1
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Huang X, Chen Y, Xiao Q, Shang X, Liu Y. Chemical inhibitors targeting histone methylation readers. Pharmacol Ther 2024; 256:108614. [PMID: 38401773 DOI: 10.1016/j.pharmthera.2024.108614] [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: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Histone methylation reader domains are protein modules that recognize specific histone methylation marks, such as methylated or unmethylated lysine or arginine residues on histones. These reader proteins play crucial roles in the epigenetic regulation of gene expression, chromatin structure, and DNA damage repair. Dysregulation of these proteins has been linked to various diseases, including cancer, neurodegenerative diseases, and developmental disorders. Therefore, targeting these proteins with chemical inhibitors has emerged as an attractive approach for therapeutic intervention, and significant progress has been made in this area. In this review, we will summarize the development of inhibitors targeting histone methylation readers, including MBT domains, chromodomains, Tudor domains, PWWP domains, PHD fingers, and WD40 repeat domains. For each domain, we will briefly discuss its identification and biological/biochemical functions, and then focus on the discovery of inhibitors tailored to target this domain, summarizing the property and potential application of most inhibitors. We will also discuss the structural basis for the potency and selectivity of these inhibitors, which will aid in further lead generation and optimization. Finally, we will also address the challenges and strategies involved in the development of these inhibitors. It should facilitate the rational design and development of novel chemical scaffolds and new targeting strategies for histone methylation reader domains with the help of this body of data.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China.
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2
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Wang J, Zhang S, Li Y, Xu Q, Kritzer JA. Investigating the Cytosolic Delivery of Proteins by Lipid Nanoparticles Using the Chloroalkane Penetration Assay. Biochemistry 2024. [PMID: 38334719 DOI: 10.1021/acs.biochem.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Protein therapeutics are an expanding area for research and drug development, and lipid nanoparticles (LNPs) are the most prominent nonviral vehicles for protein delivery. The most common methods for assessing protein delivery by LNPs include assays that measure the total amount of protein taken up by cells and assays that measure the phenotypic changes associated with protein delivery. However, assays for total cellular uptake include large amounts of protein that are trapped in endosomes or are otherwise nonfunctional. Assays for functional delivery are important, but the readouts are indirect and amplified, limiting the quantitative interpretation. Here, we apply an assay for cytosolic delivery, the chloroalkane penetration assay (CAPA), to measure the cytosolic delivery of a (-30) green fluorescent protein (GFP) fused to Cre recombinase (Cre(-30)GFP) fusion protein by LNPs. We compare these data to the data from total cellular uptake and functional delivery assays to provide a richer analysis of uptake and endosomal escape for LNP-mediated protein delivery. We also use CAPA for a screen of a small library of lipidoids, identifying those with a promising ability to deliver Cre(-30)GFP to the cytosol of mammalian cells. With careful controls and optimized conditions, we expect that CAPA will be a useful tool for investigating the rate, efficiency, and mechanisms of LNP-mediated delivery of therapeutic proteins.
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Affiliation(s)
- Jing Wang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Shiying Zhang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yamin Li
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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3
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Kim SH, Haynes KA. Reader-Effectors as Actuators of Epigenome Editing. Methods Mol Biol 2024; 2842:103-127. [PMID: 39012592 DOI: 10.1007/978-1-0716-4051-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenome editing applications are gaining broader use for targeted transcriptional control as more enzymes with diverse chromatin-modifying functions are being incorporated into fusion proteins. Development of these fusion proteins, called epigenome editors, has outpaced the study of proteins that interact with edited chromatin. One type of protein that acts downstream of chromatin editing is the reader-effector, which bridges epigenetic marks with biological effects like gene regulation. As the name suggests, a reader-effector protein is generally composed of a reader domain and an effector domain. Reader domains directly bind epigenetic marks, while effector domains often recruit protein complexes that mediate transcription, chromatin remodeling, and DNA repair. In this chapter, we discuss the role of reader-effectors in driving the outputs of epigenome editing and highlight instances where abnormal and context-specific reader-effectors might impair the effects of epigenome editing. Lastly, we discuss how engineered reader-effectors may complement the epigenome editing toolbox to achieve robust and reliable gene regulation.
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Affiliation(s)
- Seong Hu Kim
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA.
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4
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Krug B, Hu B, Chen H, Ptack A, Chen X, Gretarsson KH, Deshmukh S, Kabir N, Andrade AF, Jabbour E, Harutyunyan AS, Lee JJY, Hulswit M, Faury D, Russo C, Xu X, Johnston MJ, Baguette A, Dahl NA, Weil AG, Ellezam B, Dali R, Blanchette M, Wilson K, Garcia BA, Soni RK, Gallo M, Taylor MD, Kleinman CL, Majewski J, Jabado N, Lu C. H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.567931. [PMID: 38116029 PMCID: PMC10729739 DOI: 10.1101/2023.11.28.567931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing and cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools to restrict H3K27me3 deposition, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened 3D interactions mirroring chromatin architecture of pluripotency, and stringent gene repression that maintains cells in progenitor states to facilitate tumor development. Conversely, H3K27me3 spread in pluripotent stem cells, following neural differentiation or loss of the H3K36 methyltransferase NSD1, dilutes cPRC1 concentration and dissolves polycomb loops. These results identify the regulatory principles and disease implications of polycomb looping and nominate histone modification-guided distribution of reader complexes as an important mechanism for nuclear compartment organization. Highlights The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions.The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs.Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture.The cPRC1-H3K27me3 interaction is a targetable driver of aberrant self-renewal in tumor cells.
