1
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Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA. DNA glycosylases provide antiviral defence in prokaryotes. Nature 2024; 629:410-416. [PMID: 38632404 PMCID: PMC11078745 DOI: 10.1038/s41586-024-07329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Bacteria have adapted to phage predation by evolving a vast assortment of defence systems1. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data2. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library3 with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.
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Affiliation(s)
- Amer A Hossain
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Ying Z Pigli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexis Thomas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Vincent K Libis
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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2
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Notti RQ, Yi F, Heissel S, Bush MW, Molina H, Molvi Z, Klebanoff CA, Walz T. The resting state of the human T-cell receptor-CD3 complex. bioRxiv 2024:2023.08.22.554360. [PMID: 37662363 PMCID: PMC10473723 DOI: 10.1101/2023.08.22.554360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The T-cell receptor (TCR) is central to the ligand-dependent activation of T lymphocytes and as such orchestrates both adaptive and pathologic immune processes 1 . However, major questions remain regarding the structure and function of the human TCR 2-4 . Here, we present cryogenic electron microscopy structures for the unliganded human TCR-CD3 complex in a native-like lipid bilayer, revealing two related conformations that are distinct from its structure in detergent. These new "closed and compacted" conformations afford insights into the interactions between the TCR-CD3 and the membrane, including conserved surface patches that make extensive outer leaflet contact, and suggest novel conformational regulation by glycans. We show that the closed/compacted conformations, not the extended one previously reported in detergent 5-8 , represent the unliganded resting state for the TCR-CD3 in vivo , underscoring the importance of structural interrogation of membrane proteins in native-like environments. We use conformation-locking disulfide mutants to show that ectodomain opening is necessary for maximal ligand-dependent TCR-CD3 activation, demonstrating that TCR-intrinsic conformational change is necessary for full TCR-CD3 activation and opening numerous avenues for immunoreceptor engineering.
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3
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Heissel S, He Y, Jankevics A, Shi Y, Molina H, Viner R, Scheltema RA. Fast and Accurate Disulfide Bridge Detection. Mol Cell Proteomics 2024; 23:100759. [PMID: 38574859 PMCID: PMC11067345 DOI: 10.1016/j.mcpro.2024.100759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/08/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Recombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multibillion dollar industry. Essential here is the quality control assessment of critical attributes, such as sequence fidelity, proper folding, and posttranslational modifications. Errors can lead to diminished bioactivity and, in the context of therapeutic proteins, an elevated risk for immunogenicity. Over the years, many techniques were developed and applied to validate proteins in a standardized and high-throughput fashion. One parameter has, however, so far been challenging to assess. Disulfide bridges, covalent bonds linking two cysteine residues, assist in the correct folding and stability of proteins and thus have a major influence on their efficacy. Mass spectrometry promises to be an optimal technique to uncover them in a fast and accurate fashion. In this work, we present a unique combination of sample preparation, data acquisition, and analysis facilitating the rapid and accurate assessment of disulfide bridges in purified proteins. Through microwave-assisted acid hydrolysis, the proteins are digested rapidly and artifact-free into peptides, with a substantial degree of overlap over the sequence. The nonspecific nature of this procedure, however, introduces chemical background, which is efficiently removed by integrating ion mobility preceding the mass spectrometric measurement. The nonspecific nature of the digestion step additionally necessitates new developments in data analysis, for which we extended the XlinkX node in Proteome Discoverer to efficiently process the data and ensure correctness through effective false discovery rate correction. The entire workflow can be completed within 1 h, allowing for high-throughput, high-accuracy disulfide mapping.
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Affiliation(s)
- Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA.
| | - Yi He
- Thermo Fisher Scientific, San Jose, California, USA
| | - Andris Jankevics
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Structural Proteomics Group, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, California, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, California, USA.
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands; Structural Proteomics Group, Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, UK.
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4
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Zong Y, Weiss N, Wang K, Pagano AE, Heissel S, Perveen S, Huang J. Development of Complementary Photo-arginine/lysine to Promote Discovery of Arg/Lys hPTMs Interactomes. Adv Sci (Weinh) 2024; 11:e2307526. [PMID: 38298064 PMCID: PMC11005723 DOI: 10.1002/advs.202307526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/03/2023] [Indexed: 02/02/2024]
Abstract
Arginine and lysine, frequently appearing as a pair on histones, have been proven to carry diverse modifications and execute various epigenetic regulatory functions. However, the most context-specific and transient effectors of these marks, while significant, have evaded study as detection methods have thus far not reached a standard to capture these ephemeral events. Herein, a pair of complementary photo-arginine/δ-photo-lysine (R-dz/K-dz) probes is developed and involve these into histone peptide, nucleosome, and chromatin substrates to capture and explore the interactomes of Arg and Lys hPTMs. By means of these developed tools, this study identifies that H3R2me2a can recruit MutS protein homolog 6 (MSH6), otherwise repelDouble PHD fingers 2 (DPF2), Retinoblastoma binding protein 4/7 (RBBP4/7). And it is disclosed that H3R2me2a inhibits the chromatin remodeling activity of the cBAF complex by blocking the interaction between DPF2 (one component of cBAF) and the nucleosome. In addition, the novel pairs of H4K5 PTMs and respective readers are highlighted, namely H4K5me-Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2), H4K5me2-L3MBTL2, and H4K5acK8ac-YEATS domain-containing protein 4 (YEATS4). These powerful tools pave the way for future investigation of related epigenetic mechanisms including but not limited to hPTMs.
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Affiliation(s)
- Yu Zong
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | - Nicole Weiss
- Program of PharmacologyWeill Cornell Medical College of Cornell UniversityNew York10065USA
| | - Ke Wang
- Chemical Biology ProgramMemorial Sloan Kettering Cancer CenterNew York10065USA
| | | | - Søren Heissel
- Proteomics Resource CenterRockefeller UniversityNew York10065USA
| | - Sumera Perveen
- Structural Genomics ConsortiumUniversity of TorontoTorontoM5S3H2Canada
| | - Jian Huang
- Department of Molecular BiologyPrinceton UniversityPrinceton08544USA
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5
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Wu X, Yuan H, Wu Q, Gao Y, Duan T, Yang K, Huang T, Wang S, Yuan F, Lee D, Taori S, Plute T, Heissel S, Alwaseem H, Isay-Del Viscio M, Molina H, Agnihotri S, Hsu DJ, Zhang N, Rich JN. Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming. Nat Cancer 2024:10.1038/s43018-024-00748-7. [PMID: 38519786 DOI: 10.1038/s43018-024-00748-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Cancers commonly reprogram translation and metabolism, but little is known about how these two features coordinate in cancer stem cells. Here we show that glioblastoma stem cells (GSCs) display elevated protein translation. To dissect underlying mechanisms, we performed a CRISPR screen and identified YRDC as the top essential transfer RNA (tRNA) modification enzyme in GSCs. YRDC catalyzes the formation of N6-threonylcarbamoyladenosine (t6A) on ANN-decoding tRNA species (A denotes adenosine, and N denotes any nucleotide). Targeting YRDC reduced t6A formation, suppressed global translation and inhibited tumor growth both in vitro and in vivo. Threonine is an essential substrate of YRDC. Threonine accumulated in GSCs, which facilitated t6A formation through YRDC and shifted the proteome to support mitosis-related genes with ANN codon bias. Dietary threonine restriction (TR) reduced tumor t6A formation, slowed xenograft growth and augmented anti-tumor efficacy of chemotherapy and anti-mitotic therapy, providing a molecular basis for a dietary intervention in cancer treatment.
