1
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Perez VA, Sanders DW, Mendoza-Oliva A, Stopschinski BE, Mullapudi V, White CL, Joachimiak LA, Diamond MI. DnaJC7 specifically regulates tau seeding. eLife 2023; 12:e86936. [PMID: 37387473 PMCID: PMC10473839 DOI: 10.7554/elife.86936] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/29/2023] [Indexed: 07/01/2023] Open
Abstract
Neurodegenerative tauopathies are caused by accumulation of toxic tau protein assemblies. This appears to involve template-based seeding events, whereby tau monomer changes conformation and is recruited to a growing aggregate. Several large families of chaperone proteins, including Hsp70s and J domain proteins (JDPs), cooperate to regulate the folding of intracellular proteins such as tau, but the factors that coordinate this activity are not well known. The JDP DnaJC7 binds tau and reduces its intracellular aggregation. However, it is unknown whether this is specific to DnaJC7 or if other JDPs might be similarly involved. We used proteomics within a cell model to determine that DnaJC7 co-purified with insoluble tau and colocalized with intracellular aggregates. We individually knocked out every possible JDP and tested the effect on intracellular aggregation and seeding. DnaJC7 knockout decreased aggregate clearance and increased intracellular tau seeding. This depended on the ability of the J domain (JD) of DnaJC7 to stimulate Hsp70 ATPase activity, as JD mutations that block this interaction abrogated the protective activity. Disease-associated mutations in the JD and substrate binding site of DnaJC7 also abolished its protective activity. DnaJC7 thus specifically regulates tau aggregation in cooperation with Hsp70.
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Affiliation(s)
- Valerie Ann Perez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - David W Sanders
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Barbara Elena Stopschinski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Charles L White
- Department of Pathology, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biochemistry, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Neurology, Peter O’Donnell Jr. Brain Institute, The University of Texas Southwestern Medical CenterDallasUnited States
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2
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McCoy CJ, Paupelin-Vaucelle H, Gorilak P, Beneke T, Varga V, Gluenz E. ULK4 and Fused/STK36 interact to mediate assembly of a motile flagellum. Mol Biol Cell 2023; 34:ar66. [PMID: 36989043 PMCID: PMC10295485 DOI: 10.1091/mbc.e22-06-0222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Unc-51-like kinase (ULK) family serine-threonine protein kinase homologues have been linked to the function of motile cilia in diverse species. Mutations in Fused/STK36 and ULK4 in mice resulted in hydrocephalus and other phenotypes consistent with ciliary defects. How either protein contributes to the assembly and function of motile cilia is not well understood. Here we studied the phenotypes of ULK4 and Fused gene knockout (KO) mutants in the flagellated protist Leishmania mexicana. Both KO mutants exhibited a variety of structural defects of the flagellum cytoskeleton. Biochemical approaches indicate spatial proximity of these proteins and indicate a direct interaction between the N-terminus of LmxULK4 and LmxFused. Both proteins display a dispersed localization throughout the cell body and flagellum, with enrichment near the flagellar base and tip. The stable expression of LmxULK4 was dependent on the presence of LmxFused. Fused/STK36 was previously shown to localize to mammalian motile cilia, and we demonstrate here that ULK4 also localizes to the motile cilia in mouse ependymal cells. Taken together these data suggest a model where the pseudokinase ULK4 is a positive regulator of the kinase Fused/ STK36 in a pathway required for stable assembly of motile cilia.
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Affiliation(s)
- Ciaran J. McCoy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | - Peter Gorilak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 142 20 Prague 4, Czech Republic
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Vladimir Varga
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 142 20 Prague 4, Czech Republic
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
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3
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Perez VA, Sanders DW, Mendoza-Oliva A, Stopschinski BE, Mullapudi V, White CL, Joachimiak LA, Diamond MI. DnaJC7 specifically regulates tau seeding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532880. [PMID: 36993367 PMCID: PMC10055123 DOI: 10.1101/2023.03.16.532880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neurodegenerative tauopathies are caused by accumulation of toxic tau protein assemblies. This appears to involve template-based seeding events, whereby tau monomer changes conformation and is recruited to a growing aggregate. Several large families of chaperone proteins, including Hsp70s and J domain proteins (JDPs) cooperate to regulate the folding of intracellular proteins such as tau, but the factors that coordinate this activity are not well known. The JDP DnaJC7 binds tau and reduces its intracellular aggregation. However, it is unknown whether this is specific to DnaJC7 or if other JDPs might be similarly involved. We used proteomics within a cell model to determine that DnaJC7 co-purified with insoluble tau and colocalized with intracellular aggregates. We individually knocked out every possible JDP and tested the effect on intracellular aggregation and seeding. DnaJC7 knockout decreased aggregate clearance and increased intracellular tau seeding. This depended on the ability of the J domain (JD) of DnaJC7 to bind to Hsp70, as JD mutations that block binding to Hsp70 abrogated the protective activity. Disease-associated mutations in the JD and substrate binding site of DnaJC7 also abrogated its protective activity. DnaJC7 thus specifically regulates tau aggregation in cooperation with Hsp70.