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5
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Mathis N, Allam A, Kissling L, Marquart KF, Schmidheini L, Solari C, Balázs Z, Krauthammer M, Schwank G. Predicting prime editing efficiency and product purity by deep learning. Nat Biotechnol 2023; 41:1151-1159. [PMID: 36646933 PMCID: PMC7614945 DOI: 10.1038/s41587-022-01613-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/15/2022] [Indexed: 01/18/2023]
Abstract
Prime editing is a versatile genome editing tool but requires experimental optimization of the prime editing guide RNA (pegRNA) to achieve high editing efficiency. Here we conducted a high-throughput screen to analyze prime editing outcomes of 92,423 pegRNAs on a highly diverse set of 13,349 human pathogenic mutations that include base substitutions, insertions and deletions. Based on this dataset, we identified sequence context features that influence prime editing and trained PRIDICT (prime editing guide prediction), an attention-based bidirectional recurrent neural network. PRIDICT reliably predicts editing rates for all small-sized genetic changes with a Spearman's R of 0.85 and 0.78 for intended and unintended edits, respectively. We validated PRIDICT on endogenous editing sites as well as an external dataset and showed that pegRNAs with high (>70) versus low (<70) PRIDICT scores showed substantially increased prime editing efficiencies in different cell types in vitro (12-fold) and in hepatocytes in vivo (tenfold), highlighting the value of PRIDICT for basic and for translational research applications.
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Affiliation(s)
- Nicolas Mathis
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Ahmed Allam
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Lucas Kissling
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Kim Fabiano Marquart
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lukas Schmidheini
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Cristina Solari
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Zsolt Balázs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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6
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Kim S, Yuan JB, Woods WS, Newton DA, Perez-Pinera P, Song JS. Chromatin structure and context-dependent sequence features control prime editing efficiency. Front Genet 2023; 14:1222112. [PMID: 37456665 PMCID: PMC10344898 DOI: 10.3389/fgene.2023.1222112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Prime editing (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer-binding site (PBS) and reverse transcription (RT) template regions of PE guide RNA (pegRNA) yield high editing efficiency, especially for short PBS designs. The presence of G/C nucleotides was most critical immediately 5' to the protospacer adjacent motif (PAM) site for all designs. The effects of different last templated nucleotides were quantified and observed to depend on the length of both PBS and RT templates. Our models found AGG to be the preferred PAM and detected a guanine nucleotide four bases downstream of the PAM to facilitate editing, suggesting a hitherto-unrecognized interaction with Cas9. A neural network interpretation method based on nonextensive statistical mechanics further revealed multi-nucleotide preferences, indicating dependency among several bases across pegRNA. Our work clarifies previous conflicting observations and uncovers context-dependent features important for optimizing PE designs.
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Affiliation(s)
- Somang Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jimmy B. Yuan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Destry A. Newton
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Pablo Perez-Pinera
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jun S. Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Center for Theoretical Physics, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Statistics, Harvard University, Cambridge, MA, United States
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7
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Ortiz G, Kutateladze TG, Fujimori DG. Chemical tools targeting readers of lysine methylation. Curr Opin Chem Biol 2023; 74:102286. [PMID: 36948085 PMCID: PMC10264141 DOI: 10.1016/j.cbpa.2023.102286] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 03/22/2023]
Abstract
Reader domains that recognize methylated lysine and arginine residues on histones play a role in the recruitment, stabilization, and regulation of chromatin regulatory proteins. Targeting reader proteins with small molecule and peptidomimetic inhibitors has enabled the elucidation of the structure and function of specific domains and uncovered their role in diseases. Recent progress towards chemical probes that target readers of lysine methylation, including the Royal family and plant homeodomains (PHD), is discussed here. We highlight recently developed covalent cyclic peptide inhibitors of a plant homeodomain. Additionally, inhibitors targeting previously untargeted Tudor domains and chromodomains are discussed.
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Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Danica Galonic Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco San Francisco, CA 94158, USA.
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8
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Kim S, Yuan JB, Woods WS, Newton DA, Perez-Pinera P, Song JS. Chromatin structure and context-dependent sequence features control prime editing efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536944. [PMID: 37162994 PMCID: PMC10168420 DOI: 10.1101/2023.04.15.536944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Prime editor (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer binding site (PBS) and reverse transcription (RT) template regions of PE guide-RNA (pegRNA) yield high editing efficiency, especially for short PBS designs. The presence of G/C nucleotides was most critical immediately 5' to the protospacer adjacent motif (PAM) site for all designs. The effects of different last templated nucleotides were quantified and seen to depend on both PBS and RT template lengths. Our models found AGG to be the preferred PAM and detected a guanine nucleotide four bases downstream of PAM to facilitate editing, suggesting a hitherto-unrecognized interaction with Cas9. A neural network interpretation method based on nonextensive statistical mechanics further revealed multi-nucleotide preferences, indicating dependency among several bases across pegRNA. Our work clarifies previous conflicting observations and uncovers context-dependent features important for optimizing PE designs.
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9
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Glancy E, Wang C, Tuck E, Healy E, Amato S, Neikes HK, Mariani A, Mucha M, Vermeulen M, Pasini D, Bracken AP. PRC2.1- and PRC2.2-specific accessory proteins drive recruitment of different forms of canonical PRC1. Mol Cell 2023; 83:1393-1411.e7. [PMID: 37030288 PMCID: PMC10168607 DOI: 10.1016/j.molcel.2023.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/19/2023] [Accepted: 03/16/2023] [Indexed: 04/10/2023]
Abstract
Polycomb repressive complex 2 (PRC2) mediates H3K27me3 deposition, which is thought to recruit canonical PRC1 (cPRC1) via chromodomain-containing CBX proteins to promote stable repression of developmental genes. PRC2 forms two major subcomplexes, PRC2.1 and PRC2.2, but their specific roles remain unclear. Through genetic knockout (KO) and replacement of PRC2 subcomplex-specific subunits in naïve and primed pluripotent cells, we uncover distinct roles for PRC2.1 and PRC2.2 in mediating the recruitment of different forms of cPRC1. PRC2.1 catalyzes the majority of H3K27me3 at Polycomb target genes and is sufficient to promote recruitment of CBX2/4-cPRC1 but not CBX7-cPRC1. Conversely, while PRC2.2 is poor at catalyzing H3K27me3, we find that its accessory protein JARID2 is essential for recruitment of CBX7-cPRC1 and the consequent 3D chromatin interactions at Polycomb target genes. We therefore define distinct contributions of PRC2.1- and PRC2.2-specific accessory proteins to Polycomb-mediated repression and uncover a new mechanism for cPRC1 recruitment.