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Affiliation(s)
- Xujia Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China
| | - Huairui Yuan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Qiulian Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yixin Gao
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China
| | - Tingting Duan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Tengfei Huang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Shuai Wang
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Fanen Yuan
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Derrick Lee
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Suchet Taori
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tritan Plute
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Søren Heissel
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | | | - Henrik Molina
- Proteomics Resource Center, the Rockefeller University, New York, NY, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- John G. Rangos Sr. Research Center, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dennis J Hsu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nu Zhang
- Department of Neurosurgery, the First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou, China.
| | - Jeremy N Rich
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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6
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Bojmar L, Kim HS, Sugiura K, Heissel S, Lucotti S, Cioffi M, Johnson KE, Cohen-Gould L, Zhang H, Molina H, Matei IR, Lyden D, Hoshino A. Protocol for cross-platform characterization of human and murine extracellular vesicles and particles. STAR Protoc 2024; 5:102754. [PMID: 38096060 PMCID: PMC10762520 DOI: 10.1016/j.xpro.2023.102754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/04/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024] Open
Abstract
Characterization of isolated extracellular vesicles and particles (EVPs) is crucial for determining functions and biomarker potential. Here, we present a protocol to analyze size, number, morphology, and EVP protein cargo and to validate EVP proteins in both humans and mice. We describe steps for nanoparticle tracking analysis, transmission electron microscopy, single-EVP immunodetection, EVP proteomic mass spectrometry and bioinformatic analysis, and EVP protein validation by ExoELISA and western blot analysis. This allows for EVP cross-validation across different platforms. For complete details on the use and execution of this protocol, please refer to Hoshino et al.1.
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Affiliation(s)
- Linda Bojmar
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Han Sang Kim
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 FOUR Project, Yonsei University College of Medicine, Seoul, Korea
| | - Kei Sugiura
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michele Cioffi
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Kofi Ennu Johnson
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Leona Cohen-Gould
- Microscopy & Image Analysis, Core Facilities, Weill Cornell Medicine, New York, NY, USA
| | - Haiying Zhang
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Irina R Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Ayuko Hoshino
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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7
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Hanzel M, Fernando K, Maloney SE, Gong S, Mätlik K, Zhao J, Pasolli HA, Heissel S, Dougherty JD, Hull C, Hatten ME. Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties. bioRxiv 2024:2024.02.18.580354. [PMID: 38405978 PMCID: PMC10888872 DOI: 10.1101/2024.02.18.580354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Astrotactin 2 (ASTN2) is a transmembrane neuronal protein highly expressed in the cerebellum that functions in receptor trafficking and modulates cerebellar Purkinje cell (PC) synaptic activity. We recently reported a family with a paternally inherited intragenic ASTN2 duplication with a range of neurodevelopmental disorders, including autism spectrum disorder (ASD), learning difficulties, and speech and language delay. To provide a genetic model for the role of the cerebellum in ASD-related behaviors and study the role of ASTN2 in cerebellar circuit function, we generated global and PC-specific conditional Astn2 knockout (KO and cKO, respectively) mouse lines. Astn2 KO mice exhibit strong ASD-related behavioral phenotypes, including a marked decrease in separation-induced pup ultrasonic vocalization calls, hyperactivity and repetitive behaviors, altered social behaviors, and impaired cerebellar-dependent eyeblink conditioning. Hyperactivity and repetitive behaviors were also prominent in Astn2 cKO animals. By Golgi staining, Astn2 KO PCs have region-specific changes in dendritic spine density and filopodia numbers. Proteomic analysis of Astn2 KO cerebellum reveals a marked upregulation of ASTN2 family member, ASTN1, a neuron-glial adhesion protein. Immunohistochemistry and electron microscopy demonstrates a significant increase in Bergmann glia volume in the molecular layer of Astn2 KO animals. Electrophysiological experiments indicate a reduced frequency of spontaneous excitatory postsynaptic currents (EPSCs), as well as increased amplitudes of both spontaneous EPSCs and inhibitory postsynaptic currents (IPSCs) in the Astn2 KO animals, suggesting that pre- and postsynaptic components of synaptic transmission are altered. Thus, ASTN2 regulates ASD-like behaviors and cerebellar circuit properties.
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Affiliation(s)
- Michalina Hanzel
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA 10065
| | - Kayla Fernando
- Neurobiology Department, Duke University, Durham, NC, USA
| | - Susan E Maloney
- Dept of Psychiatry and the Intellectual and Developmental Disabilities Research Center, Washington University Medical School, St Louis, MO, USA
| | | | - Kärt Mätlik
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA 10065
| | - Jiajia Zhao
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA 10065
| | - H Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA 10065
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA 10065
| | - Joseph D Dougherty
- Dept of Psychiatry and the Intellectual and Developmental Disabilities Research Center, Washington University Medical School, St Louis, MO, USA
- Dept of Genetics, Washington University Medical School, St Louis, MO, USA
| | - Court Hull
- Neurobiology Department, Duke University, Durham, NC, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, USA 10065
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8
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Liu Y, Liu S, Tomar A, Yen FS, Unlu G, Ropek N, Weber RA, Wang Y, Khan A, Gad M, Peng J, Terzi E, Alwaseem H, Pagano AE, Heissel S, Molina H, Allwein B, Kenny TC, Possemato RL, Zhao L, Hite RK, Vinogradova EV, Mansy SS, Birsoy K. Autoregulatory control of mitochondrial glutathione homeostasis. Science 2023; 382:820-828. [PMID: 37917749 DOI: 10.1126/science.adf4154] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Mitochondria must maintain adequate amounts of metabolites for protective and biosynthetic functions. However, how mitochondria sense the abundance of metabolites and regulate metabolic homeostasis is not well understood. In this work, we focused on glutathione (GSH), a critical redox metabolite in mitochondria, and identified a feedback mechanism that controls its abundance through the mitochondrial GSH transporter, SLC25A39. Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. Depletion of GSH dissociates AFG3L2 from SLC25A39, causing a compensatory increase in mitochondrial GSH uptake. Genetic and proteomic analyses identified a putative iron-sulfur cluster in the matrix-facing loop of SLC25A39 as essential for this regulation, coupling mitochondrial iron homeostasis to GSH import. Altogether, our work revealed a paradigm for the autoregulatory control of metabolic homeostasis in organelles.
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Affiliation(s)
- Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Shanshan Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Anju Tomar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Cellular, Computational and Integrative Biology, Università di Trento, Trento, TN, Italy
| | - Frederick S Yen
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Nathalie Ropek
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY, USA
| | - Ross A Weber
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Ying Wang
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Mark Gad
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erdem Terzi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hanan Alwaseem
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexandra E Pagano
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Benjamin Allwein
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy C Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Richard L Possemato
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ekaterina V Vinogradova
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY, USA
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
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9
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Levin SN, Tomasini MD, Knox J, Shirani M, Shebl B, Requena D, Clark J, Heissel S, Alwaseem H, Surjan R, Lahasky R, Molina H, Torbenson MS, Lyons B, Migler RD, Coffino P, Simon SM. Disruption of proteome by an oncogenic fusion kinase alters metabolism in fibrolamellar hepatocellular carcinoma. Sci Adv 2023; 9:eadg7038. [PMID: 37343102 PMCID: PMC10284549 DOI: 10.1126/sciadv.adg7038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a usually lethal primary liver cancer driven by a somatic dysregulation of protein kinase A. We show that the proteome of FLC tumors is distinct from that of adjacent nontransformed tissue. These changes can account for some of the cell biological and pathological alterations in FLC cells, including their drug sensitivity and glycolysis. Hyperammonemic encephalopathy is a recurrent problem in these patients, and established treatments based on the assumption of liver failure are unsuccessful. We show that many of the enzymes that produce ammonia are increased and those that consume ammonia are decreased. We also demonstrate that the metabolites of these enzymes change as expected. Thus, hyperammonemic encephalopathy in FLC may require alternative therapeutics.