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Affiliation(s)
- Valerie A Perez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - David W Sanders
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Barbara E Stopschinski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles L White
- Department of Pathology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Biochemistry, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Neurology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
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4
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Herrera LR, McGlynn K, Gibbs ZA, Davis AJ, Whitehurst AW. The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526348. [PMID: 36778501 PMCID: PMC9915569 DOI: 10.1101/2023.01.31.526348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tumors frequently activate the expression of genes that are only otherwise required for meiosis. HORMAD1, which is essential for meiotic recombination in multiple species, is expressed in over 50% of human lung adenocarcinoma cells (LUAD). We previously found that HORMAD1 promotes DNA double strand break (DSB) repair in LUAD. Here, we report that HORMAD1 takes on an additional role in protecting genomic integrity. Specifically, we find HORMAD1 is critical for protecting stalled DNA replication forks in LUAD. Loss of HORMAD1 leads to nascent DNA degradation, an event which is mediated by the MRE11-DNA2-BLM pathway. Moreover, following exogenous induction of DNA replication stress, HORMAD1 deleted cells accumulate single stranded DNA (ssDNA). We find that these phenotypes are the result of a lack of RAD51 and BRCA2 loading onto stalled replication forks. Ultimately, loss of HORMAD1 leads to increased DSBs and chromosomal aberrations in response to replication stress. Collectively, our data support a model where HORMAD1 expression is selected to mitigate DNA replication stress, which would otherwise induce deleterious genomic instability.
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5
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Braunger K, Ahn J, Jore MM, Johnson S, Tang TTL, Pedersen DV, Andersen GR, Lea SM. Structure and function of a family of tick-derived complement inhibitors targeting properdin. Nat Commun 2022; 13:317. [PMID: 35031611 PMCID: PMC8760278 DOI: 10.1038/s41467-021-27920-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
Activation of the serum-resident complement system begins a cascade that leads to activation of membrane-resident complement receptors on immune cells, thus coordinating serum and cellular immune responses. Whilst many molecules act to control inappropriate activation, Properdin is the only known positive regulator of the human complement system. By stabilising the alternative pathway C3 convertase it promotes complement self-amplification and persistent activation boosting the magnitude of the serum complement response by all triggers. In this work, we identify a family of tick-derived alternative pathway complement inhibitors, hereafter termed CirpA. Functional and structural characterisation reveals that members of the CirpA family directly bind to properdin, inhibiting its ability to promote complement activation, and leading to potent inhibition of the complement response in a species specific manner. We provide a full functional and structural characterisation of a properdin inhibitor, opening avenues for future therapeutic approaches.
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Affiliation(s)
- Katharina Braunger
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Jiyoon Ahn
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Matthijs M Jore
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, 21702, Frederick, MD, USA.
| | - Terence T L Tang
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Dennis V Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, 21702, Frederick, MD, USA.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, OX1 3RE, Oxford, UK.
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6
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Cai K, Zhao Y, Zhao L, Phan N, Hou Y, Cheng X, Witman GB, Nicastro D. Structural organization of the C1b projection within the ciliary central apparatus. J Cell Sci 2021; 134:272503. [PMID: 34651179 DOI: 10.1242/jcs.254227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 09/29/2021] [Indexed: 12/23/2022] Open
Abstract
Motile cilia have a '9+2' structure containing nine doublet microtubules and a central apparatus (CA) composed of two singlet microtubules with associated projections. The CA plays crucial roles in regulating ciliary motility. Defects in CA assembly or function usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of most CA projections remain largely unknown. Here, we combined genetic, proteomic and cryo-electron tomographic approaches to compare the CA of wild-type Chlamydomonas reinhardtii with those of three CA mutants. Our results show that two proteins, FAP42 and FAP246, are localized to the L-shaped C1b projection of the CA, where they interact with the candidate CA protein FAP413. FAP42 is a large protein that forms the peripheral 'beam' of the C1b projection, and the FAP246-FAP413 subcomplex serves as the 'bracket' between the beam (FAP42) and the C1b 'pillar' that attaches the projection to the C1 microtubule. The FAP246-FAP413-FAP42 complex is essential for stable assembly of the C1b, C1f and C2b projections, and loss of these proteins leads to ciliary motility defects.
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Affiliation(s)
- Kai Cai
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75231, USA
| | - Yanhe Zhao
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75231, USA
| | - Lei Zhao
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Nhan Phan
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75231, USA
| | - Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Xi Cheng
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George B Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75231, USA
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7
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Zaman A, Wu X, Lemoff A, Yadavalli S, Lee J, Wang C, Cooper J, McMillan EA, Yeaman C, Mirzaei H, White MA, Bivona TG. Exocyst protein subnetworks integrate Hippo and mTOR signaling to promote virus detection and cancer. Cell Rep 2021; 36:109491. [PMID: 34348154 DOI: 10.1016/j.celrep.2021.109491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/20/2021] [Accepted: 07/14/2021] [Indexed: 11/25/2022] Open
Abstract
The exocyst is an evolutionarily conserved protein complex that regulates vesicular trafficking and scaffolds signal transduction. Key upstream components of the exocyst include monomeric RAL GTPases, which help mount cell-autonomous responses to trophic and immunogenic signals. Here, we present a quantitative proteomics-based characterization of dynamic and signal-dependent exocyst protein interactomes. Under viral infection, an Exo84 exocyst subcomplex assembles the immune kinase Protein Kinase R (PKR) together with the Hippo kinase Macrophage Stimulating 1 (MST1). PKR phosphorylates MST1 to activate Hippo signaling and inactivate Yes Associated Protein 1 (YAP1). By contrast, a Sec5 exocyst subcomplex recruits another immune kinase, TANK binding kinase 1 (TBK1), which interacted with and activated mammalian target of rapamycin (mTOR). RALB was necessary and sufficient for induction of Hippo and mTOR signaling through parallel exocyst subcomplex engagement, supporting the cellular response to virus infection and oncogenic signaling. This study highlights RALB-exocyst signaling subcomplexes as mechanisms for the integrated engagement of Hippo and mTOR signaling in cells challenged by viral pathogens or oncogenic signaling.