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Affiliation(s)
- Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ellen Tuck
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Simona Amato
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Andrea Mariani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Diego Pasini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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10
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Wang J, Yang B, Zhang X, Liu S, Pan X, Ma C, Ma S, Yu D, Wu W. Chromobox proteins in cancer: Multifaceted functions and strategies for modulation (Review). Int J Oncol 2023; 62:36. [PMID: 36734270 PMCID: PMC9937689 DOI: 10.3892/ijo.2023.5484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
Chromobox (CBX) proteins are important epigenetic regulatory proteins and are widely involved in biological processes, such as embryonic development, the maintenance of stem cell characteristics and the regulation of cell proliferation and apoptosis. Disorder and dysfunction of CBXs in cancer usually lead to the blockade or ectoptic activation of developmental pathways, promoting the occurrence, development and progression of cancer. In the present review, the characteristics and functions of CBXs were first introduced. Subsequently, the expression of CBXs in cancers and the relationship between CBXs and clinical characteristics (mainly cancer grade, stage, metastasis and relapse) and prognosis were discussed. Finally, it was described how CBXs regulate cell proliferation and self‑renewal, apoptosis and the acquisition of malignant phenotypes, such as invasion, migration and chemoresistance, through mechanisms involving epigenetic modification, nuclear translocation, noncoding RNA interactions, transcriptional regulation, posttranslational modifications, protein‑protein interactions, signal transduction and metabolic reprogramming. The study also focused on cancer therapies targeting CBXs. The present review provides new insight and a comprehensive basis for follow‑up research on CBXs and cancer.
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Affiliation(s)
- Jian Wang
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Bo Yang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiuhang Zhang
- Department of Burn Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shuhan Liu
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiaoqiang Pan
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Changkai Ma
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shiqiang Ma
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Dehai Yu
- Department of Public Research Platform, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China,Professor Dehai Yu, Public Research Platform, The First Hospital of Jilin University, 1 Xinmin Street, Changchun, Jilin 130021, P.R. China, E-mail:
| | - Wei Wu
- Department of Neurovascular Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China,Correspondence to: Professor Wei Wu, Department of Neurovascular Surgery, The First Hospital of Jilin University, 1 Xinmin Street, Changchun, Jilin 130021, P.R. China, E-mail:
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11
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Van Holsbeeck K, Elsocht M, Ballet S. Propargylamine Amino Acids as Constrained Nε-Substituted Lysine Mimetics. Org Lett 2023; 25:130-133. [PMID: 36546856 DOI: 10.1021/acs.orglett.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, alkylated propargylamines are reported as constrained lysine mimetics and constructed in a single step using a copper(I)-catalyzed A3-coupling reaction. Using multiple secondary amines, the reaction allowed the generation of a structurally diverse set of N-Fmoc protected amino acid derivatives. In addition, the A3-reaction was applied on solid phase via the assembly of short model tripeptides. Moreover, the internal alkyne moiety allowed further functionalization toward novel 1,4,5-trisubstituted 1,2,3-triazole-based amino acids.
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Affiliation(s)
- Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Mathias Elsocht
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
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12
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Doyle EJ, Morey L, Conway E. Know when to fold 'em: Polycomb complexes in oncogenic 3D genome regulation. Front Cell Dev Biol 2022; 10:986319. [PMID: 36105358 PMCID: PMC9464936 DOI: 10.3389/fcell.2022.986319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is spatially and temporally regulated through a series of orchestrated processes resulting in the formation of 3D chromatin structures such as topologically associating domains (TADs), loops and Polycomb Bodies. These structures are closely linked to transcriptional regulation, with loss of control of these processes a frequent feature of cancer and developmental syndromes. One such oncogenic disruption of the 3D genome is through recurrent dysregulation of Polycomb Group Complex (PcG) functions either through genetic mutations, amplification or deletion of genes that encode for PcG proteins. PcG complexes are evolutionarily conserved epigenetic complexes. They are key for early development and are essential transcriptional repressors. PcG complexes include PRC1, PRC2 and PR-DUB which are responsible for the control of the histone modifications H2AK119ub1 and H3K27me3. The spatial distribution of the complexes within the nuclear environment, and their associated modifications have profound effects on the regulation of gene transcription and the 3D genome. Nevertheless, how PcG complexes regulate 3D chromatin organization is still poorly understood. Here we glean insights into the role of PcG complexes in 3D genome regulation and compaction, how these processes go awry during tumorigenesis and the therapeutic implications that result from our insights into these mechanisms.
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Affiliation(s)
- Emma J. Doyle
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Lluis Morey
- Sylvester Comprehensive Cancer Centre, Miami, FL, United States
- Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eric Conway
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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13
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Kang Y, Jung WJ, Brent MR. Predicting which genes will respond to transcription factor perturbations. G3 (BETHESDA, MD.) 2022; 12:jkac144. [PMID: 35666184 PMCID: PMC9339286 DOI: 10.1093/g3journal/jkac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022]
Abstract
The ability to predict which genes will respond to the perturbation of a transcription factor serves as a benchmark for our systems-level understanding of transcriptional regulatory networks. In previous work, machine learning models have been trained to predict static gene expression levels in a biological sample by using data from the same or similar samples, including data on their transcription factor binding locations, histone marks, or DNA sequence. We report on a different challenge-training machine learning models to predict which genes will respond to the perturbation of a transcription factor without using any data from the perturbed cells. We find that existing transcription factor location data (ChIP-seq) from human cells have very little detectable utility for predicting which genes will respond to perturbation of a transcription factor. Features of genes, including their preperturbation expression level and expression variation, are very useful for predicting responses to perturbation of any transcription factor. This shows that some genes are poised to respond to transcription factor perturbations and others are resistant, shedding light on why it has been so difficult to predict responses from binding locations. Certain histone marks, including H3K4me1 and H3K4me3, have some predictive power when located downstream of the transcription start site. However, the predictive power of histone marks is much less than that of gene expression level and expression variation. Sequence-based or epigenetic properties of genes strongly influence their tendency to respond to direct transcription factor perturbations, partially explaining the oft-noted difficulty of predicting responsiveness from transcription factor binding location data. These molecular features are largely reflected in and summarized by the gene's expression level and expression variation. Code is available at https://github.com/BrentLab/TFPertRespExplainer.