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Affiliation(s)
- Solomon N. Levin
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michael D. Tomasini
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - James Knox
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Mahsa Shirani
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jackson Clark
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Rodrigo Surjan
- General Surgery Division, Surgery Department, Hospital Nove de Julho, São Paulo, Brazil
| | - Ron Lahasky
- Lahasky Medical Clinic, Abbeville, LA 70510, USA
- The Fibrolamellar Registry, New York, NY 10028, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | | | - Barbara Lyons
- The Fibrolamellar Registry, New York, NY 10028, USA
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | | | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sanford M. Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- The Fibrolamellar Registry, New York, NY 10028, USA
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10
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Kenny TC, Khan A, Son Y, Yue L, Heissel S, Sharma A, Pasolli HA, Liu Y, Gamazon ER, Alwaseem H, Hite RK, Birsoy K. Integrative genetic analysis identifies FLVCR1 as a plasma-membrane choline transporter in mammals. Cell Metab 2023; 35:1057-1071.e12. [PMID: 37100056 PMCID: PMC10367582 DOI: 10.1016/j.cmet.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023]
Abstract
Genome-wide association studies (GWASs) of serum metabolites have the potential to uncover genes that influence human metabolism. Here, we combined an integrative genetic analysis that associates serum metabolites to membrane transporters with a coessentiality map of metabolic genes. This analysis revealed a connection between feline leukemia virus subgroup C cellular receptor 1 (FLVCR1) and phosphocholine, a downstream metabolite of choline metabolism. Loss of FLVCR1 in human cells strongly impairs choline metabolism due to the inhibition of choline import. Consistently, CRISPR-based genetic screens identified phospholipid synthesis and salvage machinery as synthetic lethal with FLVCR1 loss. Cells and mice lacking FLVCR1 exhibit structural defects in mitochondria and upregulate integrated stress response (ISR) through heme-regulated inhibitor (HRI) kinase. Finally, Flvcr1 knockout mice are embryonic lethal, which is partially rescued by choline supplementation. Altogether, our findings propose FLVCR1 as a major choline transporter in mammals and provide a platform to discover substrates for unknown metabolite transporters.
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Affiliation(s)
- Timothy C Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Yeeun Son
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lishu Yue
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Anurag Sharma
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - H Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
| | - Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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11
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Kenari AN, Bojmar L, Heissel S, Molina H, Lyden D, Hoshino A. Protocol for Plasma Extracellular Vesicle and Particle Isolation and Mass Spectrometry-Based Proteomic Identification. Methods Mol Biol 2023; 2628:291-300. [PMID: 36781793 DOI: 10.1007/978-1-0716-2978-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Plasma extracellular vesicles and particles (EVPs) are enriched in biomolecules that reflect individuals' physiological and pathological states. Several studies have demonstrated the potential of human plasma EVPs as a novel liquid biopsy. Here we describe a protocol for human plasma EVPs isolation and proteomic characterization. We isolated human plasma EVPs by the classical ultracentrifugation method and performed mass spectrometry-based proteomic profiling. Using this protocol, researchers can reveal the plasma EVPs proteome and explore the clinical application of plasma EVPs proteins for developing disease biomarkers.
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Affiliation(s)
| | - Linda Bojmar
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ayuko Hoshino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
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12
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Rosain J, Neehus AL, Manry J, Yang R, Le Pen J, Daher W, Liu Z, Chan YH, Tahuil N, Türel Ö, Bourgey M, Ogishi M, Doisne JM, Izquierdo HM, Shirasaki T, Le Voyer T, Guérin A, Bastard P, Moncada-Velez M, Han JE, Khan T, Rapaport F, Hong SH, Cheung A, Haake K, Mindt BC, Perez L, Philippot Q, Lee D, Zhang P, Rinchai D, Al Ali F, Ata MMA, Rahman M, Peel JN, Heissel S, Molina H, Kendir-Demirkol Y, Bailey R, Zhao S, Bohlen J, Mancini M, Seeleuthner Y, Roelens M, Lorenzo L, Soudée C, Paz MEJ, Gonzalez ML, Jeljeli M, Soulier J, Romana S, L’Honneur AS, Materna M, Martínez-Barricarte R, Pochon M, Oleaga-Quintas C, Michev A, Migaud M, Lévy R, Alyanakian MA, Rozenberg F, Croft CA, Vogt G, Emile JF, Kremer L, Ma CS, Fritz JH, Lemon SM, Spaan AN, Manel N, Abel L, MacDonald MR, Boisson-Dupuis S, Marr N, Tangye SG, Di Santo JP, Zhang Q, Zhang SY, Rice CM, Béziat V, Lachmann N, Langlais D, Casanova JL, Gros P, Bustamante J. Human IRF1 governs macrophagic IFN-γ immunity to mycobacteria. Cell 2023; 186:621-645.e33. [PMID: 36736301 PMCID: PMC9907019 DOI: 10.1016/j.cell.2022.12.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023]
Abstract
Inborn errors of human IFN-γ-dependent macrophagic immunity underlie mycobacterial diseases, whereas inborn errors of IFN-α/β-dependent intrinsic immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria and related intramacrophagic pathogens. These children have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2, which is life-threatening in individuals with impaired IFN-α/β immunity. In leukocytes or fibroblasts stimulated in vitro, IRF1-dependent responses to IFN-γ are, both quantitatively and qualitatively, much stronger than those to IFN-α/β. Moreover, IRF1-deficient mononuclear phagocytes do not control mycobacteria and related pathogens normally when stimulated with IFN-γ. By contrast, IFN-α/β-dependent intrinsic immunity to nine viruses, including SARS-CoV-2, is almost normal in IRF1-deficient fibroblasts. Human IRF1 is essential for IFN-γ-dependent macrophagic immunity to mycobacteria, but largely redundant for IFN-α/β-dependent antiviral immunity.
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Affiliation(s)
- Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France; Paris Cité University, Imagine Institute, 75015 Paris, France.