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Affiliation(s)
- Aubhishek Zaman
- Department of Medicine, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA; UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
| | - Xiaofeng Wu
- Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Sivaramakrishna Yadavalli
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Jeon Lee
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Bioinformatics Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Chensu Wang
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Jonathan Cooper
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Elizabeth A McMillan
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Charles Yeaman
- Department of Anatomy and Cell Biology, University of Iowa, 51 Newton Road, Iowa City, IA 52242, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Michael A White
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA; UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
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8
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Fu G, Scarbrough C, Song K, Phan N, Wirschell M, Nicastro D. Structural organization of the intermediate and light chain complex of Chlamydomonas ciliary I1 dynein. FASEB J 2021; 35:e21646. [PMID: 33993568 DOI: 10.1096/fj.202001857r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Axonemal I1 dynein (dynein f) is the largest inner dynein arm in cilia and a key regulator of ciliary beating. It consists of two dynein heavy chains, and an intermediate chain/light chain (ICLC) complex. However, the structural organization of the nine ICLC subunits remains largely unknown. Here, we used biochemical and genetic approaches, and cryo-electron tomography imaging in Chlamydomonas to dissect the molecular architecture of the I1 dynein ICLC complex. Using a strain expressing SNAP-tagged IC140, tomography revealed the location of the IC140 N-terminus at the proximal apex of the ICLC structure. Mass spectrometry of a tctex2b mutant showed that TCTEX2B dynein light chain is required for the stable assembly of TCTEX1 and inner dynein arm interacting proteins IC97 and FAP120. The structural defects observed in tctex2b located these 4 subunits in the center and bottom regions of the ICLC structure, which overlaps with the location of the IC138 regulatory subcomplex, which contains IC138, IC97, FAP120, and LC7b. These results reveal the three-dimensional organization of the native ICLC complex and indicate potential protein-protein interactions that are involved in the pathway by which I1 regulates ciliary motility.
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Affiliation(s)
- Gang Fu
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Chasity Scarbrough
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kangkang Song
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nhan Phan
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maureen Wirschell
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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9
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Gupte R, Nandu T, Kraus WL. Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun 2021; 12:3931. [PMID: 34168143 PMCID: PMC8225886 DOI: 10.1038/s41467-021-24225-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/04/2021] [Indexed: 02/01/2023] Open
Abstract
STAT1α is a key transcription factor driving pro-inflammatory responses in macrophages. We found that the interferon gamma (IFNγ)-regulated transcriptional program in macrophages is controlled by ADP-ribosylation (ADPRylation) of STAT1α, a post-translational modification resulting in the site-specific covalent attachment of ADP-ribose moieties. PARP-1, the major nuclear poly(ADP-ribose) polymerase (PARP), supports IFNγ-stimulated enhancer formation by regulating the genome-wide binding and IFNγ-dependent transcriptional activation of STAT1α. It does so by ADPRylating STAT1α on specific residues in its DNA-binding domain (DBD) and transcription activation (TA) domain. ADPRylation of the DBD controls STAT1α binding to its cognate DNA elements, whereas ADPRylation of the TA domain regulates enhancer activation by modulating STAT1α phosphorylation and p300 acetyltransferase activity. Loss of ADPRylation at either site leads to diminished IFNγ-dependent transcription and downstream pro-inflammatory responses. We conclude that PARP-1-mediated ADPRylation of STAT1α drives distinct enhancer activation mechanisms and is a critical regulator of inflammatory responses in macrophages.
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Affiliation(s)
- Rebecca Gupte
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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10
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Somatilaka BN, Hwang SH, Palicharla VR, White KA, Badgandi H, Shelton JM, Mukhopadhyay S. Ankmy2 Prevents Smoothened-Independent Hyperactivation of the Hedgehog Pathway via Cilia-Regulated Adenylyl Cyclase Signaling. Dev Cell 2020; 54:710-726.e8. [PMID: 32702291 PMCID: PMC9042708 DOI: 10.1016/j.devcel.2020.06.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/12/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
The mechanisms underlying subcellular targeting of cAMP-generating adenylyl cyclases and processes regulated by their compartmentalization are poorly understood. Here, we identify Ankmy2 as a repressor of the Hedgehog pathway via adenylyl cyclase targeting. Ankmy2 binds to multiple adenylyl cyclases, determining their maturation and trafficking to primary cilia. Mice lacking Ankmy2 are mid-embryonic lethal. Knockout embryos have increased Hedgehog signaling and completely open neural tubes showing co-expansion of all ventral neuroprogenitor markers, comparable to the loss of the Hedgehog receptor Patched1. Ventralization in Ankmy2 knockout is completely independent of the Hedgehog pathway transducer Smoothened. Instead, ventralization results from the reduced formation of Gli2 and Gli3 repressors and early depletion of adenylyl cyclase III in neuroepithelial cilia, implicating deficient pathway repression. Ventralization in Ankmy2 knockout requires both cilia and Gli2 activation. These findings indicate that cilia-dependent adenylyl cyclase signaling represses the Hedgehog pathway and promotes morphogenetic patterning.