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Affiliation(s)
- Yiming Kang
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108, USA
| | - Wooseok J Jung
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108, USA
| | - Michael R Brent
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Computer Science and Engineering, Washington University, St. Louis, MO 63108, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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14
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Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer. Cancers (Basel) 2022; 14:cancers14122866. [PMID: 35740532 PMCID: PMC9221043 DOI: 10.3390/cancers14122866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/27/2023] Open
Abstract
3D chromatin organization plays an important role in transcription regulation and gene expression. The 3D genome is highly maintained by several architectural proteins, such as CTCF, Yin Yang 1, and cohesin complex. This structural organization brings regulatory DNA elements in close proximity to their target promoters. In this review, we discuss the 3D chromatin organization of super-enhancers and their relationship to phase-separated condensates. Super-enhancers are large clusters of DNA elements. They can physically contact with their target promoters by chromatin looping during transcription. Multiple transcription factors can bind to enhancer and promoter sequences and recruit a complex array of transcriptional co-activators and RNA polymerase II to effect transcriptional activation. Phase-separated condensates of transcription factors and transcriptional co-activators have been implicated in assembling the transcription machinery at particular enhancers. Cancer cells can hijack super-enhancers to drive oncogenic transcription to promote cell survival and proliferation. These dysregulated transcriptional programs can cause cancer cells to become highly dependent on transcriptional regulators, such as Mediator and BRD4. Moreover, the expression of oncogenes that are driven by super-enhancers is sensitive to transcriptional perturbation and often occurs in phase-separated condensates, supporting therapeutic rationales of targeting SE components, 3D genome organization, or dysregulated condensates in cancer.
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15
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Mustafi P, Hu M, Kumari S, Das C, Li G, Kundu TK. Phosphorylation-dependent association of human chromatin protein PC4 to linker histone H1 regulates genome organization and transcription. Nucleic Acids Res 2022; 50:6116-6136. [PMID: 35670677 PMCID: PMC9226532 DOI: 10.1093/nar/gkac450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Human Positive Coactivator 4 (PC4) is a multifaceted chromatin protein involved in diverse cellular processes including genome organization, transcription regulation, replication, DNA repair and autophagy. PC4 exists as a phospho-protein in cells which impinges on its acetylation by p300 and thereby affects its transcriptional co-activator functions via double-stranded DNA binding. Despite the inhibitory effects, the abundance of phosphorylated PC4 in cells intrigued us to investigate its role in chromatin functions in a basal state of the cell. We found that casein kinase-II (CKII)-mediated phosphorylation of PC4 is critical for its interaction with linker histone H1. By employing analytical ultracentrifugation and electron microscopy imaging of in vitro reconstituted nucleosomal array, we observed that phospho-mimic (PM) PC4 displays a superior chromatin condensation potential in conjunction with linker histone H1. ATAC-sequencing further unveiled the role of PC4 phosphorylation to be critical in inducing chromatin compaction of a wide array of coding and non-coding genes in vivo. Concordantly, phospho-PC4 mediated changes in chromatin accessibility led to gene repression and affected global histone modifications. We propose that the abundance of PC4 in its phosphorylated state contributes to genome compaction contrary to its co-activator function in driving several cellular processes like gene transcription and autophagy.
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Affiliation(s)
- Pallabi Mustafi
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Mingli Hu
- National laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Chandrima Das
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Guohong Li
- National laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow 226031, India
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16
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Recent progress on small molecules targeting epigenetic complexes. Curr Opin Chem Biol 2022; 67:102130. [DOI: 10.1016/j.cbpa.2022.102130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 12/16/2022]
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17
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Kean KM, Baril SA, Lamb KN, Dishman SN, Treacy JW, Houk KN, Brustad EM, James LI, Waters ML. Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding. J Med Chem 2022; 65:2646-2655. [PMID: 35014255 PMCID: PMC9048841 DOI: 10.1021/acs.jmedchem.1c02049] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.
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Affiliation(s)
- Kelsey M. Kean
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Stefanie A. Baril
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Sarah N. Dishman
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, Box 951569, University of California, Los Angeles, CA 90095 USA
| | - Eric M. Brustad
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA,Corresponding Author: Marcey L. Waters – Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States;
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18
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Lamb KN, Dishman SN, Waybright JM, Engelberg IA, Rectenwald JM, Norris-Drouin JL, Cholensky SH, Pearce KH, James LI, Frye SV. Discovery of Potent Peptidomimetic Antagonists for Heterochromatin Protein 1 Family Proteins. ACS OMEGA 2022; 7:716-732. [PMID: 35036738 PMCID: PMC8757366 DOI: 10.1021/acsomega.1c05381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The heterochromatin protein 1 (HP1) sub-family of CBX chromodomains are responsible for the recognition of histone H3 lysine 9 tri-methyl (H3K9me3)-marked nucleosomal substrates through binding of the N-terminal chromodomain. These HP1 proteins, namely, CBX1 (HP1β), CBX3 (HP1γ), and CBX5 (HP1α), are commonly associated with regions of pericentric heterochromatin, but recent literature studies suggest that regulation by these proteins is likely more dynamic and includes other loci. Importantly, there are no chemical tools toward HP1 chromodomains to spatiotemporally explore the effects of HP1-mediated processes, underscoring the need for novel HP1 chemical probes. Here, we report the discovery of HP1 targeting peptidomimetic compounds, UNC7047 and UNC7560, and a biotinylated derivative tool compound, UNC7565. These compounds represent an important milestone, as they possess nanomolar affinity for the CBX5 chromodomain by isothermal titration calorimetry (ITC) and bind HP1-containing complexes in cell lysates. These chemical tools provide a starting point for further optimization and the study of CBX5-mediated processes.