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,Institute of Experimental Hematology, REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Wassim Daher
- Infectious Disease Research Institute of Montpellier (IRIM), Montpellier University, 34000 Montpellier, France,Inserm, IRIM, 34293 Montpellier, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Yi-Hao Chan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Natalia Tahuil
- Department of Immunology, Del Niño Jesus Hospital, T4000 San Miguel de Tucuman, Tucuman, Argentina
| | - Özden Türel
- Department of Pediatric Infectious Disease, Bezmialem Vakif University Faculty of Medicine, 34093 İstanbul, Turkey
| | - Mathieu Bourgey
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Canadian Centre for Computation Genomics, Montreal, QC H3A 0G1, Canada
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France,Inserm U1223, 75015 Paris, France
| | | | - Takayoshi Shirasaki
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Antoine Guérin
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2052, Australia
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA,Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Taushif Khan
- Department of Immunology, Sidra Medicine, Doha, Qatar
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Seon-Hui Hong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Andrew Cheung
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Kathrin Haake
- Institute of Experimental Hematology, REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Barbara C. Mindt
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3A 0G1, Canada,FOCiS Centre of Excellence in Translational Immunology, McGill University, Montreal, QC H3A 0G1, Canada
| | - Laura Perez
- Department of Immunology and Rheumatology, “J. P. Garrahan” National Hospital of Pediatrics, C1245 CABA, Buenos Aires, Argentina
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Danyel Lee
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Fatima Al Ali
- Department of Immunology, Sidra Medicine, Doha, Qatar
| | | | | | - Jessica N. Peel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Yasemin Kendir-Demirkol
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA,Umraniye Education and Research Hospital, Department of Pediatric Genetics, 34764 İstanbul, Turkey
| | - Rasheed Bailey
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Shuxiang Zhao
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Mathieu Mancini
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3A 0G1, Canada
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Marie Roelens
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France,Paris Cité University, 75006 Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Camille Soudée
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - María Elvira Josefina Paz
- Department of Pediatric Pathology, Del Niño Jesus Hospital, T4000 San Miguel de Tucuman, Tucuman, Argentina
| | - Maria Laura Gonzalez
- Central Laboratory, Del Niño Jesus Hospital, T4000 San Miguel de Tucuman, Tucuman, Argentina
| | - Mohamed Jeljeli
- Cochin University Hospital, Biological Immunology Unit, AP-HP, 75014 Paris, France
| | - Jean Soulier
- Inserm/CNRS U944/7212, Paris Cité University, 75006 Paris, France,Hematology Laboratory, Saint-Louis Hospital, AP-HP, 75010 Paris, France,,National Reference Center for Bone Marrow Failures, Saint-Louis and Robert Debré Hospitals, 75010 Paris, France
| | - Serge Romana
- Rare Disease Genomic Medicine Department, Paris Cité University, Necker Hospital for Sick Children, 75015 Paris, France
| | | | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Rubén Martínez-Barricarte
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mathieu Pochon
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Alexandre Michev
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France
| | - Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | | | - Flore Rozenberg
- Department of Virology, Paris Cité University, Cochin Hospital, 75014 Paris, France
| | - Carys A. Croft
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France,Inserm U1223, 75015 Paris, France,Paris Cité University, 75006 Paris, France
| | - Guillaume Vogt
- Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes, Lille University, Lille Pasteur Institute, Lille University Hospital, 59000 Lille, France,Neglected Human Genetics Laboratory, Paris Cité University, 75006 Paris, France
| | - Jean-François Emile
- Pathology Department, Ambroise-Paré Hospital, AP-HP, 92100 Boulogne-Billancourt, France
| | - Laurent Kremer
- Infectious Disease Research Institute of Montpellier (IRIM), Montpellier University, 34000 Montpellier, France,Inserm, IRIM, 34293 Montpellier, France
| | - Cindy S. Ma
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2052, Australia
| | - Jörg H. Fritz
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3A 0G1, Canada,FOCiS Centre of Excellence in Translational Immunology, McGill University, Montreal, QC H3A 0G1, Canada,Department of Physiology, McGill University, Montreal, QC H3A 0G1, Canada
| | - Stanley M. Lemon
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
| | - András N. Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584CX Utrecht, The Netherlands
| | - Nicolas Manel
- Institut Curie, PSL Research University, Inserm U932, 75005 Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nico Marr
- Department of Immunology, Sidra Medicine, Doha, Qatar,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of NSW, Sydney, NSW 2052, Australia
| | - James P. Di Santo
- Innate Immunity Unit, Institut Pasteur, 75015 Paris, France,Inserm U1223, 75015 Paris, France
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France,Paris Cité University, Imagine Institute, 75015 Paris, France,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Nico Lachmann
- Institute of Experimental Hematology, REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany,Department of Pediatric Pulmonology, Allergology and Neonatology and Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover Medical School, 30625 Hannover, Germany, EU,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - David Langlais
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France; Paris Cité University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA; Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065, USA.
| | - Philippe Gros
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada,Department of Biochemistry, McGill University, Montreal, QC H3A 0G1, Canada
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Inserm U1163, 75015 Paris, France; Paris Cité University, Imagine Institute, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA; Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France.
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13
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Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Wu Q, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF. Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells. Sci Adv 2023; 9:eade9120. [PMID: 36608131 PMCID: PMC9821863 DOI: 10.1126/sciadv.ade9120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/01/2022] [Indexed: 05/18/2023]
Abstract
Utilization of specific codons varies between organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine limitation-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced an adaptive proteomic shift toward low-arginine codon-containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.
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Affiliation(s)
- Dennis J. Hsu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Gao
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexandra Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Qiushuang Wu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Maria Liberti
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
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14
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Mighty J, Rubio-Navarro A, Shi C, Zhou J, Flores-Bellver M, Heissel S, Onwumere O, Einbond L, Gharbaran R, Casper DS, Benito-Martin A, Redenti S. Extracellular vesicles of human diabetic retinopathy retinal tissue and urine of diabetic retinopathy patients are enriched for the junction plakoglo bin protein. Front Endocrinol (Lausanne) 2023; 13:1077644. [PMID: 36686464 PMCID: PMC9854122 DOI: 10.3389/fendo.2022.1077644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Diabetic Retinopathy (DR) is a potentially blinding retinal disorder that develops through the pathogenesis of diabetes. The lack of disease predictors implies a poor prognosis with frequent irreversible retinal damage and vision loss. Extracellular Vesicles (EVs) present a novel opportunity for pre-symptomatic disease diagnosis and prognosis, both severely limited in DR. All biological fluids contain EVs, which are currently being studied as disease biomarkers. EV proteins derived from urine have emerged as potential noninvasive biomarkers. Methods In this study, we isolated EVs from DR retinal tissue explants and from DR patients' urine, and characterized the vesicles, finding differences in particle number and size. Next, we performed proteomic analysis on human explanted DR retinal tissue conditioned media, DR retinal EVs and DR urinary EVs and compared to normal human retinal tissue, retinal EVs, and urinary EVs, respectively. Results Our system biology analysis of DR tissue and EV expression profiles revealed biological pathways related to cell-to-cell junctions, vesicle biology, and degranulation processes. Junction Plakoglobin (JUP), detected in DR tissue-derived EVs and DR urinary EVs, but not in controls, was revealed to be a central node in many identified pathogenic pathways. Proteomic results were validated by western blot. Urinary EVs obtained from healthy donors and diabetic patient without DR did not contain JUP. Conclusion The absence of JUP in healthy urinary EVs provide the basis for development of a novel Diabetic Retinopathy biomarker, potentially facilitating diagnosis.
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Affiliation(s)
- Jason Mighty
- Lehman College, City University of New York, Bronx, NY, United States
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, NY, United States
| | - Alfonso Rubio-Navarro
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
- Instituto de Investigación Biosanitaria ibs GRANADA, University Hospitals of Granada-University of Granada, Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, Granada, Spain
| | - Cui Shi
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, NY, United States
| | - Jing Zhou
- Lehman College, City University of New York, Bronx, NY, United States
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, NY, United States
| | - Miguel Flores-Bellver
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, Aurora, CO, United States
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, United States
| | - Onyekwere Onwumere
- Lehman College, City University of New York, Bronx, NY, United States
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, NY, United States
| | - Linda Einbond
- Lehman College, City University of New York, Bronx, NY, United States
| | | | - Daniel S. Casper
- Department of Ophthalmology, Columbia University Vagelos College of Physicians & Surgeons Naomi Berrie Diabetes Center, New York, NY, United States
| | - Alberto Benito-Martin
- Lehman College, City University of New York, Bronx, NY, United States
- Universidad Alfonso X El Sabio, Facultad de Medicina. Unidad de Investigación Biomédica, Madrid, Spain
| | - Stephen Redenti
- Lehman College, City University of New York, Bronx, NY, United States
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, New York, NY, United States
- Department of Ophthalmology, Columbia University Vagelos College of Physicians & Surgeons Naomi Berrie Diabetes Center, New York, NY, United States
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15
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Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF. Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells. bioRxiv 2023:2023.01.02.521806. [PMID: 36711568 PMCID: PMC9881871 DOI: 10.1101/2023.01.02.521806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Utilization of specific codons varies significantly across organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine restriction-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced a proteomic shift towards low arginine codon containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.
