi Prakash Sanyal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Ajay Saini
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
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Soliva-Estruch M, Tamashiro KL, Daskalakis NP. Genetics and epigenetics of stress: New avenues for an old concept. Neurobiol Stress 2023; 23:100525. [PMID: 36873728 PMCID: PMC9975307 DOI: 10.1016/j.ynstr.2023.100525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Affiliation(s)
- Marina Soliva-Estruch
- Department of Psychiatry, McLean Hospital and Harvard Medical School, Belmont, MA, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Limburg, The Netherlands
| | - Kellie L. Tamashiro
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nikolaos P. Daskalakis
- Department of Psychiatry, McLean Hospital and Harvard Medical School, Belmont, MA, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Corresponding author. Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, USA.
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Walker RR, Rentia Z, Chiappinelli KB. Epigenetically programmed resistance to chemo- and immuno-therapies. Adv Cancer Res 2023; 158:41-71. [PMID: 36990538 PMCID: PMC10184181 DOI: 10.1016/bs.acr.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Resistance to cancer treatments remains a major barrier in developing cancer cures. While promising combination chemotherapy treatments and novel immunotherapies have improved patient outcomes, resistance to these treatments remains poorly understood. New insights into the dysregulation of the epigenome show how it promotes tumor growth and resistance to therapy. By altering control of gene expression, tumor cells can evade immune cell recognition, ignore apoptotic cues, and reverse DNA damage induced by chemotherapies. In this chapter, we summarize the data on epigenetic remodeling during cancer progression and treatment that enable cancer cell survival and describe how these epigenetic changes are being targeted clinically to overcome resistance.
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Affiliation(s)
- Reddick R Walker
- The George Washington University Cancer Center (GWCC), Washington, DC, United States; Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States
| | - Zainab Rentia
- The George Washington University Cancer Center (GWCC), Washington, DC, United States
| | - Katherine B Chiappinelli
- The George Washington University Cancer Center (GWCC), Washington, DC, United States; Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States.
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50
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Wang S, Zeng Y, He X, Liu F, Pei P, Zhang T. Folate-deficiency induced acyl-CoA synthetase short-chain family member 2 increases lysine crotonylome involved in neural tube defects. Front Mol Neurosci 2023; 15:1064509. [PMID: 36743291 PMCID: PMC9895841 DOI: 10.3389/fnmol.2022.1064509] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/28/2022] [Indexed: 01/22/2023] Open
Abstract
Maternal folate deficiency increases the risk of neural tube defects (NTDs), but the mechanism remains unclear. Here, we established a mouse model of NTDs via low folate diets combined with MTX-induced conditions. We found that a significant increase in butyrate acid was observed in mouse NTDs brains. In addition, aberrant key crotonyl-CoA-producing enzymes acyl-CoA synthetase short-chain family member 2 (ACSS2) levels and lysine crotonylation (Kcr) were elevated high in corresponding low folate content maternal serum samples from mouse NTD model. Next, proteomic analysis revealed that folate deficiency led to global proteomic modulation, especially in key crotonyl-CoA-producing enzymes, and dramatic ultrastructural changes in mouse embryonic stem cells (mESCs). Furthermore, we determined that folate deficiency induced ACSS2 and Kcr in mESCs. Surprisingly, folic acid supplementation restored level of ACSS2 and Kcr. We also investigated overall protein post-translational Kcr under folate deficiency, revealing the key regulation of Kcr in glycolysis/gluconeogenesis, and the citric acid cycle. Our findings suggest folate deficiency leads to the occurrence of NTDs by altering ACSS2. Protein crotonylation may be the molecular basis for NTDs remodeling by folate deficiency.
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Affiliation(s)
- Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China,Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing, China,Graduate School of Peking Union Medical College, Capital Institute of Pediatrics, Beijing, China,*Correspondence: Shan Wang, ; Ting Zhang,
| | - Yubing Zeng
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Xuejia He
- Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing, China
| | - Fan Liu
- Graduate School of Peking Union Medical College, Capital Institute of Pediatrics, Beijing, China
| | - Pei Pei
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China,Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing, China,Graduate School of Peking Union Medical College, Capital Institute of Pediatrics, Beijing, China,*Correspondence: Shan Wang, ; Ting Zhang,
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