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Affiliation(s)
- Kelsey N. Lamb
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sarah N. Dishman
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jarod M. Waybright
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Isabelle A. Engelberg
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Justin M. Rectenwald
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L. Norris-Drouin
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie H. Cholensky
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- Center
for Integrative Chemical Biology and Drug Discovery, Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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19
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Trotman JB, Braceros KCA, Cherney RE, Murvin MM, Calabrese JM. The control of polycomb repressive complexes by long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1657. [PMID: 33861025 PMCID: PMC8500928 DOI: 10.1002/wrna.1657] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
The polycomb repressive complexes 1 and 2 (PRCs; PRC1 and PRC2) are conserved histone-modifying enzymes that often function cooperatively to repress gene expression. The PRCs are regulated by long noncoding RNAs (lncRNAs) in complex ways. On the one hand, specific lncRNAs cause the PRCs to engage with chromatin and repress gene expression over genomic regions that can span megabases. On the other hand, the PRCs bind RNA with seemingly little sequence specificity, and at least in the case of PRC2, direct RNA-binding has the effect of inhibiting the enzyme. Thus, some RNAs appear to promote PRC activity, while others may inhibit it. The reasons behind this apparent dichotomy are unclear. The most potent PRC-activating lncRNAs associate with chromatin and are predominantly unspliced or harbor unusually long exons. Emerging data imply that these lncRNAs promote PRC activity through internal RNA sequence elements that arise and disappear rapidly in evolutionary time. These sequence elements may function by interacting with common subsets of RNA-binding proteins that recruit or stabilize PRCs on chromatin. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jackson B. Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keean C. A. Braceros
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rachel E. Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - McKenzie M. Murvin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - J. Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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20
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Suh JL, Bsteh D, Hart B, Si Y, Weaver TM, Pribitzer C, Lau R, Soni S, Ogana H, Rectenwald JM, Norris JL, Cholensky SH, Sagum C, Umana JD, Li D, Hardy B, Bedford MT, Mumenthaler SM, Lenz HJ, Kim YM, Wang GG, Pearce KH, James LI, Kireev DB, Musselman CA, Frye SV, Bell O. Reprogramming CBX8-PRC1 function with a positive allosteric modulator. Cell Chem Biol 2021; 29:555-571.e11. [PMID: 34715055 PMCID: PMC9035045 DOI: 10.1016/j.chembiol.2021.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/19/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022]
Abstract
Canonical targeting of Polycomb repressive complex 1 (PRC1) to repress developmental genes is mediated by cell-type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7, and 8). Based on their central role in silencing and their dysregulation associated with human disease including cancer, CBX proteins are attractive targets for small-molecule chemical probe development. Here, we have used a quantitative and target-specific cellular assay to discover a potent positive allosteric modulator (PAM) of CBX8. The PAM activity of UNC7040 antagonizes H3K27me3 binding by CBX8 while increasing interactions with nucleic acids. We show that treatment with UNC7040 leads to efficient and selective eviction of CBX8-containing PRC1 from chromatin, loss of silencing, and reduced proliferation across different cancer cell lines. Our discovery and characterization of UNC7040 not only reveals the most cellularly potent CBX8-specific chemical probe to date, but also corroborates a mechanism of Polycomb regulation by non-specific CBX nucleotide binding activity.
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Affiliation(s)
- Junghyun L Suh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel Bsteh
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Bryce Hart
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yibo Si
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Tyler M Weaver
- University of Iowa, Department of Biochemistry, Iowa City, IA 52242, USA
| | - Carina Pribitzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Roy Lau
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Heather Ogana
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90027, USA
| | - Justin M Rectenwald
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jacqueline L Norris
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie H Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jessica D Umana
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dongxu Li
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian Hardy
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA 90033, USA; Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yong-Mi Kim
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90027, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ken H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dmitri B Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Catherine A Musselman
- University of Iowa, Department of Biochemistry, Iowa City, IA 52242, USA; University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Oliver Bell
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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21
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Wang S, C Ordonez-Rubiano S, Dhiman A, Jiao G, Strohmier BP, Krusemark CJ, Dykhuizen EC. Polycomb group proteins in cancer: multifaceted functions and strategies for modulation. NAR Cancer 2021; 3:zcab039. [PMID: 34617019 PMCID: PMC8489530 DOI: 10.1093/narcan/zcab039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022] Open
Abstract
Polycomb repressive complexes (PRCs) are a heterogenous collection of dozens, if not hundreds, of protein complexes composed of various combinations of subunits. PRCs are transcriptional repressors important for cell-type specificity during development, and as such, are commonly mis-regulated in cancer. PRCs are broadly characterized as PRC1 with histone ubiquitin ligase activity, or PRC2 with histone methyltransferase activity; however, the mechanism by which individual PRCs, particularly the highly diverse set of PRC1s, alter gene expression has not always been clear. Here we review the current understanding of how PRCs act, both individually and together, to establish and maintain gene repression, the biochemical contribution of individual PRC subunits, the mis-regulation of PRC function in different cancers, and the current strategies for modulating PRC activity. Increased mechanistic understanding of PRC function, as well as cancer-specific roles for individual PRC subunits, will uncover better targets and strategies for cancer therapies.