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Affiliation(s)
- Dennis J. Hsu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Gao
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexandra Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Maria Liberti
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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16
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Spaan AN, Neehus AL, Laplantine E, Staels F, Ogishi M, Seeleuthner Y, Rapaport F, Lacey KA, Van Nieuwenhove E, Chrabieh M, Hum D, Migaud M, Izmiryan A, Lorenzo L, Kochetkov T, Heesterbeek DAC, Bardoel BW, DuMont AL, Dobbs K, Chardonnet S, Heissel S, Baslan T, Zhang P, Yang R, Bogunovic D, Wunderink HF, Haas PJA, Molina H, Van Buggenhout G, Lyonnet S, Notarangelo LD, Seppänen MRJ, Weil R, Seminario G, Gomez-Tello H, Wouters C, Mesdaghi M, Shahrooei M, Bossuyt X, Sag E, Topaloglu R, Ozen S, Leavis HL, van Eijk MMJ, Bezrodnik L, Blancas Galicia L, Hovnanian A, Nassif A, Bader-Meunier B, Neven B, Meyts I, Schrijvers R, Puel A, Bustamante J, Aksentijevich I, Kastner DL, Torres VJ, Humblet-Baron S, Liston A, Abel L, Boisson B, Casanova JL. Human OTULIN haploinsufficiency impairs cell-intrinsic immunity to staphylococcal α-toxin. Science 2022; 376:eabm6380. [PMID: 35587511 PMCID: PMC9233084 DOI: 10.1126/science.abm6380] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The molecular basis of interindividual clinical variability upon infection with Staphylococcus aureus is unclear. We describe patients with haploinsufficiency for the linear deubiquitinase OTULIN, encoded by a gene on chromosome 5p. Patients suffer from episodes of life-threatening necrosis, typically triggered by S. aureus infection. The disorder is phenocopied in patients with the 5p- (Cri-du-Chat) chromosomal deletion syndrome. OTULIN haploinsufficiency causes an accumulation of linear ubiquitin in dermal fibroblasts, but tumor necrosis factor receptor-mediated nuclear factor κB signaling remains intact. Blood leukocyte subsets are unaffected. The OTULIN-dependent accumulation of caveolin-1 in dermal fibroblasts, but not leukocytes, facilitates the cytotoxic damage inflicted by the staphylococcal virulence factor α-toxin. Naturally elicited antibodies against α-toxin contribute to incomplete clinical penetrance. Human OTULIN haploinsufficiency underlies life-threatening staphylococcal disease by disrupting cell-intrinsic immunity to α-toxin in nonleukocytic cells.
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Affiliation(s)
- András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Institute of Experimental Hematology, REBIRTH Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Emmanuel Laplantine
- Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, CNRS ERL8255, Sorbonne University, 75724 Paris, France
- Institut de Recherche St. Louis, Hôpital St. Louis, INSERM U944, CNRS U7212, Paris Cité University, 75010 Paris, France
| | - Frederik Staels
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Keenan A Lacey
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Erika Van Nieuwenhove
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatric Rheumatology and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - David Hum
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Araksya Izmiryan
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Laboratory of Genetic Skin Diseases, INSERM U1163, 75015 Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Tatiana Kochetkov
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Dani A C Heesterbeek
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Bart W Bardoel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Ashley L DuMont
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20852, USA
| | - Solenne Chardonnet
- Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, UMS Production et Analyse de données en Sciences de la vie et en Santé, PASS, INSERM, Sorbonne University, 75013 Paris, France
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Dusan Bogunovic
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Herman F Wunderink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Pieter-Jan A Haas
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Griet Van Buggenhout
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Stanislas Lyonnet
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Laboratory Embryology and Genetics of Malformations, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD 20852, USA
| | - Mikko R J Seppänen
- Rare Disease and Pediatric Research Centers, Children and Adolescents, University of Helsinki and HUS Helsinki University Hospital, 00260 Helsinki, Finland
| | - Robert Weil
- Centre d'Immunologie et des Maladies Infectieuses, INSERM U1135, CNRS ERL8255, Sorbonne University, 75724 Paris, France
| | - Gisela Seminario
- Center for Clinical Immunology, Immunology Group Children's Hospital Ricardo Gutiérrez, C1425EFD Buenos Aires, Argentina
| | - Héctor Gomez-Tello
- Immunology Department, Poblano Children's Hospital, 72190 Puebla, Mexico
| | - Carine Wouters
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Mehrnaz Mesdaghi
- Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, 15468-155514 Tehran, Iran
| | - Mohammad Shahrooei
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, 15468-155514 Ahvaz, Iran
| | - Xavier Bossuyt
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Erdal Sag
- Department of Pediatric Rheumatology, Hacettepe University, 06230 Ankara, Turkey
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University School of Medicine, Hacettepe University, 06230 Ankara, Turkey
| | - Seza Ozen
- Department of Pediatric Rheumatology, Hacettepe University, 06230 Ankara, Turkey
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Maarten M J van Eijk
- Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Liliana Bezrodnik
- Center for Clinical Immunology, Immunology Group Children's Hospital Ricardo Gutiérrez, C1425EFD Buenos Aires, Argentina
| | | | - Alain Hovnanian
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Laboratory of Genetic Skin Diseases, INSERM U1163, 75015 Paris, France
- Department of Genetics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Aude Nassif
- Centre Médical, Institut Pasteur, 75724 Paris, France
| | - Brigitte Bader-Meunier
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Bénédicte Neven
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmunity, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Isabelle Meyts
- Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, Jeffrey Modell Diagnostic and Research Network Center, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Rik Schrijvers
- Allergy and Clinical Immunology Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Daniel L Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Victor J Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Stéphanie Humblet-Baron
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Adrian Liston
- Laboratory for Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
- VIB Center for Brain and Disease Research, Leuven 3000, Belgium
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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17
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Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S. Author Correction: Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nat Commun 2021; 12:7263. [PMID: 34880236 PMCID: PMC8654860 DOI: 10.1038/s41467-021-27501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- J Blaze
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - A Navickas
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H L Phillips
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - S Heissel
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - A Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Miglani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H Asgharian
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - M Foo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Z T Pennington
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Espeso-Gil
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Rostandy
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - H Alwaseem
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - C G Hahn
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - D J Cai
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - W D Yao
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - H Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - F Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Research and Development Service, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
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18
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Flores‐Bellver M, Mighty J, Aparicio‐Domingo S, Li KV, Shi C, Zhou J, Cobb H, McGrath P, Michelis G, Lenhart P, Bilousova G, Heissel S, Rudy MJ, Coughlan C, Goodspeed AE, Becerra SP, Redenti S, Canto‐Soler MV. Extracellular vesicles released by human retinal pigment epithelium mediate increased polarised secretion of drusen proteins in response to AMD stressors. J Extracell Vesicles 2021; 10:e12165. [PMID: 34750957 PMCID: PMC8575963 DOI: 10.1002/jev2.12165] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/06/2021] [Accepted: 10/25/2021] [Indexed: 12/22/2022] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness worldwide. Drusen are key contributors to the etiology of AMD and the ability to modulate drusen biogenesis could lead to therapeutic strategies to slow or halt AMD progression. The mechanisms underlying drusen biogenesis, however, remain mostly unknown. Here we demonstrate that under homeostatic conditions extracellular vesicles (EVs) secreted by retinal pigment epithelium (RPE) cells are enriched in proteins associated with mechanisms involved in AMD pathophysiology, including oxidative stress, immune response, inflammation, complement system and drusen composition. Furthermore, we provide first evidence that drusen-associated proteins are released as cargo of extracellular vesicles secreted by RPE cells in a polarised apical:basal mode. Notably, drusen-associated proteins exhibited distinctive directional secretion modes in homeostatic conditions and, differential modulation of this directional secretion in response to AMD stressors. These observations underpin the existence of a finely-tuned mechanism regulating directional apical:basal sorting and secretion of drusen-associated proteins via EVs, and its modulation in response to mechanisms involved in AMD pathophysiology. Collectively, our results strongly support an active role of RPE-derived EVs as a key source of drusen proteins and important contributors to drusen development and growth.
