1
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Lee K, Barone M, Waterbury AL, Jiang H, Nam E, DuBois-Coyne SE, Whedon SD, Wang ZA, Caroli J, Neal K, Ibeabuchi B, Dhoondia Z, Kuroda MI, Liau BB, Beck S, Mattevi A, Cole PA. Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1. Nat Chem Biol 2024:10.1038/s41589-024-01671-9. [PMID: 38965385 DOI: 10.1038/s41589-024-01671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
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Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marco Barone
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eunju Nam
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jonatan Caroli
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Katherine Neal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brian Ibeabuchi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zuzer Dhoondia
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samuel Beck
- Department of Dermatology, Boston University School of Medicine & Boston Medical Center, Boston, MA, USA.
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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2
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Pastoors D, Havermans M, Mulet-Lazaro R, Brian D, Noort W, Grasel J, Hoogenboezem R, Smeenk L, Demmers JAA, Milsom MD, Enver T, Groen RWJ, Bindels E, Delwel R. Oncogene EVI1 drives acute myeloid leukemia via a targetable interaction with CTBP2. SCIENCE ADVANCES 2024; 10:eadk9076. [PMID: 38748792 PMCID: PMC11095456 DOI: 10.1126/sciadv.adk9076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
Acute myeloid leukemia (AML) driven by the activation of EVI1 due to chromosome 3q26/MECOM rearrangements is incurable. Because transcription factors such as EVI1 are notoriously hard to target, insight into the mechanism by which EVI1 drives myeloid transformation could provide alternative avenues for therapy. Applying protein folding predictions combined with proteomics technologies, we demonstrate that interaction of EVI1 with CTBP1 and CTBP2 via a single PLDLS motif is indispensable for leukemic transformation. A 4× PLDLS repeat construct outcompetes binding of EVI1 to CTBP1 and CTBP2 and inhibits proliferation of 3q26/MECOM rearranged AML in vitro and in xenotransplant models. This proof-of-concept study opens the possibility to target one of the most incurable forms of AML with specific EVI1-CTBP inhibitors. This has important implications for other tumor types with aberrant expression of EVI1 and for cancers transformed by different CTBP-dependent oncogenic transcription factors.
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Affiliation(s)
- Dorien Pastoors
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Marije Havermans
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Duncan Brian
- Stem Cell Group, UCL Cancer Institute, University College London, London, UK
| | - Willy Noort
- Department of Hematology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer biology and immunology, Amsterdam, Netherlands
| | - Julius Grasel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
- Division of Experimental Hematology, German Cancer Research Center, DKFZ69120 Heidelberg, Germany
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Leonie Smeenk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Michael D. Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
- Division of Experimental Hematology, German Cancer Research Center, DKFZ69120 Heidelberg, Germany
| | - Tariq Enver
- Stem Cell Group, UCL Cancer Institute, University College London, London, UK
| | - Richard W. J. Groen
- Department of Hematology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer biology and immunology, Amsterdam, Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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3
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Gawriyski L, Tan Z, Liu X, Chowdhury I, Malaymar Pinar D, Zhang Q, Weltner J, Jouhilahti EM, Wei GH, Kere J, Varjosalo M. Interaction network of human early embryonic transcription factors. EMBO Rep 2024; 25:1589-1622. [PMID: 38297188 PMCID: PMC10933267 DOI: 10.1038/s44319-024-00074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaonan Liu
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | | | - Dicle Malaymar Pinar
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Qin Zhang
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Markku Varjosalo
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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4
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Torres HM, Fang F, May DG, Bosshardt P, Hinojosa L, Roux KJ, Tao J. Comprehensive analysis of the proximity-dependent nuclear interactome for the oncoprotein NOTCH1 in live cells. J Biol Chem 2024; 300:105522. [PMID: 38043798 PMCID: PMC10788534 DOI: 10.1016/j.jbc.2023.105522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/25/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023] Open
Abstract
Notch signaling plays a critical role in cell fate decisions in all cell types. Furthermore, gain-of-function mutations in NOTCH1 have been uncovered in many human cancers. Disruption of Notch signaling has recently emerged as an attractive disease treatment strategy. However, the nuclear interaction landscape of the oncoprotein NOTCH1 remains largely unexplored. We therefore employed here a proximity-dependent biotin identification approach to identify in vivo protein associations with the nuclear Notch1 intracellular domain in live cells. We identified a large set of previously reported and unreported proteins that associate with NOTCH1, including general transcription and elongation factors, DNA repair and replication factors, coactivators, corepressors, and components of the NuRD and SWI/SNF chromatin remodeling complexes. We also found that Notch1 intracellular domain associates with protein modifiers and components of other signaling pathways that may influence Notch signal transduction and protein stability such as USP7. We further validated the interaction of NOTCH1 with histone deacetylase 1 or GATAD2B using protein network analysis, proximity-based ligation, in vivo cross-linking and coimmunoprecipitation assays in several Notch-addicted cancer cell lines. Through data mining, we also revealed potential drug targets for the inhibition of Notch signaling. Collectively, these results provide a valuable resource to uncover the mechanisms that fine-tune Notch signaling in tumorigenesis and inform therapeutic targets for Notch-addicted tumors.
