1
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Lopes M, Lund PJ, Garcia BA. An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.596744. [PMID: 38915586 PMCID: PMC11195131 DOI: 10.1101/2024.06.11.596744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The eukaryotic genome is packaged around histone proteins, which are subject to a myriad of post-translational modifications. By controlling DNA accessibility and the recruitment of protein complexes that mediate chromatin-related processes, these modifications constitute a key mechanism of epigenetic regulation. Since mass spectrometry can easily distinguish between these different modifications, it has become an essential technique in deciphering the histone code. Although robust LC-MS/MS methods are available to analyze modifications on the histone N-terminal tails, routine methods for characterizing ubiquitin marks on histone C-terminal regions, especially H2AK119ub, are less robust. Here we report the development of a simple workflow for the detection and improved quantification of the canonical histone ubiquitination marks H2AK119ub and H2BK120ub. The method entails a fully tryptic digestion of acid-extracted histones followed by derivatization with heavy or light propionic anhydride. A pooled sample is then spiked into oppositely labeled single samples as a reference channel for relative quantification, and data is acquired using PRM-based nanoLC-MS/MS. We validated our approach with synthetic peptides as well as treatments known to modulate the levels of H2AK119ub and H2BK120ub. This new method complements existing histone workflows, largely focused on the lysine-rich N-terminal regions, by extending modification analysis to other sequence contexts.
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Affiliation(s)
- Mariana Lopes
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peder J. Lund
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Benjamin A. Garcia
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Dept. of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110
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2
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Gates LA, Reis BS, Lund PJ, Paul MR, Leboeuf M, Djomo AM, Nadeem Z, Lopes M, Vitorino FN, Unlu G, Carroll TS, Birsoy K, Garcia BA, Mucida D, Allis CD. Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression. Nat Metab 2024; 6:697-707. [PMID: 38413806 DOI: 10.1038/s42255-024-00992-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Post-translational modifications (PTMs) on histones are a key source of regulation on chromatin through impacting cellular processes, including gene expression1. These PTMs often arise from metabolites and are thus impacted by metabolism and environmental cues2-7. One class of metabolically regulated PTMs are histone acylations, which include histone acetylation, butyrylation, crotonylation and propionylation3,8. As these PTMs can be derived from short-chain fatty acids, which are generated by the commensal microbiota in the intestinal lumen9-11, we aimed to define how microbes impact the host intestinal chromatin landscape, mainly in female mice. Here we show that in addition to acetylation, intestinal epithelial cells from the caecum and distal mouse intestine also harbour high levels of butyrylation and propionylation on lysines 9 and 27 of histone H3. We demonstrate that these acylations are regulated by the microbiota and that histone butyrylation is additionally regulated by the metabolite tributyrin. Tributyrin-regulated gene programmes are correlated with histone butyrylation, which is associated with active gene-regulatory elements and levels of gene expression. Together, our study uncovers a regulatory layer of how the microbiota and metabolites influence the intestinal epithelium through chromatin, demonstrating a physiological setting in which histone acylations are dynamically regulated and associated with gene regulation.
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Affiliation(s)
- Leah A Gates
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA.
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | | | - Peder J Lund
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Marylene Leboeuf
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Annaelle M Djomo
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Zara Nadeem
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
- Hunter College of the City University of New York, Yalow Honors Scholar Program, New York, NY, USA
| | - Mariana Lopes
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Francisca N Vitorino
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation & Genetics, The Rockefeller University, New York, NY, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Kivanç Birsoy
- Laboratory of Metabolic Regulation & Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
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3
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Kitamura N, Galligan JJ. A global view of the human post-translational modification landscape. Biochem J 2023; 480:1241-1265. [PMID: 37610048 PMCID: PMC10586784 DOI: 10.1042/bcj20220251] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology and as instrumentation continues to improve, this list will surely grow. While many PTMs have been studied in detail (e.g. phosphorylation, acetylation), the vast majority lack defined mechanisms for their regulation and impact on cell fate. In this review, we will highlight the field of PTM research as it currently stands, discussing the mechanisms that dictate site specificity, analytical methods for their detection and study, and the chemical tools that can be leveraged to define PTM regulation. In addition, we will highlight the approaches needed to discover and validate novel PTMs. Lastly, this review will provide a starting point for those interested in PTM biology, providing a comprehensive list of PTMs and what is known regarding their regulation and metabolic origins.