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Affiliation(s)
| | - Sun-Hee Hwang
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vivek Reddy Palicharla
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin Andrew White
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hemant Badgandi
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Michael Shelton
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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11
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Wang J, Paz C, Padalino G, Coghlan A, Lu Z, Gradinaru I, Collins JNR, Berriman M, Hoffmann KF, Collins JJ. Large-scale RNAi screening uncovers therapeutic targets in the parasite Schistosoma mansoni. Science 2020; 369:1649-1653. [PMID: 32973031 PMCID: PMC7877197 DOI: 10.1126/science.abb7699] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
Schistosome parasites kill 250,000 people every year. Treatment of schistosomiasis relies on the drug praziquantel. Unfortunately, a scarcity of molecular tools has hindered the discovery of new drug targets. Here, we describe a large-scale RNA interference (RNAi) screen in adult Schistosoma mansoni that examined the function of 2216 genes. We identified 261 genes with phenotypes affecting neuromuscular function, tissue integrity, stem cell maintenance, and parasite survival. Leveraging these data, we prioritized compounds with activity against the parasites and uncovered a pair of protein kinases (TAO and STK25) that cooperate to maintain muscle-specific messenger RNA transcription. Loss of either of these kinases results in paralysis and worm death in a mammalian host. These studies may help expedite therapeutic development and invigorate studies of these neglected parasites.
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Affiliation(s)
- Jipeng Wang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carlos Paz
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gilda Padalino
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Zhigang Lu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Irina Gradinaru
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Julie N R Collins
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Karl F Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, UK
| | - James J Collins
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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12
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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13
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Tao L, Lemoff A, Wang G, Zarek C, Lowe A, Yan N, Reese TA. Reactive oxygen species oxidize STING and suppress interferon production. eLife 2020; 9:e57837. [PMID: 32886065 PMCID: PMC7473769 DOI: 10.7554/elife.57837] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) are by-products of cellular respiration that can promote oxidative stress and damage cellular proteins and lipids. One canonical role of ROS is to defend the cell against invading bacterial and viral pathogens. Curiously, some viruses, including herpesviruses, thrive despite the induction of ROS, suggesting that ROS are beneficial for the virus. However, the underlying mechanisms remain unclear. Here, we found that ROS impaired interferon response during murine herpesvirus infection and that the inhibition occurred downstream of cytoplasmic DNA sensing. We further demonstrated that ROS suppressed the type I interferon response by oxidizing Cysteine 147 on murine stimulator of interferon genes (STING), an ER-associated protein that mediates interferon response after cytoplasmic DNA sensing. This inhibited STING polymerization and activation of downstream signaling events. These data indicate that redox regulation of Cysteine 147 of mouse STING, which is equivalent to Cysteine 148 of human STING, controls interferon production. Together, our findings reveal that ROS orchestrates anti-viral immune responses, which can be exploited by viruses to evade cellular defenses.
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Affiliation(s)
- Lili Tao
- Department of Immunology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - Guoxun Wang
- Department of Immunology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Christina Zarek
- Department of Immunology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Alexandria Lowe
- Department of Immunology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nan Yan
- Department of Immunology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Microbiology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Tiffany A Reese
- Department of Immunology, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Microbiology, University of Texas Southwestern Medical CenterDallasUnited States
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14
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Noor Z, Ahn SB, Baker MS, Ranganathan S, Mohamedali A. Mass spectrometry-based protein identification in proteomics-a review. Brief Bioinform 2020; 22:1620-1638. [PMID: 32047889 DOI: 10.1093/bib/bbz163] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.
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15
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Beneke T, Banecki K, Fochler S, Gluenz E. LAX28 is required for the stable assembly of the inner dynein arm f complex, and the tether and tether head complex in Leishmania flagella. J Cell Sci 2020; 133:jcs239855. [PMID: 31932510 PMCID: PMC7747692 DOI: 10.1242/jcs.239855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/12/2019] [Indexed: 12/26/2022] Open
Abstract
Motile eukaryotic flagella beat through coordinated activity of dynein motor proteins; however, the mechanisms of dynein coordination and regulation are incompletely understood. The inner dynein arm (IDA) f complex (also known as the I1 complex), and the tether and tether head (T/TH) complex are thought to be key regulators of dynein action but, unlike the IDA f complex, T/TH proteins remain poorly characterised. Here, we characterised T/TH-associated proteins in the protist Leishmania mexicana Proteome analysis of axonemes from null mutants for the CFAP44 T/TH protein showed that they lacked the IDA f protein IC140 and a novel 28-kDa axonemal protein, LAX28. Sequence analysis identified similarities between LAX28 and the uncharacterised human sperm tail protein TEX47, both sharing features with sensory BLUF-domain-containing proteins. Leishmania lacking LAX28, CFAP44 or IC140 retained some motility, albeit with reduced swimming speed and directionality and a propensity for flagellar curling. Expression of tagged proteins in different null mutant backgrounds showed that the axonemal localisation of LAX28 requires CFAP44 and IC140, and the axonemal localisations of CFAP44 and IC140 both depend on LAX28. These data demonstrate a role for LAX28 in motility and show mutual dependencies of IDA f and T/TH-associated proteins for axonemal assembly in Leishmania.
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Affiliation(s)
- Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Katherine Banecki
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sophia Fochler
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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16
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Abstract
The complement system is a crucial antimicrobial system in the human body. However, controlling its regulation is essential, and failure to do so is implicated in a number of clinical inflammatory pathologies leading to great interest in therapeutic complement inhibition. We have identified and characterized a class of complement inhibitors from biting ticks. Utilizing both cryoelectron microscopy and X-ray crystallography we provide a comprehensive understanding of their mechanism of inhibition at the level of the terminal pathway of complement. We present a high-resolution cryoelectron microscopy structure of complement C5, the molecule targeted by the major therapeutic Eculizumab. In addition, we reveal the fold of the CirpT family of tick inhibitors and their unique mode of inhibition. The complement system is a crucial part of innate immune defenses against invading pathogens. The blood-meal of the tick Rhipicephalus pulchellus lasts for days, and the tick must therefore rely on inhibitors to counter complement activation. We have identified a class of inhibitors from tick saliva, the CirpT family, and generated detailed structural data revealing their mechanism of action. We show direct binding of a CirpT to complement C5 and have determined the structure of the C5–CirpT complex by cryoelectron microscopy. This reveals an interaction with the peripheral macro globulin domain 4 (C5_MG4) of C5. To achieve higher resolution detail, the structure of the C5_MG4–CirpT complex was solved by X-ray crystallography (at 2.7 Å). We thus present the fold of the CirpT protein family, and provide detailed mechanistic insights into its inhibitory function. Analysis of the binding interface reveals a mechanism of C5 inhibition, and provides information to expand our biological understanding of the activation of C5, and thus the terminal complement pathway.