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Affiliation(s)
- Haydee M Torres
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA
| | - Fang Fang
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Danielle G May
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Paige Bosshardt
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Leetoria Hinojosa
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA
| | - Jianning Tao
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
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5
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Vcelkova T, Reiter W, Zylka M, Hollenstein D, Schuckert S, Hartl M, Seiser C. GSE1 links the HDAC1/CoREST co-repressor complex to DNA damage. Nucleic Acids Res 2023; 51:11748-11769. [PMID: 37878419 PMCID: PMC10681733 DOI: 10.1093/nar/gkad911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023] Open
Abstract
Post-translational modifications of histones are important regulators of the DNA damage response (DDR). By using affinity purification mass spectrometry (AP-MS) we discovered that genetic suppressor element 1 (GSE1) forms a complex with the HDAC1/CoREST deacetylase/demethylase co-repressor complex. In-depth phosphorylome analysis revealed that loss of GSE1 results in impaired DDR, ATR signalling and γH2AX formation upon DNA damage induction. Altered profiles of ATR target serine-glutamine motifs (SQ) on DDR-related hallmark proteins point to a defect in DNA damage sensing. In addition, GSE1 knock-out cells show hampered DNA damage-induced phosphorylation on SQ motifs of regulators of histone post-translational modifications, suggesting altered histone modification. While loss of GSE1 does not affect the histone deacetylation activity of CoREST, GSE1 appears to be essential for binding of the deubiquitinase USP22 to CoREST and for the deubiquitination of H2B K120 in response to DNA damage. The combination of deacetylase, demethylase, and deubiquitinase activity makes the USP22-GSE1-CoREST subcomplex a multi-enzymatic eraser that seems to play an important role during DDR. Since GSE1 has been previously associated with cancer progression and survival our findings are potentially of high medical relevance.
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Affiliation(s)
- Terezia Vcelkova
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Martha Zylka
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - David M Hollenstein
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Stefan Schuckert
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
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6
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Zeng C, Chen J, Cooke EW, Subuddhi A, Roodman ET, Chen FX, Cao K. Demethylase-independent roles of LSD1 in regulating enhancers and cell fate transition. Nat Commun 2023; 14:4944. [PMID: 37607921 PMCID: PMC10444793 DOI: 10.1038/s41467-023-40606-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
The major enhancer regulator lysine-specific histone demethylase 1A (LSD1) is required for mammalian embryogenesis and is implicated in human congenital diseases and multiple types of cancer; however, the underlying mechanisms remain enigmatic. Here, we dissect the role of LSD1 and its demethylase activity in gene regulation and cell fate transition. Surprisingly, the catalytic inactivation of LSD1 has a mild impact on gene expression and cellular differentiation whereas the loss of LSD1 protein de-represses enhancers globally and impairs cell fate transition. LSD1 deletion increases H3K27ac levels and P300 occupancy at LSD1-targeted enhancers. The gain of H3K27ac catalyzed by P300/CBP, not the loss of CoREST complex components from chromatin, contributes to the transcription de-repression of LSD1 targets and differentiation defects caused by LSD1 loss. Together, our study demonstrates a demethylase-independent role of LSD1 in regulating enhancers and cell fate transition, providing insight into treating diseases driven by LSD1 mutations and misregulation.