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Affiliation(s)
- Naoya Kitamura
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
| | - James J. Galligan
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
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4
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Khazaei S, Chen CCL, Andrade AF, Kabir N, Azarafshar P, Morcos SM, França JA, Lopes M, Lund PJ, Danieau G, Worme S, Adnani L, Nzirorera N, Chen X, Yogarajah G, Russo C, Zeinieh M, Wong CJ, Bryant L, Hébert S, Tong B, Sihota TS, Faury D, Puligandla E, Jawhar W, Sandy V, Cowan M, Nakada EM, Jerome-Majewska LA, Ellezam B, Gomes CC, Denecke J, Lessel D, McDonald MT, Pizoli CE, Taylor K, Cocanougher BT, Bhoj EJ, Gingras AC, Garcia BA, Lu C, Campos EI, Kleinman CL, Garzia L, Jabado N. Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration. Cell 2023; 186:1162-1178.e20. [PMID: 36931244 PMCID: PMC10112048 DOI: 10.1016/j.cell.2023.02.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
Germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated H3.3G34R/V/W knock-in mice and identified strikingly distinct developmental defects for each mutation. H3.3G34R-mutants exhibited progressive microcephaly and neurodegeneration, with abnormal accumulation of disease-associated microglia and concurrent neuronal depletion. G34R severely decreased H3K36me2 on the mutant H3.3 tail, impairing recruitment of DNA methyltransferase DNMT3A and its redistribution on chromatin. These changes were concurrent with sustained expression of complement and other innate immune genes possibly through loss of non-CG (CH) methylation and silencing of neuronal gene promoters through aberrant CG methylation. Complement expression in G34R brains may lead to neuroinflammation possibly accounting for progressive neurodegeneration. Our study reveals that H3.3G34-substitutions have differential impact on the epigenome, which underlie the diverse phenotypes observed, and uncovers potential roles for H3K36me2 and DNMT3A-dependent CH-methylation in modulating synaptic pruning and neuroinflammation in post-natal brains.
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Affiliation(s)
- Sima Khazaei
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | | | - Nisha Kabir
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Pariya Azarafshar
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Shahir M Morcos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Josiane Alves França
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana Lopes
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Peder J Lund
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Geoffroy Danieau
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Samantha Worme
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Lata Adnani
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nadine Nzirorera
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Marine College, Shandong University, Weihai 264209, China
| | - Gayathri Yogarajah
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Caterina Russo
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michele Zeinieh
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven Hébert
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Bethany Tong
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Tianna S Sihota
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Damien Faury
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Evan Puligandla
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wajih Jawhar
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Child Health and Human Development, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Veronica Sandy
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada
| | - Emily M Nakada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Loydie A Jerome-Majewska
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Marie T McDonald
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | - Carolyn E Pizoli
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Kathryn Taylor
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | | | | | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Livia Garzia
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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5
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Chen LY, Wang WW, Wozniak JM, Parker CG. A heterobifunctional molecule system for targeted protein acetylation in cells. Methods Enzymol 2023; 681:287-323. [PMID: 36764762 DOI: 10.1016/bs.mie.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Protein acetylation is a vital biological process that regulates myriad cellular events. Despite its profound effects on protein function, there are limited research tools to dynamically and selectively regulate protein acetylation. To address this, we developed an acetylation tagging system, called AceTAG, to target proteins for chemically induced acetylation directly in live cells. AceTAG uses heterobifunctional molecules composed of a ligand for the lysine acetyltransferase p300/CBP and a FKBP12F36V ligand. Target proteins are genetically tagged with FKBP12F36V and brought in proximity with p300/CBP by AceTAG molecules to subsequently undergo protein-specific acetylation. Targeted acetylation of proteins in cells using AceTAG is selective, rapid, and can be modulated in a dose-dependent fashion, enabling controlled investigations of acetylated protein targets directly in cells. In this protocol, we focus on (1) generation of AceTAG constructs and cell lines, (2) in vitro characterization of AceTAG mediated ternary complex formation and cellular target engagement studies; and (3) in situ characterization of AceTAG induced acetylation of targeted proteins by immunoblotting and quantitative proteomics. The robust procedures described herein should enable the use of AceTAG to explore the roles of acetylation for a variety of protein targets.
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Affiliation(s)
- Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Wesley Wei Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, United States.