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17
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Xu CC, Mau T. A tissue-specific, injectable acellular gel for the treatment of chronic vocal fold scarring. Acta Biomater 2019; 99:141-153. [PMID: 31425889 PMCID: PMC6851489 DOI: 10.1016/j.actbio.2019.08.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/27/2019] [Accepted: 08/13/2019] [Indexed: 02/08/2023]
Abstract
Gel-based injectable biomaterials have significant potential for treating vocal fold defects such as scarring. An ideal injectable for vocal fold lamina propria restoration should mimic the microenvironment of the lamina propria to induce scarless wound healing and functional tissue regeneration. Most current synthetic or natural injectable biomaterials do not possess the same level of complex, tissue-specific constituents as the natural vocal fold lamina propria. In this study we present a newly-developed injectable gel fabricated from decellularized bovine vocal fold lamina propria. Blyscan assay and mass spectrometry indicated that the vocal fold-specific gel contained a large amount of sulfated glycosaminoglycans and over 250 proteins. Gene Ontology overrepresentation analysis revealed that the proteins in the gel dominantly promote antifibrotic biological process. In vivo study using a rabbit vocal fold injury model showed that the injectable gel significantly reduced collagen density and decreased tissue contraction of the lamina propria in vocal folds with chronic scarring. Furthermore, this acellular gel only elicited minimal humoral immune response after injection. Our findings suggested that the tissue-specific, injectable extracellular matrix gel could be a promising biomaterial for treating vocal fold scarring, even after the formation of mature scar. STATEMENT OF SIGNIFICANCE: Vocal fold lamina propria scarring remains among the foremost therapeutic challenges in the management of patients with voice disorders. Surgical excision of scar may cause secondary scarring and yield inconsistent results. The present study reports an extracellular matrix-derived biomaterial that demonstrated antifibrotic effect on chronic scarring in vocal fold lamina propria. Its injectability minimizes the invasiveness of the delivery procedure and the degree of mucosal violation. In this work we also describe a new methodology which can more accurately identify proteins from the complex mixture of an acellular extracellular matrix gel by excluding interfering peptides produced during the enzymatic digestion in gel fabrication.
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Affiliation(s)
- Chet C Xu
- Department of Otolaryngology-Head and Neck Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Biomedical Engineering Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ted Mau
- Department of Otolaryngology-Head and Neck Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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18
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Beneke T, Demay F, Hookway E, Ashman N, Jeffery H, Smith J, Valli J, Becvar T, Myskova J, Lestinova T, Shafiq S, Sadlova J, Volf P, Wheeler RJ, Gluenz E. Genetic dissection of a Leishmania flagellar proteome demonstrates requirement for directional motility in sand fly infections. PLoS Pathog 2019; 15:e1007828. [PMID: 31242261 PMCID: PMC6615630 DOI: 10.1371/journal.ppat.1007828] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 07/09/2019] [Accepted: 05/08/2019] [Indexed: 11/29/2022] Open
Abstract
The protozoan parasite Leishmania possesses a single flagellum, which is remodelled during the parasite’s life cycle from a long motile flagellum in promastigote forms in the sand fly to a short immotile flagellum in amastigotes residing in mammalian phagocytes. This study examined the protein composition and in vivo function of the promastigote flagellum. Protein mass spectrometry and label free protein enrichment testing of isolated flagella and deflagellated cell bodies defined a flagellar proteome for L. mexicana promastigote forms (available via ProteomeXchange with identifier PXD011057). This information was used to generate a CRISPR-Cas9 knockout library of 100 mutants to screen for flagellar defects. This first large-scale knockout screen in a Leishmania sp. identified 56 mutants with altered swimming speed (52 reduced and 4 increased) and defined distinct mutant categories (faster swimmers, slower swimmers, slow uncoordinated swimmers and paralysed cells, including aflagellate promastigotes and cells with curled flagella and disruptions of the paraflagellar rod). Each mutant was tagged with a unique 17-nt barcode, providing a simple barcode sequencing (bar-seq) method for measuring the relative fitness of L. mexicana mutants in vivo. In mixed infections of the permissive sand fly vector Lutzomyia longipalpis, paralysed promastigotes and uncoordinated swimmers were severely diminished in the fly after defecation of the bloodmeal. Subsequent examination of flies infected with a single paralysed mutant lacking the central pair protein PF16 or an uncoordinated swimmer lacking the axonemal protein MBO2 showed that these promastigotes did not reach anterior regions of the fly alimentary tract. These data show that L. mexicana need directional motility for successful colonisation of sand flies. Leishmania are protozoan parasites, transmitted between mammals by the bite of phlebotomine sand flies. Promastigote forms in the sand fly have a long flagellum, which is motile and used for anchoring the parasites to prevent clearance with the digested blood meal remnants. To dissect flagellar functions and their importance in life cycle progression, we generated here a comprehensive list of >300 flagellar proteins and produced a CRISPR-Cas9 gene knockout library of 100 mutant Leishmania. We studied their behaviour in vitro before examining their fate in the sand fly Lutzomyia longipalpis. Measuring mutant swimming speeds showed that about half behaved differently compared to the wild type: a few swam faster, many slower and some were completely paralysed. We also found a group of uncoordinated swimmers. To test whether flagellar motility is required for parasite migration from the fly midgut to the foregut from where they reach the next host, we infected sand flies with a mixed mutant population. Each mutant carried a unique tag and tracking these tags up to nine days after infection showed that paralysed and uncoordinated Leishmania were rapidly lost from flies. These data indicate that directional swimming is important for successful colonisation of sand flies.