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Affiliation(s)
- Cheng Zeng
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Jiwei Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai, China
| | - Emmalee W Cooke
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Arijita Subuddhi
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Eliana T Roodman
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai, China
| | - Kaixiang Cao
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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7
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Gräwe C, Hernandez-Quiles M, Jansen PWTC, Brimmers A, Vermeulen M. Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy. J Proteome Res 2023; 22:2683-2693. [PMID: 37466164 PMCID: PMC10407929 DOI: 10.1021/acs.jproteome.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 07/20/2023]
Abstract
In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS1-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and determination of apparent binding affinities. We benchmarked PASMAN using the SP/KLF motif and further applied it to gain insights into two CGCG-containing consensus DNA motifs. These motifs are recognized by two BEN domain-containing proteins, BANP and BEND3, which we find to interact with these motifs with distinct affinities. Finally, we profiled the BEND3 proximal proteome, revealing the NuRD complex as the major BEND3 proximal protein complex in vivo. In summary, PASMAN represents, to our knowledge, the first higher-order multiplexing-based interaction proteomics method that can be used to decipher specific DNA-protein interactions and their apparent affinities in various biological and pathological contexts.
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Affiliation(s)
- Cathrin Gräwe
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Miguel Hernandez-Quiles
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| | - Pascal W. T. C. Jansen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Annika Brimmers
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - 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
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
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8
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Investigation of SAMD1 ablation in mice. Sci Rep 2023; 13:3000. [PMID: 36810619 PMCID: PMC9944271 DOI: 10.1038/s41598-023-29779-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
SAM domain-containing protein 1 (SAMD1) has been implicated in atherosclerosis, as well as in chromatin and transcriptional regulation, suggesting a versatile and complex biological function. However, its role at an organismal level is currently unknown. Here, we generated SAMD1-/- and SAMD1+/- mice to explore the role of SAMD1 during mouse embryogenesis. Homozygous loss of SAMD1 was embryonic lethal, with no living animals seen after embryonic day 18.5. At embryonic day 14.5, organs were degrading and/or incompletely developed, and no functional blood vessels were observed, suggesting failed blood vessel maturation. Sparse red blood cells were scattered and pooled, primarily near the embryo surface. Some embryos had malformed heads and brains at embryonic day 15.5. In vitro, SAMD1 absence impaired neuronal differentiation processes. Heterozygous SAMD1 knockout mice underwent normal embryogenesis and were born alive. Postnatal genotyping showed a reduced ability of these mice to thrive, possibly due to altered steroidogenesis. In summary, the characterization of SAMD1 knockout mice suggests a critical role of SAMD1 during developmental processes in multiple organs and tissues.
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9
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LSD1 for the Targeted Regulation of Adipose Tissue. Curr Issues Mol Biol 2022; 45:151-163. [PMID: 36661498 PMCID: PMC9857158 DOI: 10.3390/cimb45010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/23/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
White and thermal (brown and beige) adipose tissue energy storage and oxidative regulation pathways play a central role in maintaining the energy balance throughout the body, and the dysregulation of these pathways is closely related to glucose and lipid metabolism disorders and adipose tissue dysfunction, including obesity, chronic inflammation, insulin resistance, mitochondrial dysfunction, and fibrosis. Recent epigenetic studies have identified the novel regulatory element LSD1, which controls the above parameters, and have provided new mechanistic possibilities for re-encoding the fate and function of adipocytes. In this review, we outline the current advances in adipocyte metabolism in physiology and disease and discuss possible strategies for LSD1 to alter the phenotype of adipose tissue and thus influence energy utilization to improve metabolic health.
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10
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Lee K, Whedon SD, Wang ZA, Cole PA. Distinct biochemical properties of the class I histone deacetylase complexes. Curr Opin Chem Biol 2022; 70:102179. [PMID: 35803024 PMCID: PMC10786639 DOI: 10.1016/j.cbpa.2022.102179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/22/2022]
Abstract
Classical histone deacetylases (HDACs) are enzymes that can hydrolytically cleave acetyl-Lys in histones and other proteins and serve as established drug targets in some forms of cancer. Class I HDACs 1-3 typically exist in a range of multiprotein complexes inside cells and show distinct biological functions in modulating gene expression. In recent years, it has become possible to purify and analyze the structure and enzymatic properties of several of these HDAC complexes, including CoREST, MiDAC, NuRD, Sin3, SMRT, MIER, and RERE. Here, we summarize what is experimentally established and/or computationally predicted about the structure of these complexes to describe their particular catalytic activities and site-specificities with modified nucleosome substrates.
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Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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