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6
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Lund PJ, Gates LA, Leboeuf M, Smith SA, Chau L, Lopes M, Friedman ES, Saiman Y, Kim MS, Shoffler CA, Petucci C, Allis CD, Wu GD, Garcia BA. Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation. Cell Rep 2022; 41:111809. [PMID: 36516747 PMCID: PMC9994635 DOI: 10.1016/j.celrep.2022.111809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 03/09/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota influences acetylation on host histones by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-coenzyme A (CoA), a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis.
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Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah A Gates
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Marylene Leboeuf
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Sarah A Smith
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lillian Chau
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariana Lopes
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elliot S Friedman
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yedidya Saiman
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Min Soo Kim
- Metabolomics Core, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clarissa A Shoffler
- Metabolomics Core, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Petucci
- Metabolomics Core, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Gary D Wu
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Wenes M, Jaccard A, Wyss T, Maldonado-Pérez N, Teoh ST, Lepez A, Renaud F, Franco F, Waridel P, Yacoub Maroun C, Tschumi B, Dumauthioz N, Zhang L, Donda A, Martín F, Migliorini D, Lunt SY, Ho PC, Romero P. The mitochondrial pyruvate carrier regulates memory T cell differentiation and antitumor function. Cell Metab 2022; 34:731-746.e9. [PMID: 35452600 PMCID: PMC9116152 DOI: 10.1016/j.cmet.2022.03.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/25/2022] [Accepted: 03/30/2022] [Indexed: 12/26/2022]
Abstract
Glycolysis, including both lactate fermentation and pyruvate oxidation, orchestrates CD8+ T cell differentiation. However, how mitochondrial pyruvate metabolism and uptake controlled by the mitochondrial pyruvate carrier (MPC) impact T cell function and fate remains elusive. We found that genetic deletion of MPC drives CD8+ T cell differentiation toward a memory phenotype. Metabolic flexibility induced by MPC inhibition facilitated acetyl-coenzyme-A production by glutamine and fatty acid oxidation that results in enhanced histone acetylation and chromatin accessibility on pro-memory genes. However, in the tumor microenvironment, MPC is essential for sustaining lactate oxidation to support CD8+ T cell antitumor function. We further revealed that chimeric antigen receptor (CAR) T cell manufacturing with an MPC inhibitor imprinted a memory phenotype and demonstrated that infusing MPC inhibitor-conditioned CAR T cells resulted in superior and long-lasting antitumor activity. Altogether, we uncover that mitochondrial pyruvate uptake instructs metabolic flexibility for guiding T cell differentiation and antitumor responses.
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Affiliation(s)
- Mathias Wenes
- Department of Oncology, University of Lausanne, Épalinges, Switzerland.
| | - Alison Jaccard
- Department of Oncology, University of Lausanne, Épalinges, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Épalinges, Switzerland
| | - Tania Wyss
- Department of Oncology, University of Lausanne, Épalinges, Switzerland
| | - Noelia Maldonado-Pérez
- Gene and Cell Therapy Unit, Genomic Medicine Department, Pfizer-University of Granada-Junta de Andalucía, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Shao Thing Teoh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Anouk Lepez
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland; Swiss Cancer Center Léman, Geneva and Lausanne, Switzerland
| | - Fabrice Renaud
- Department of Oncology, University of Lausanne, Épalinges, Switzerland
| | - Fabien Franco
- Department of Oncology, University of Lausanne, Épalinges, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Épalinges, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, University of Lausanne, Lausanne, Switzerland
| | | | - Benjamin Tschumi
- Department of Oncology, University of Lausanne, Épalinges, Switzerland
| | - Nina Dumauthioz
- Department of Oncology, University of Lausanne, Épalinges, Switzerland
| | - Lianjun Zhang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Alena Donda
- Department of Oncology, University of Lausanne, Épalinges, Switzerland
| | - Francisco Martín
- Gene and Cell Therapy Unit, Genomic Medicine Department, Pfizer-University of Granada-Junta de Andalucía, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Denis Migliorini
- Brain Tumor and Immune Cell Engineering Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland; Swiss Cancer Center Léman, Geneva and Lausanne, Switzerland; Department of Oncology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Épalinges, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, Épalinges, Switzerland
| | - Pedro Romero
- Department of Oncology, University of Lausanne, Épalinges, Switzerland.