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Affiliation(s)
- Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - François Demay
- University of Lille 1, Cité Scientifique, Villeneuve d’Ascq, France
| | - Edward Hookway
- Research Department of Pathology, University College London, London, United Kingdom
| | - Nicole Ashman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Heather Jeffery
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - James Smith
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jessica Valli
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Tomas Becvar
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jitka Myskova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tereza Lestinova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shahaan Shafiq
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, United Kingdom
| | - Jovana Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Richard John Wheeler
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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19
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Huang L, Chambliss KL, Gao X, Yuhanna IS, Behling-Kelly E, Bergaya S, Ahmed M, Michaely P, Luby-Phelps K, Darehshouri A, Xu L, Fisher EA, Ge WP, Mineo C, Shaul PW. SR-B1 drives endothelial cell LDL transcytosis via DOCK4 to promote atherosclerosis. Nature 2019; 569:565-569. [PMID: 31019307 PMCID: PMC6631346 DOI: 10.1038/s41586-019-1140-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 03/25/2019] [Indexed: 01/15/2023]
Abstract
Atherosclerosis, which underlies life-threatening cardiovascular disorders including myocardial infarction and stroke1, is initiated by low density lipoprotein cholesterol (LDL) passage into the artery wall and engulfment by macrophages, leading to foam cell formation and lesion development2, 2, 3, 3. How circulating LDL enters the artery wall to instigate atherosclerosis is unknown. Here we show in mice that scavenger receptor, class B type 1 (SR-B1) in endothelial cells mediates LDL delivery into arteries and its accumulation by artery wall macrophages, thereby promoting atherosclerosis. LDL particles are colocalized with SR-B1 in endothelial cell intracellular vesicles in vivo, and LDL transcytosis across endothelial monolayers requires its direct binding to SR-B1 and an 8 amino acid cytoplasmic domain of the receptor that recruits the guanine nucleotide exchange factor dedicator of cytokinesis 4 (DOCK4)4. DOCK4 promotes SR-B1 internalization and LDL transport by coupling LDL binding to SR-B1 with Rac1 activation. SR-B1 and DOCK4 expression are increased in atherosclerosis-prone regions of the mouse aorta prior to lesion formation, and in human atherosclerotic versus normal arteries. These findings challenge the long-held concept that atherogenesis involves passive LDL movement across a compromised endothelial barrier. Interventions inhibiting endothelial delivery of LDL into the artery wall may represent a new therapeutic category in the battle against cardiovascular disease.
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Affiliation(s)
- Linzhang Huang
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ken L Chambliss
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofei Gao
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan S Yuhanna
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Erica Behling-Kelly
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sonia Bergaya
- Department of Medicine, New York University School of Medicine, New York, NY, USA.,Leon H. Charney Division of Cardiology, New York University School of Medicine, New York, NY, USA.,Marc and Ruti Bell Program in Vascular Biology, New York University School of Medicine, New York, NY, USA
| | - Mohamed Ahmed
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Michaely
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kate Luby-Phelps
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anza Darehshouri
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Edward A Fisher
- Department of Medicine, New York University School of Medicine, New York, NY, USA.,Leon H. Charney Division of Cardiology, New York University School of Medicine, New York, NY, USA.,Marc and Ruti Bell Program in Vascular Biology, New York University School of Medicine, New York, NY, USA
| | - Woo-Ping Ge
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chieko Mineo
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Philip W Shaul
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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20
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Bricogne C, Fine M, Pereira PM, Sung J, Tijani M, Wang Y, Henriques R, Collins MK, Hilgemann DW. TMEM16F activation by Ca 2+ triggers plasma membrane expansion and directs PD-1 trafficking. Sci Rep 2019; 9:619. [PMID: 30679690 PMCID: PMC6345885 DOI: 10.1038/s41598-018-37056-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
TMEM16F is a Ca2+ -gated ion channel that is required for Ca2+ -activated phosphatidylserine exposure on the surface of many eukaryotic cells. TMEM16F is widely expressed and has roles in platelet activation during blood clotting, bone formation and T cell activation. By combining microscopy and patch clamp recording we demonstrate that activation of TMEM16F by Ca2+ ionophores in Jurkat T cells triggers large-scale surface membrane expansion in parallel with phospholipid scrambling. With continued ionophore application,TMEM16F-expressing cells then undergo extensive shedding of ectosomes. The T cell co-receptor PD-1 is selectively incorporated into ectosomes. This selectivity depends on its transmembrane sequence. Surprisingly, cells lacking TMEM16F not only fail to expand surface membrane in response to elevated cytoplasmic Ca2+, but instead undergo rapid massive endocytosis with PD-1 internalisation. These results establish a new role for TMEM16F as a regulator of Ca2+ activated membrane trafficking.
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Affiliation(s)
| | - Michael Fine
- University of Texas Southwestern Medical Center, Department of Physiology, Dallas, Texas, USA
| | - Pedro M Pereira
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St, London, UK
| | - Julia Sung
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Herts, UK
| | - Maha Tijani
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Herts, UK
| | - Youxue Wang
- University of Texas Southwestern Medical Center, Department of Physiology, Dallas, Texas, USA
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St, London, UK
| | - Mary K Collins
- UCL Cancer Institute, University College London, Gower St, London, UK.