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Affiliation(s)
- Miguel Flores‐Bellver
- CellSight Ocular Stem Cell and Regeneration ProgramDepartment of OphthalmologySue Anschutz‐Rodgers Eye CenterUniversity of Colorado, School of MedicineAuroraColoradoUSA
| | - Jason Mighty
- Lehman CollegeBronxNew YorkUSA
- Biology Doctoral ProgramThe Graduate School and University CenterCity University of New YorkNew YorkNew YorkUSA
| | - Silvia Aparicio‐Domingo
- CellSight Ocular Stem Cell and Regeneration ProgramDepartment of OphthalmologySue Anschutz‐Rodgers Eye CenterUniversity of Colorado, School of MedicineAuroraColoradoUSA
| | - Kang V. Li
- CellSight Ocular Stem Cell and Regeneration ProgramDepartment of OphthalmologySue Anschutz‐Rodgers Eye CenterUniversity of Colorado, School of MedicineAuroraColoradoUSA
| | - Cui Shi
- Lehman CollegeBronxNew YorkUSA
- Biology Doctoral ProgramThe Graduate School and University CenterCity University of New YorkNew YorkNew YorkUSA
| | | | - Hannah Cobb
- CellSight Ocular Stem Cell and Regeneration ProgramDepartment of OphthalmologySue Anschutz‐Rodgers Eye CenterUniversity of Colorado, School of MedicineAuroraColoradoUSA
| | - Patrick McGrath
- Department of DermatologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - German Michelis
- Section of Protein Structure and FunctionNEINIHBethesdaMarylandUSA
| | - Patricia Lenhart
- CellSight Ocular Stem Cell and Regeneration ProgramDepartment of OphthalmologySue Anschutz‐Rodgers Eye CenterUniversity of Colorado, School of MedicineAuroraColoradoUSA
| | - Ganna Bilousova
- Department of DermatologyUniversity of Colorado School of MedicineAuroraColoradoUSA
- Charles C. Gates Center for Regenerative MedicineUniversity of Colorado School of MedicineAuroraColoradoUSA
- Linda Crnic Institute for Down SyndromeUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Søren Heissel
- Proteomics Resource CenterThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Michael J. Rudy
- Department of NeurologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Christina Coughlan
- University of Colorado Alzheimer's and Cognition CenterDepartment of NeurologyLinda Crnic Institute for Down SyndromeUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Andrew E. Goodspeed
- Department of PharmacologyUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- University of Colorado Cancer CenterUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | | | - Stephen Redenti
- Lehman CollegeBronxNew YorkUSA
- Biology Doctoral ProgramThe Graduate School and University CenterCity University of New YorkNew YorkNew YorkUSA
- Biochemistry Doctoral ProgramThe Graduate SchoolCity University of New YorkNew YorkNew YorkUSA
| | - M. Valeria Canto‐Soler
- CellSight Ocular Stem Cell and Regeneration ProgramDepartment of OphthalmologySue Anschutz‐Rodgers Eye CenterUniversity of Colorado, School of MedicineAuroraColoradoUSA
- Charles C. Gates Center for Regenerative MedicineUniversity of Colorado School of MedicineAuroraColoradoUSA
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19
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Wang Y, Yen FS, Zhu XG, Timson RC, Weber R, Xing C, Liu Y, Allwein B, Luo H, Yeh HW, Heissel S, Unlu G, Gamazon ER, Kharas MG, Hite R, Birsoy K. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells. Nature 2021; 599:136-140. [PMID: 34707288 PMCID: PMC10981497 DOI: 10.1038/s41586-021-04025-w] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/09/2021] [Indexed: 01/20/2023]
Abstract
Glutathione (GSH) is a small-molecule thiol that is abundant in all eukaryotes and has key roles in oxidative metabolism1. Mitochondria, as the major site of oxidative reactions, must maintain sufficient levels of GSH to perform protective and biosynthetic functions2. GSH is synthesized exclusively in the cytosol, yet the molecular machinery involved in mitochondrial GSH import remains unknown. Here, using organellar proteomics and metabolomics approaches, we identify SLC25A39, a mitochondrial membrane carrier of unknown function, as a regulator of GSH transport into mitochondria. Loss of SLC25A39 reduces mitochondrial GSH import and abundance without affecting cellular GSH levels. Cells lacking both SLC25A39 and its paralogue SLC25A40 exhibit defects in the activity and stability of proteins containing iron-sulfur clusters. We find that mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. Heterologous expression of an engineered bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria enables mitochondrial GSH production and ameliorates the metabolic and proliferative defects caused by its depletion. Finally, GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import in mammalian cells. Our work identifies SLC25A39 as an essential and regulated component of the mitochondrial GSH-import machinery.
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Affiliation(s)
- Ying Wang
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Frederick S Yen
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Xiphias Ge Zhu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Rebecca C Timson
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Ross Weber
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Changrui Xing
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin Allwein
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hsi-Wen Yeh
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Clare Hall and MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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20
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Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S. Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nat Commun 2021; 12:4913. [PMID: 34389722 PMCID: PMC8363735 DOI: 10.1038/s41467-021-24969-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Epitranscriptomic mechanisms linking tRNA function and the brain proteome to cognition and complex behaviors are not well described. Here, we report bi-directional changes in depression-related behaviors after genetic disruption of neuronal tRNA cytosine methylation, including conditional ablation and transgene-derived overexpression of Nsun2 in the mouse prefrontal cortex (PFC). Neuronal Nsun2-deficiency was associated with a decrease in tRNA m5C levels, resulting in deficits in expression of 70% of tRNAGly isodecoders. Altogether, 1488/5820 proteins changed upon neuronal Nsun2-deficiency, in conjunction with glycine codon-specific defects in translational efficiencies. Loss of Gly-rich proteins critical for glutamatergic neurotransmission was associated with impaired synaptic signaling at PFC pyramidal neurons and defective contextual fear memory. Changes in the neuronal translatome were also associated with a 146% increase in glycine biosynthesis. These findings highlight the methylation sensitivity of glycinergic tRNAs in the adult PFC. Furthermore, they link synaptic plasticity and complex behaviors to epitranscriptomic modifications of cognate tRNAs and the proteomic homeostasis associated with specific amino acids.