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Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
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22
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Milosevich N, Wilson CR, Brown TM, Alpsoy A, Wang S, Connelly KE, Sinclair KAD, Ponio FR, Hof R, Dykhuizen EC, Hof F. Polycomb Paralog Chromodomain Inhibitors Active against Both CBX6 and CBX8*. ChemMedChem 2021; 16:3027-3034. [PMID: 34174168 PMCID: PMC8497432 DOI: 10.1002/cmdc.202100262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/20/2021] [Indexed: 02/06/2023]
Abstract
Methyllysine reader proteins bind to methylated lysine residues and alter gene transcription by changing either the compaction state of chromatin or by the recruitment of other multiprotein complexes. The polycomb paralog family of methyllysine readers bind to trimethylated lysine on the tail of histone 3 (H3) via a highly conserved aromatic cage located in their chromodomains. Each of the polycomb paralogs are implicated in several disease states. CBX6 and CBX8 are members of the polycomb paralog family with two structurally similar chromodomains. By exploring the structure-activity relationships of a previously reported CBX6 inhibitor we have discovered more potent and cell permeable analogs. Our current report includes potent, dual-selective inhibitors of CBX6 and CBX8. We have shown that the -2 position in our scaffold is an important residue for selectivity amongst the polycomb paralogs. Preliminary cell-based studies show that the new inhibitors impact cell proliferation in a rhabdoid tumor cell line.
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Affiliation(s)
- Natalia Milosevich
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Chelsea R. Wilson
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Tyler M. Brown
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Katelyn E. Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | | | - Felino R. Ponio
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Rebecca Hof
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Emily C. Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada
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23
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Waybright JM, Clinkscales SE, Barnash KD, Budziszewski GR, Rectenwald JM, Chiarella AM, Norris-Drouin JL, Cholensky SH, Pearce KH, Herring LE, McGinty RK, Hathaway NA, James LI. A Peptidomimetic Ligand Targeting the Chromodomain of MPP8 Reveals HRP2's Association with the HUSH Complex. ACS Chem Biol 2021; 16:1721-1736. [PMID: 34415726 DOI: 10.1021/acschembio.1c00429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interpretation of histone post-translational modifications (PTMs), specifically lysine methylation, by specific classes of "reader" proteins marks an important aspect of epigenetic control of gene expression. Methyl-lysine (Kme) readers often regulate gene expression patterns through the recognition of a specific Kme PTM while participating in or recruiting large protein complexes that contain enzymatic or chromatin remodeling activity. Understanding the composition of these Kme-reader-containing protein complexes can serve to further our understanding of the biological roles of Kme readers, while small molecule chemical tools can be valuable reagents in interrogating novel protein-protein interactions. Here, we describe our efforts to target the chromodomain of M-phase phosphoprotein 8 (MPP8), a member of the human silencing hub (HUSH) complex and a histone 3 lysine 9 trimethyl (H3K9me3) reader that is vital for heterochromatin formation and has specific roles in cancer metastasis. Utilizing a one-bead, one-compound (OBOC) combinatorial screening approach, we identified UNC5246, a peptidomimetic ligand capable of interacting with the MPP8 chromodomain in the context of the HUSH complex. Additionally, a biotinylated derivative of UNC5246 facilitated chemoproteomics studies which revealed hepatoma-derived growth factor-related protein 2 (HRP2) as a novel protein associated with MPP8. HRP2 was further shown to colocalize with MPP8 at the E-cadherin gene locus, suggesting a possible role in cancer cell plasticity.
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Affiliation(s)
- Jarod M. Waybright
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sarah E. Clinkscales
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | | | - Gabrielle R. Budziszewski
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Justin M. Rectenwald
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Anna M. Chiarella
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L. Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie H. Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Laura E. Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Robert K. McGinty
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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24
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Tamburri S, Conway E, Pasini D. Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer. Trends Genet 2021; 38:333-352. [PMID: 34426021 DOI: 10.1016/j.tig.2021.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
Cell identity is tightly controlled by specific transcriptional programs which require post-translational modifications of histones. These histone modifications allow the establishment and maintenance of active and repressed chromatin domains. Histone H2A lysine 119 ubiquitination (H2AK119ub1) has an essential role in building repressive chromatin domains during development. It is regulated by the counteracting activities of the Polycomb repressive complex 1 (PRC1) and the Polycomb repressive-deubiquitinase (PR-DUB) complexes, two multi-subunit ensembles that write and erase this modification, respectively. We have catalogued the recurrent genetic alterations in subunits of the PRC1 and PR-DUB complexes in both neurodevelopmental disorders and cancer. These genetic lesions are often shared across disorders, and we highlight common mechanisms of H2AK119ub1 dysregulation and how they affect development in multiple disease contexts.
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Affiliation(s)
- Simone Tamburri
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
| | - Eric Conway
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
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25
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Engelberg IA, Liu J, Norris-Drouin JL, Cholensky SH, Ottavi SA, Frye SV, Kutateladze TG, James LI. Discovery of an H3K36me3-Derived Peptidomimetic Ligand with Enhanced Affinity for Plant Homeodomain Finger Protein 1 (PHF1). J Med Chem 2021; 64:8510-8522. [PMID: 33999620 DOI: 10.1021/acs.jmedchem.1c00430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plant homeodomain finger protein 1 (PHF1) is an accessory component of the gene silencing complex polycomb repressive complex 2 and recognizes the active chromatin mark, trimethylated lysine 36 of histone H3 (H3K36me3). In addition to its role in transcriptional regulation, PHF1 has been implicated as a driver of endometrial stromal sarcoma and fibromyxoid tumors. We report the discovery and characterization of UNC6641, a peptidomimetic antagonist of the PHF1 Tudor domain which was optimized through in silico modeling and incorporation of non-natural amino acids. UNC6641 binds the PHF1 Tudor domain with a Kd value of 0.96 ± 0.03 μM while also binding the related protein PHF19 with similar potency. A crystal structure of PHF1 in complex with UNC6641, along with NMR and site-directed mutagenesis data, provided insight into the binding mechanism and requirements for binding. Additionally, UNC6641 enabled the development of a high-throughput assay to identify small molecule binders of PHF1.