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Herts, UK.
- Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan.
| | - Donald W Hilgemann
- University of Texas Southwestern Medical Center, Department of Physiology, Dallas, Texas, USA.
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21
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Moussa EM, Huang H, Thézénas ML, Fischer R, Ramaprasad A, Sisay-Joof F, Jallow M, Pain A, Kwiatkowski D, Kessler BM, Casals-Pascual C. Proteomic profiling of the plasma of Gambian children with cerebral malaria. Malar J 2018; 17:337. [PMID: 30249265 PMCID: PMC6154937 DOI: 10.1186/s12936-018-2487-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cerebral malaria (CM) is a severe neurological complication of Plasmodium falciparum infection. A number of pathological findings have been correlated with pediatric CM including sequestration, platelet accumulation, petechial haemorrhage and retinopathy. However, the molecular mechanisms leading to death in CM are not yet fully understood. METHODS A shotgun plasma proteomic study was conducted using samples form 52 Gambian children with CM admitted to hospital. Based on clinical outcome, children were assigned to two groups: reversible and fatal CM. Label-free liquid chromatography-tandem mass spectrometry was used to identify and compare plasma proteins that were differentially regulated in children who recovered from CM and those who died. Candidate biomarkers were validated using enzyme immunoassays. RESULTS The plasma proteomic signature of children with CM identified 266 proteins differentially regulated in children with fatal CM. Proteins from the coagulation cascade were consistently decreased in fatal CM, whereas the plasma proteomic signature associated with fatal CM underscored the importance of endothelial activation, tissue damage, inflammation, haemolysis and glucose metabolism. The concentration of circulating proteasomes or PSMB9 in plasma was not significantly different in fatal CM when compared with survivors. Plasma PSMB9 concentration was higher in patients who presented with seizures and was significantly correlated with the number of seizures observed in patients with CM during admission. CONCLUSIONS The results indicate that increased tissue damage and hypercoagulability may play an important role in fatal CM. The diagnostic value of this molecular signature to identify children at high risk of dying to optimize patient referral practices should be validated prospectively.
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Affiliation(s)
- Ehab M Moussa
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- King Abdulla University of Science and Technology, Thuwal, Saudi Arabia
| | - Honglei Huang
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | | | - Roman Fischer
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Abhinay Ramaprasad
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- King Abdulla University of Science and Technology, Thuwal, Saudi Arabia
| | | | | | - Arnab Pain
- King Abdulla University of Science and Technology, Thuwal, Saudi Arabia
| | | | | | - Climent Casals-Pascual
- Wellcome Trust Centre for Human Genetics, Oxford, UK.
- Hospital Clinic i Provincial de Barcelona, CDB and ISGlobal, Barcelona, Spain.
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22
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Stegmann M, Barclay AN, Metcalfe C. Reduction of leucocyte cell surface disulfide bonds during immune activation is dynamic as revealed by a quantitative proteomics workflow (SH-IQ). Open Biol 2018; 8:rsob.180079. [PMID: 30232098 PMCID: PMC6170505 DOI: 10.1098/rsob.180079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/17/2018] [Indexed: 11/16/2022] Open
Abstract
Communication through cell surface receptors is crucial for maintaining immune homeostasis, coordinating the immune response and pathogen clearance. This is dependent on the interaction of cell surface receptors with their ligands and requires functionally active conformational states. Thus, immune cell function can be controlled by modulating the structure of either the receptor or the ligand. Reductive cleavage of labile disulfide bonds can mediate such an allosteric change, resulting in modulation of the immune system by a hitherto little studied mechanism. Identifying proteins with labile disulfide bonds and determining the extent of reduction is crucial in elucidating the functional result of reduction. We describe a mass spectrometry-based method—thiol identification and quantitation (SH-IQ)—to identify, quantify and monitor such reduction of labile disulfide bonds in primary cells during immune activation. These results provide the first insight into the extent and dynamics of labile disulfide bond reduction in leucocyte cell surface proteins upon immune activation. We show that this process is thiol oxidoreductase-dependent and mainly affects activatory (e.g. CD132, SLAMF1) and adhesion (CD44, ICAM1) molecules, suggesting a mechanism to prevent over-activation of the immune system and excessive accumulation of leucocytes at sites of inflammation.
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Affiliation(s)
- Monika Stegmann
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - A Neil Barclay
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Clive Metcalfe
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK .,National Institute of Biological Standards and Control, Blanche Lane, South Mimms, UK
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23
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Stallings NR, O'Neal MA, Hu J, Kavalali ET, Bezprozvanny I, Malter JS. Pin1 mediates Aβ 42-induced dendritic spine loss. Sci Signal 2018; 11:11/522/eaap8734. [PMID: 29559586 PMCID: PMC6136423 DOI: 10.1126/scisignal.aap8734] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Early-stage Alzheimer's disease is characterized by the loss of dendritic spines in the neocortex of the brain. This phenomenon precedes tau pathology, plaque formation, and neurodegeneration and likely contributes to synaptic loss, memory impairment, and behavioral changes in patients. Studies suggest that dendritic spine loss is induced by soluble, multimeric amyloid-β (Aβ42), which, through postsynaptic signaling, activates the protein phosphatase calcineurin. We investigated how calcineurin caused spine pathology and found that the cis-trans prolyl isomerase Pin1 was a critical downstream target of Aβ42-calcineurin signaling. In dendritic spines, Pin1 interacted with and was dephosphorylated by calcineurin, which rapidly suppressed its isomerase activity. Knockout of Pin1 or exposure to Aβ42 induced the loss of mature dendritic spines, which was prevented by exogenous Pin1. The calcineurin inhibitor FK506 blocked dendritic spine loss in Aβ42-treated wild-type cells but had no effect on Pin1-null neurons. These data implicate Pin1 in dendritic spine maintenance and synaptic loss in early Alzheimer's disease.