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Affiliation(s)
- J Blaze
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - A Navickas
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H L Phillips
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - S Heissel
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - A Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Miglani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H Asgharian
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - M Foo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Z T Pennington
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Espeso-Gil
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Rostandy
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - H Alwaseem
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - C G Hahn
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - D J Cai
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - W D Yao
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - H Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - F Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Research and Development Service, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
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21
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Zhu XG, Chudnovskiy A, Baudrier L, Prizer B, Liu Y, Ostendorf BN, Yamaguchi N, Arab A, Tavora B, Timson R, Heissel S, de Stanchina E, Molina H, Victora GD, Goodarzi H, Birsoy K. Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells. Cell Metab 2021; 33:211-221.e6. [PMID: 33152324 PMCID: PMC7790894 DOI: 10.1016/j.cmet.2020.10.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/12/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) cells require substantial metabolic rewiring to overcome nutrient limitations and immune surveillance. However, the metabolic pathways necessary for pancreatic tumor growth in vivo are poorly understood. To address this, we performed metabolism-focused CRISPR screens in PDAC cells grown in culture or engrafted in immunocompetent mice. While most metabolic gene essentialities are unexpectedly similar under these conditions, a small fraction of metabolic genes are differentially required for tumor progression. Among these, loss of heme synthesis reduces tumor growth due to a limiting role of heme in vivo, an effect independent of tissue origin or immune system. Our screens also identify autophagy as a metabolic requirement for pancreatic tumor immune evasion. Mechanistically, autophagy protects cancer cells from CD8+ T cell killing through TNFα-induced cell death in vitro. Altogether, this resource provides metabolic dependencies arising from microenvironmental limitations and the immune system, nominating potential anti-cancer targets.
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Affiliation(s)
- Xiphias Ge Zhu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Lou Baudrier
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin Prizer
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Yuyang Liu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin N Ostendorf
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Abolfozl Arab
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Bernardo Tavora
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Rebecca Timson
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henrik Molina
- The Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA.
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22
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Hoshino A, Kim HS, Bojmar L, Gyan KE, Cioffi M, Hernandez J, Zambirinis CP, Rodrigues G, Molina H, Heissel S, Mark MT, Steiner L, Benito-Martin A, Lucotti S, Di Giannatale A, Offer K, Nakajima M, Williams C, Nogués L, Pelissier Vatter FA, Hashimoto A, Davies AE, Freitas D, Kenific CM, Ararso Y, Buehring W, Lauritzen P, Ogitani Y, Sugiura K, Takahashi N, Alečković M, Bailey KA, Jolissant JS, Wang H, Harris A, Schaeffer LM, García-Santos G, Posner Z, Balachandran VP, Khakoo Y, Raju GP, Scherz A, Sagi I, Scherz-Shouval R, Yarden Y, Oren M, Malladi M, Petriccione M, De Braganca KC, Donzelli M, Fischer C, Vitolano S, Wright GP, Ganshaw L, Marrano M, Ahmed A, DeStefano J, Danzer E, Roehrl MHA, Lacayo NJ, Vincent TC, Weiser MR, Brady MS, Meyers PA, Wexler LH, Ambati SR, Chou AJ, Slotkin EK, Modak S, Roberts SS, Basu EM, Diolaiti D, Krantz BA, Cardoso F, Simpson AL, Berger M, Rudin CM, Simeone DM, Jain M, Ghajar CM, Batra SK, Stanger BZ, Bui J, Brown KA, Rajasekhar VK, Healey JH, de Sousa M, Kramer K, Sheth S, Baisch J, Pascual V, Heaton TE, La Quaglia MP, Pisapia DJ, Schwartz R, Zhang H, Liu Y, Shukla A, Blavier L, DeClerck YA, LaBarge M, Bissell MJ, Caffrey TC, Grandgenett PM, Hollingsworth MA, Bromberg J, Costa-Silva B, Peinado H, Kang Y, Garcia BA, O'Reilly EM, Kelsen D, Trippett TM, Jones DR, Matei IR, Jarnagin WR, Lyden D. Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers. Cell 2020; 182:1044-1061.e18. [PMID: 32795414 DOI: 10.1016/j.cell.2020.07.009] [Citation(s) in RCA: 607] [Impact Index Per Article: 151.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/23/2020] [Accepted: 07/09/2020] [Indexed: 01/08/2023]
Abstract
There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n = 151) and plasma-derived (n = 120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer. Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.
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Affiliation(s)
- Ayuko Hoshino
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Japan Science and Technology Agency, PRESTO, Tokyo, Japan.
| | - Han Sang Kim
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Brain Korea 21 Plus Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Linda Bojmar
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Kofi Ennu Gyan
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Michele Cioffi
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Hernandez
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Constantinos P Zambirinis
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gonçalo Rodrigues
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Milica Tesic Mark
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Loïc Steiner
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Alberto Benito-Martin
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Angela Di Giannatale
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Pediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Katharine Offer
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Miho Nakajima
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Caitlin Williams
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Laura Nogués
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Fanny A Pelissier Vatter
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ayako Hashimoto
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Alexander E Davies
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Daniela Freitas
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; i3S-Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen 208, Porto, Portugal
| | - Candia M Kenific
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yonathan Ararso
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Weston Buehring
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Pernille Lauritzen
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yusuke Ogitani
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Kei Sugiura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoko Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Maša Alečković
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Kayleen A Bailey
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Joshua S Jolissant
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huajuan Wang
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ashton Harris
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - L Miles Schaeffer
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Guillermo García-Santos
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of General and Gastrointestinal Surgery, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Zoe Posner
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Vinod P Balachandran
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasmin Khakoo
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Praveen Raju
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avigdor Scherz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mahathi Malladi
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary Petriccione
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin C De Braganca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Donzelli
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cheryl Fischer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie Vitolano
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geraldine P Wright
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lee Ganshaw
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariel Marrano
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amina Ahmed
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe DeStefano
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Enrico Danzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael H A Roehrl
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Norman J Lacayo
- Lucile Packard Children's Hospital Stanford, Stanford, CA, USA
| | - Theresa C Vincent
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden; Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Martin R Weiser
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary S Brady
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Srikanth R Ambati
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander J Chou
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ellen M Basu
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Diolaiti
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Benjamin A Krantz
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatima Cardoso
- Breast Unit, Champalimaud Clinical Center/Champalimaud Foundation, Lisbon, Portugal
| | - Amber L Simpson
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diane M Simeone
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Maneesh Jain
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Cyrus M Ghajar
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Surinder K Batra
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ben Z Stanger
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jack Bui
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Kristy A Brown
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Vinagolu K Rajasekhar
- Orthopedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John H Healey
- Orthopedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria de Sousa
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Kim Kramer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sujit Sheth
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Jeanine Baisch
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA; Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Virginia Pascual
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA; Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Todd E Heaton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael P La Quaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert Schwartz
- Division of Gastroenterology & Hepatology, Weill Cornell Medicine, New York, NY, USA
| | - Haiying Zhang
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Liu
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arti Shukla
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Laurence Blavier
- Department of Pediatrics and Biochemistry and Molecular Medicine, University of Southern California, CA, USA
| | - Yves A DeClerck
- Department of Pediatrics and Biochemistry and Molecular Medicine, University of Southern California, CA, USA
| | - Mark LaBarge
- Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Mina J Bissell
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas C Caffrey
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paul M Grandgenett
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael A Hollingsworth
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jacqueline Bromberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tanya M Trippett
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina R Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - William R Jarnagin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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23
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Nguyen AH, Thomsen ARB, Cahill TJ, Huang R, Huang LY, Marcink T, Clarke OB, Heissel S, Masoudi A, Ben-Hail D, Samaan F, Dandey VP, Tan YZ, Hong C, Mahoney JP, Triest S, Little J, Chen X, Sunahara R, Steyaert J, Molina H, Yu Z, des Georges A, Lefkowitz RJ. Structure of an endosomal signaling GPCR-G protein-β-arrestin megacomplex. Nat Struct Mol Biol 2019; 26:1123-1131. [PMID: 31740855 PMCID: PMC7108872 DOI: 10.1038/s41594-019-0330-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023]
Abstract
Classically, G-protein-coupled receptors (GPCRs) are thought to activate G protein from the plasma membrane and are subsequently desensitized by β-arrestin (β-arr). However, some GPCRs continue to signal through G protein from internalized compartments, mediated by a GPCR-G protein-β-arr 'megaplex'. Nevertheless, the molecular architecture of the megaplex remains unknown. Here, we present its cryo-electron microscopy structure, which shows simultaneous engagement of human G protein and bovine β-arr to the core and phosphorylated tail, respectively, of a single active human chimeric β2-adrenergic receptor with the C-terminal tail of the arginine vasopressin type 2 receptor (β2V2R). All three components adopt their canonical active conformations, suggesting that a single megaplex GPCR is capable of simultaneously activating G protein and β-arr. Our findings provide a structural basis for GPCR-mediated sustained internalized G protein signaling.