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Affiliation(s)
- Isabelle A Engelberg
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Jacqueline L Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie H Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Samantha A Ottavi
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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26
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Engelberg IA, Foley CA, James LI, Frye SV. Improved methods for targeting epigenetic reader domains of acetylated and methylated lysine. Curr Opin Chem Biol 2021; 63:132-144. [PMID: 33852996 DOI: 10.1016/j.cbpa.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 01/20/2023]
Abstract
Responsible for interpreting histone post-translational modifications, epigenetic reader proteins have emerged as novel therapeutic targets for a wide range of diseases. Chemical probes have been critical in enabling target validation studies and have led to translational advances in cancer and inflammation-related pathologies. Here, we present the most recently reported probes of reader proteins that recognize acylated and methylated lysine. We will discuss challenges associated with achieving potent antagonism of reader domains and review ongoing efforts to overcome these hurdles, focusing on targeting strategies including the use of peptidomimetic ligands, allosteric modulators, and protein degraders.
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Affiliation(s)
- Isabelle A Engelberg
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Caroline A Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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27
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Mariani M, Zimmerman C, Rodriguez P, Hasenohr E, Aimola G, Gerrard DL, Richman A, Dest A, Flamand L, Kaufer B, Frietze S. Higher-Order Chromatin Structures of Chromosomally Integrated HHV-6A Predict Integration Sites. Front Cell Infect Microbiol 2021; 11:612656. [PMID: 33718266 PMCID: PMC7953476 DOI: 10.3389/fcimb.2021.612656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/20/2021] [Indexed: 12/31/2022] Open
Abstract
Human herpesvirus -6A and 6B (HHV-6A/B) can integrate their genomes into the telomeres of human chromosomes. Viral integration can occur in several cell types, including germinal cells, resulting in individuals that harbor the viral genome in every cell of their body. The integrated genome is efficiently silenced but can sporadically reactivate resulting in various clinical symptoms. To date, the integration mechanism and the subsequent silencing of HHV-6A/B genes remains poorly understood. Here we investigate the genome-wide chromatin contacts of the integrated HHV-6A in latently-infected cells. We show that HHV-6A becomes transcriptionally silent upon infection of these cells over the course of seven days. In addition, we established an HHV-6-specific 4C-seq approach, revealing that the HHV-6A 3D interactome is associated with quiescent chromatin states in cells harboring integrated virus. Furthermore, we observed that the majority of virus chromatin interactions occur toward the distal ends of specific human chromosomes. Exploiting this finding, we established a 4C-seq method that accurately detects the chromosomal integration sites. We further implement long-read minION sequencing in the 4C-seq assay and developed a method to identify HHV-6A/B integration sites in clinical samples.
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Affiliation(s)
- Michael Mariani
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Cosima Zimmerman
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Princess Rodriguez
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Ellie Hasenohr
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Giulia Aimola
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Diana Lea Gerrard
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Alyssa Richman
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Andrea Dest
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States
| | - Louis Flamand
- Division of Infectious Disease and Immunity, CHU de Québec Research Center-Université Laval, Quebec City, QC, Canada
| | - Benedikt Kaufer
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Seth Frietze
- Department of Biomedical and Health Sciences, College of Nursing and Health Sciences, University of Vermont, Burlington, VT, United States.,University of Vermont Cancer Center, Burlington, VT, United States
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28
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Horn V, Jongkees SAK, van Ingen H. Mimicking the Nucleosomal Context in Peptide-Based Binders of a H3K36me Reader Increases Binding Affinity While Altering the Binding Mode. Molecules 2020; 25:molecules25214951. [PMID: 33114657 PMCID: PMC7662849 DOI: 10.3390/molecules25214951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/29/2022] Open
Abstract
Targeting of proteins in the histone modification machinery has emerged as a promising new direction to fight disease. The search for compounds that inhibit proteins that readout histone modification has led to several new epigenetic drugs, mostly for proteins involved in recognition of acetylated lysines. However, this approach proved to be a challenging task for methyllysine readers, which typically feature shallow binding pockets. Moreover, reader proteins of trimethyllysine K36 on the histone H3 (H3K36me3) not only bind the methyllysine but also the nucleosomal DNA. Here, we sought to find peptide-based binders of H3K36me3 reader PSIP1, which relies on DNA interactions to tightly bind H3K36me3 modified nucleosomes. We designed several peptides that mimic the nucleosomal context of H3K36me3 recognition by including negatively charged Glu-rich regions. Using a detailed NMR analysis, we find that addition of negative charges boosts binding affinity up to 50-fold while decreasing binding to the trimethyllysine binding pocket. Since screening and selection of compounds for reader domains is typically based solely on affinity measurements due to their lack of enzymatic activity, our case highlights the need to carefully control for the binding mode, in particular for the challenging case of H3K36me3 readers.
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Affiliation(s)
- Velten Horn
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502 Leiden, The Netherlands;
| | - Seino A. K. Jongkees
- Chemical Biology and Drug Discovery Group, Utrecht University, P.O. Box 80082 Utrecht, The Netherlands;
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502 Leiden, The Netherlands;
- NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-30-253-9934
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29
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Vaughan RM, Kupai A, Foley CA, Sagum CA, Tibben BM, Eden HE, Tiedemann RL, Berryhill CA, Patel V, Shaw KM, Krajewski K, Strahl BD, Bedford MT, Frye SV, Dickson BM, Rothbart SB. The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells. Epigenetics Chromatin 2020; 13:44. [PMID: 33097091 PMCID: PMC7585203 DOI: 10.1186/s13072-020-00366-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
The chromatin-binding E3 ubiquitin ligase ubiquitin-like with PHD and RING finger domains 1 (UHRF1) contributes to the maintenance of aberrant DNA methylation patterning in cancer cells through multivalent histone and DNA recognition. The tandem Tudor domain (TTD) of UHRF1 is well-characterized as a reader of lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and, more recently, lysine 126 di- and tri-methylation on DNA ligase 1 (LIG1K126me2/me3). However, the functional significance and selectivity of these interactions remain unclear. In this study, we used protein domain microarrays to search for additional readers of LIG1K126me2, the preferred methyl state bound by the UHRF1 TTD. We show that the UHRF1 TTD binds LIG1K126me2 with high affinity and selectivity compared to other known methyllysine readers. Notably, and unlike H3K9me2/me3, the UHRF1 plant homeodomain (PHD) and its N-terminal linker (L2) do not contribute to multivalent LIG1K126me2 recognition along with the TTD. To test the functional significance of this interaction, we designed a LIG1K126me2 cell-penetrating peptide (CPP). Consistent with LIG1 knockdown, uptake of the CPP had no significant effect on the propagation of DNA methylation patterning across the genomes of bulk populations from high-resolution analysis of several cancer cell lines. Further, we did not detect significant changes in DNA methylation patterning from bulk cell populations after chemical or genetic disruption of lysine methyltransferase activity associated with LIG1K126me2 and H3K9me2. Collectively, these studies identify UHRF1 as a selective reader of LIG1K126me2 in vitro and further implicate the histone and non-histone methyllysine reader activity of the UHRF1 TTD as a dispensable domain function for cancer cell DNA methylation maintenance.