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8
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Hermann J, Schurgers L, Jankowski V. Identification and characterization of post-translational modifications: Clinical implications. Mol Aspects Med 2022; 86:101066. [PMID: 35033366 DOI: 10.1016/j.mam.2022.101066] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Post-translational modifications (PTMs) generate marginally modified isoforms of native peptides, proteins and lipoproteins thereby regulating protein functions, molecular interactions, and localization. With a key role in functional proteomics, post-translational modifications are recently also associated with the onsets and progressions of various diseases, such as cancer, cardiovascular, renal, and metabolic diseases. With the impact of post-translational modifications becoming increasingly clear, its reliable detection and quantification remain a major obstacle in the translation of these novel pathological markers into clinical diagnosis. While current antibody-based clinical diagnostics struggle to detect and quantify these marginal protein and lipoprotein alterations, state-of-the-art mass spectrometric, proteomic approaches provide the mass accuracy and resolving power necessary to isolate, identify and quantify novel and pathological post-translational modifications; however clinical translation of mass spectrometric applications are still facing major challenges. Here we review the status quo of the clinical translation of mass-spectrometric applications as novel diagnostic tools for the identification and quantification of post-translational modifications and focus on the emerging role of mass spectrometric methods in the clinical assessment of PTMs in disease states.
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Affiliation(s)
- Juliane Hermann
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Leon Schurgers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200, MD, Maastricht, the Netherlands
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.
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Karlstaedt A. Stable Isotopes for Tracing Cardiac Metabolism in Diseases. Front Cardiovasc Med 2021; 8:734364. [PMID: 34859064 PMCID: PMC8631909 DOI: 10.3389/fcvm.2021.734364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Although metabolic remodeling during cardiovascular diseases has been well-recognized for decades, the recent development of analytical platforms and mathematical tools has driven the emergence of assessing cardiac metabolism using tracers. Metabolism is a critical component of cellular functions and adaptation to stress. The pathogenesis of cardiovascular disease involves metabolic adaptation to maintain cardiac contractile function even in advanced disease stages. Stable-isotope tracer measurements are a powerful tool for measuring flux distributions at the whole organism level and assessing metabolic changes at a systems level in vivo. The goal of this review is to summarize techniques and concepts for in vivo or ex vivo stable isotope labeling in cardiovascular research, to highlight mathematical concepts and their limitations, to describe analytical methods at the tissue and single-cell level, and to discuss opportunities to leverage metabolic models to address important mechanistic questions relevant to all patients with cardiovascular disease.
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Affiliation(s)
- Anja Karlstaedt
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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10
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Saiman Y, David Shen TC, Lund PJ, Gershuni VM, Jang C, Patel S, Jung S, Furth EE, Friedman ES, Chau L, Garcia BA, Wu GD. Global Microbiota-Dependent Histone Acetylation Patterns Are Irreversible and Independent of Short Chain Fatty Acids. Hepatology 2021; 74:3427-3440. [PMID: 34233020 PMCID: PMC9867598 DOI: 10.1002/hep.32043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND AIMS Although germ-free mice are an indispensable tool in studying the gut microbiome and its effects on host physiology, they are phenotypically different than their conventional counterparts. While antibiotic-mediated microbiota depletion in conventional mice leads to physiologic alterations that often mimic the germ-free state, the degree to which the effects of microbial colonization on the host are reversible is unclear. The gut microbiota produce abundant short chain fatty acids (SCFAs), and previous studies have demonstrated a link between microbial-derived SCFAs and global hepatic histone acetylation in germ-free mice. APPROACH AND RESULTS We demonstrate that global hepatic histone acetylation states measured by mass spectrometry remained largely unchanged despite loss of luminal and portal vein SCFAs after antibiotic-mediated microbiota depletion. In contrast to stable hepatic histone acetylation states, we see robust hepatic transcriptomic alterations after microbiota depletion. Additionally, neither dietary supplementation with supraphysiologic levels of SCFA nor the induction of hepatocyte proliferation in the absence of microbiota-derived SCFAs led to alterations in global hepatic histone acetylation. CONCLUSIONS These results suggest that microbiota-dependent landscaping of the hepatic epigenome through global histone acetylation is static in nature, while the hepatic transcriptome is responsive to alterations in the gut microbiota.
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Affiliation(s)
- Yedidya Saiman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ting-Chin David Shen
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peder J. Lund
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Victoria M. Gershuni
- Department of Surgery, Perelman School of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Cholsoon Jang
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Shivali Patel
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Emma E. Furth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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11
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Dunphy K, Dowling P, Bazou D, O’Gorman P. Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers. Cancers (Basel) 2021; 13:1930. [PMID: 33923680 PMCID: PMC8072572 DOI: 10.3390/cancers13081930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
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