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Affiliation(s)
- Anthony H. Nguyen
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Alex R. B. Thomsen
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Thomas J. Cahill
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Rick Huang
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Li-Yin Huang
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Tara Marcink
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA.,Center for Host-Pathogen Interaction, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Oliver B. Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.,The Irving Center for Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, USA
| | - Ali Masoudi
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Danya Ben-Hail
- Structural Biology Initiative, CUNY Advanced Science Research Center, NY 10031, USA
| | - Fadi Samaan
- Structural Biology Initiative, CUNY Advanced Science Research Center, NY 10031, USA
| | - Venkata P. Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA,Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chuan Hong
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Jacob P. Mahoney
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA,Present Address: Department of Structural Biology, Stanford University, Stanford, CA
| | - Sarah Triest
- Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium; Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussels, Belgium
| | - John Little
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Xin Chen
- School of Pharmaceutical Engineering and Life Sciences, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Roger Sunahara
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussels, B-1050 Brussels, Belgium; Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussels, Belgium
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York 10065, USA
| | - Zhiheng Yu
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, NY 10031, USA,Department of Chemistry and Biochemistry, City College of New York, NY, USA,Biochemistry and Chemistry Ph.D. Programs, Graduate Center, City University of New York, NY, USA,Corresponding authors: (A.d.G.); (R.J.L.)
| | - Robert J. Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Corresponding authors: (A.d.G.); (R.J.L.)
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24
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Heissel S, Frederiksen SJ, Bunkenborg J, Højrup P. Enhanced trypsin on a budget: Stabilization, purification and high-temperature application of inexpensive commercial trypsin for proteomics applications. PLoS One 2019; 14:e0218374. [PMID: 31246970 PMCID: PMC6597055 DOI: 10.1371/journal.pone.0218374] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/02/2019] [Indexed: 01/22/2023] Open
Abstract
Trypsin is by far the most commonly used protease in proteomics. Even though the amount of protease used in each experiment is very small, digestion of large amounts of protein prior to enrichment can be rather costly. The price of commercial trypsin is highly dependent on the quality of the enzyme, which is determined by its purity, activity, and chemical modifications. In this study we evaluated several strategies for improving the quality of crude trypsin by reductive methylation and affinity purification. We present a protocol applicable to most proteomics laboratories for obtaining a highly stable and pure trypsin preparation using reductive methylation and purification by benzamidine-sepharose. The entire workflow can be performed within a day and yields ~4 mg per batch but is completely scalable. The methylated product was benchmarked against sequencing grade trypsin from Promega and they were found to be comparable for one hour digestions at elevated temperatures, where residual chymotryptic activity was found to be negligible.
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Affiliation(s)
- Søren Heissel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Sigurd J. Frederiksen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | | | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- * E-mail:
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25
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Affiliation(s)
- Sheila Maibom-Thomsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
- Alphalyse A/S, Unsbjergvej 4D, Odense SØ 5220, Denmark
| | - Søren Heissel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Ejvind Mørtz
- Alphalyse A/S, Unsbjergvej 4D, Odense SØ 5220, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
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26
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Heissel S, Bunkenborg J, Kristiansen MP, Holmbjerg AF, Grimstrup M, Mørtz E, Kofoed T, Højrup P. Evaluation of spectral libraries and sample preparation for DIA-LC-MS analysis of host cell proteins: A case study of a bacterially expressed recombinant biopharmaceutical protein. Protein Expr Purif 2018. [DOI: 10.1016/j.pep.2018.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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Schjoeth-Eskesen C, Nielsen CH, Heissel S, Højrup P, Hansen PR, Gillings N, Kjaer A. [(64) Cu]-labelled trastuzumab: optimisation of labelling by DOTA and NODAGA conjugation and initial evaluation in mice. J Labelled Comp Radiopharm 2015; 58:227-33. [PMID: 25906708 PMCID: PMC5029596 DOI: 10.1002/jlcr.3287] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 12/28/2022]
Abstract
The human epidermal growth factor receptor‐2 (HER2) is overexpressed in 20–30% of all breast cancer cases, leading to increased cell proliferation, growth and migration. The monoclonal antibody, trastuzumab, binds to HER2 and is used for treatment of HER2‐positive breast cancer. Trastuzumab has previously been labelled with copper‐64 by conjugation of a 1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA) chelator. The aim of this study was to optimise the 64Cu‐labelling of DOTA‐trastuzumab and as the first to produce and compare with its 1,4,7‐triazacyclononane, 1‐glutaric acid‐5,7 acetic acid (NODAGA) analogue in a preliminary HER2 tumour mouse model. The chelators were conjugated to trastuzumab using the activated esters DOTA mono‐N‐hydroxysuccinimide (NHS) and NODAGA‐NHS. 64Cu‐labelling of DOTA‐trastuzumab was studied by varying the amount of DOTA‐trastuzumab used, reaction temperature and time. Full 64Cu incorporation could be achieved using a minimum of 10‐µg DOTA‐trastuzumab, but the fastest labelling was obtained after 15 min at room temperature using 25 µg of DOTA‐trastuzumab. In comparison, 80% incorporation was achieved for 64Cu‐labelling of NODAGA‐trastuzumab. Both [64Cu]DOTA‐trastuzumab and [64Cu]NODAGA‐trastuzumab were produced after purification with radiochemical purities of >97%. The tracers were injected into mice with HER2 expressing tumours. The mice were imaged by positron emission tomography and showed high tumour uptake of 3–9% ID/g for both tracers.
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Affiliation(s)
- Christina Schjoeth-Eskesen
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Haagen Nielsen
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, University of Copenhagen, Copenhagen, Denmark
| | - Søren Heissel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Nic Gillings
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, University of Copenhagen, Copenhagen, Denmark
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