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Affiliation(s)
- Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Ariana Kupai
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Caroline A Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Cari A Sagum
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Bailey M Tibben
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Hope E Eden
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | | | | | - Varun Patel
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Kevin M Shaw
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bradley M Dickson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA.
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30
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Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
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31
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Wang ZA, Cole PA. The Chemical Biology of Reversible Lysine Post-translational Modifications. Cell Chem Biol 2020; 27:953-969. [PMID: 32698016 PMCID: PMC7487139 DOI: 10.1016/j.chembiol.2020.07.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/09/2020] [Accepted: 07/01/2020] [Indexed: 12/31/2022]
Abstract
Lysine (Lys) residues in proteins undergo a wide range of reversible post-translational modifications (PTMs), which can regulate enzyme activities, chromatin structure, protein-protein interactions, protein stability, and cellular localization. Here we discuss the "writers," "erasers," and "readers" of some of the common protein Lys PTMs and summarize examples of their major biological impacts. We also review chemical biology approaches, from small-molecule probes to protein chemistry technologies, that have helped to delineate Lys PTM functions and show promise for a diverse set of biomedical applications.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Avenue Louis Pasteur NRB, Boston, MA 02115, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Avenue Louis Pasteur NRB, Boston, MA 02115, USA.
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32
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Cipriano A, Sbardella G, Ciulli A. Targeting epigenetic reader domains by chemical biology. Curr Opin Chem Biol 2020; 57:82-94. [DOI: 10.1016/j.cbpa.2020.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 12/17/2022]
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Deprey K, Kritzer JA. Quantitative measurement of cytosolic penetration using the chloroalkane penetration assay. Methods Enzymol 2020; 641:277-309. [PMID: 32713526 PMCID: PMC7872221 DOI: 10.1016/bs.mie.2020.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A major barrier for drug development is ensuring molecules can access intracellular targets. This is especially true for biomolecules, which are notoriously difficult to deliver to the cytosol. Many current methods for measuring the internalization of therapeutic biomolecules are largely indirect and qualitative, and they do not offer information about subcellular localization. We recently reported a new assay, called the ChloroAlkane Penetration Assay (CAPA), that addresses some of the drawbacks of existing methods. CAPA is high-throughput, quantitative, and compartment-specific, and can be used to monitor cytosolic penetration over time and under a variety of culture conditions. We have used CAPA to investigate the cytosolic localization of peptides, proteins, and oligonucleotides. In this chapter, we discuss the materials, protocols, and troubleshooting necessary to perform CAPA and appropriately analyze the data. We end with a discussion about the applications and limitations of CAPA, and we speculate on the potential of the assay and its variations.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, MA, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, MA, United States.
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Design and Construction of a Focused DNA-Encoded Library for Multivalent Chromatin Reader Proteins. Molecules 2020; 25:molecules25040979. [PMID: 32098353 PMCID: PMC7070942 DOI: 10.3390/molecules25040979] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and function, and consequently cellular phenotype, is regulated in part by a network of chromatin-modifying enzymes that place post-translational modifications (PTMs) on histone tails. These marks serve as recruitment sites for other chromatin regulatory complexes that ‘read’ these PTMs. High-quality chemical probes that can block reader functions of proteins involved in chromatin regulation are important tools to improve our understanding of pathways involved in chromatin dynamics. Insight into the intricate system of chromatin PTMs and their context within the epigenome is also therapeutically important as misregulation of this complex system is implicated in numerous human diseases. Using computational methods, along with structure-based knowledge, we have designed and constructed a focused DNA-Encoded Library (DEL) containing approximately 60,000 compounds targeting bi-valent methyl-lysine (Kme) reader domains. Additionally, we have constructed DNA-barcoded control compounds to allow optimization of selection conditions using a model Kme reader domain. We anticipate that this target-class focused approach will serve as a new method for rapid discovery of inhibitors for multivalent chromatin reader domains.
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Foley CA, Potjewyd F, Lamb KN, James LI, Frye SV. Assessing the Cell Permeability of Bivalent Chemical Degraders Using the Chloroalkane Penetration Assay. ACS Chem Biol 2020; 15:290-295. [PMID: 31846298 DOI: 10.1021/acschembio.9b00972] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bivalent chemical degraders provide a catalytic route to selectively degrade disease-associated proteins. By linking target-specific ligands with E3 ubiquitin ligase recruiting ligands, these compounds facilitate targeted protein ubiquitination and degradation by the proteasome. Due to the complexity of this multistep mechanism, the development of effective degrader molecules remains a difficult, lengthy, and unpredictable process. Since degraders are large heterobifunctional molecules, the efficacy of these compounds may be limited by poor cell permeability, and an efficient and reliable method to quantify the cell permeability of these compounds is lacking. Herein, we demonstrate that by the addition of a chloroalkane tag on the BRD4 specific degrader, MZ1, cell permeability can be quantified via the chloroalkane penetration assay. By extending this analysis to individual components of the degrader molecule, we have obtained structure-permeability relationships that will be informative for future degrader development, particularly as degraders move into the clinic as potential therapeutics.
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Affiliation(s)
- Caroline A. Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Frances Potjewyd
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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