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Affiliation(s)
- Nancy R Stallings
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Melissa A O'Neal
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Jie Hu
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ege T Kavalali
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ilya Bezprozvanny
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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24
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Antiphospholipid antibodies induce thrombosis by PP2A activation via apoER2-Dab2-SHC1 complex formation in endothelium. Blood 2018; 131:2097-2110. [PMID: 29500169 DOI: 10.1182/blood-2017-11-814681] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/23/2018] [Indexed: 01/10/2023] Open
Abstract
In the antiphospholipid syndrome (APS), antiphospholipid antibody (aPL) recognition of β2 glycoprotein I promotes thrombosis, and preclinical studies indicate that this is due to endothelial nitric oxide synthase (eNOS) antagonism via apolipoprotein E receptor 2 (apoER2)-dependent processes. How apoER2 molecularly links these events is unknown. Here, we show that, in endothelial cells, the apoER2 cytoplasmic tail serves as a scaffold for aPL-induced assembly and activation of the heterotrimeric protein phosphatase 2A (PP2A). Disabled-2 (Dab2) recruitment to the apoER2 NPXY motif promotes the activating L309 methylation of the PP2A catalytic subunit by leucine methyl transferase-1. Concurrently, Src homology domain-containing transforming protein 1 (SHC1) recruits the PP2A scaffolding subunit to the proline-rich apoER2 C terminus along with 2 distinct regulatory PP2A subunits that mediate inhibitory dephosphorylation of Akt and eNOS. In mice, the coupling of these processes in endothelium is demonstrated to underlie aPL-invoked thrombosis. By elucidating these intricacies in the pathogenesis of APS-related thrombosis, numerous potential new therapeutic targets have been identified.
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25
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Qu Z, D'Mello SR. Proteomic analysis identifies NPTX1 and HIP1R as potential targets of histone deacetylase-3-mediated neurodegeneration. Exp Biol Med (Maywood) 2018; 243:627-638. [PMID: 29486577 DOI: 10.1177/1535370218761149] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A defining feature of neurodegenerative diseases is the abnormal and excessive loss of neurons. One molecule that is particularly important in promoting neuronal death in a variety of cell culture and in vivo models of neurodegeneration is histone deacetylase-3 (HDAC3), a member of the histone deacetylase family of proteins. As a step towards understanding how HDAC3 promotes neuronal death, we conducted a proteomic screen aimed at identifying proteins that were regulated by HDAC3. HDAC3 was overexpressed in cultured rat cerebellar granule neurons (CGNs) and protein lysates were analyzed by mass spectrometry. Of over 3000 proteins identified in the screen, only 21 proteins displayed a significant alteration in expression. Of these, 12 proteins were downregulated whereas 9 proteins were upregulated. The altered expression of five of these proteins, TEX10, NPTX1, TFG, TSC1, and NFL, along with another protein that was downregulated in the proteomic screen, HIP1R, was confirmed using Western blots and commercially available antibodies. Because antibodies were not available for some of the proteins and since HDAC3 is a transcriptional regulator of gene expression, we conducted RT-PCR analysis to confirm expression changes. In separate analyses, we also included other proteins that are known to regulate neurodegeneration, including HDAC9, HSF1, huntingtin, GAPDH, FUS, and p65/RELA. Based on our proteomic screen and candidate protein approach, we identify three genes, Nptx1, Hip1r, and Hdac9, all known to regulate neurodegeneration that are robustly regulated by HDAC3. Given their suggested roles in regulating neuronal death, these genes are likely to be involved in regulating HDAC3-mediated neurotoxicity. Impact statement Neurodegenerative diseases are a major medical, social, and economic problem. Recent studies by several laboratories have indicated that histone deacetylase-3 (HDAC3) plays a key role in promoting neuronal death. But the downstream mediators of HDAC3 neurotoxicity have yet to be identified. We conducted a proteomic screen to identify HDAC3 targets the results of which have been described in this report. Briefly, we identify Nptx1, Hip1r, and Hdac9 as genes whose expression is altered by HDAC3. Investigating how these genes are involved in HDAC3 neurotoxicity could shed valuable insight into neurodegenerative disease and identify molecules that can be targeted to treat these devastating disorders.
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Affiliation(s)
- Zhe Qu
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Santosh R D'Mello
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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26
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Manders DB, Kishore HA, Gazdar AF, Keller PW, Tsunezumi J, Yanagisawa H, Lea J, Word RA. Dysregulation of fibulin-5 and matrix metalloproteases in epithelial ovarian cancer. Oncotarget 2018; 9:14251-14267. [PMID: 29581841 PMCID: PMC5865667 DOI: 10.18632/oncotarget.24484] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/01/2018] [Indexed: 12/20/2022] Open
Abstract
Fibulin 5 (FBLN5) is an extracellular matrix glycoprotein that suppresses matrix metalloprotease 9 (MMP-9), angiogenesis and epithelial cell motility. Here, we investigated the regulation and function of FBLN5 in epithelial ovarian cancer (EOC). FBLN5 mRNA was down-regulated 5-fold in EOC relative to benign ovary. Not surprisingly, MMP9 mRNA and enzyme activity were increased significantly, and inversely correlated with FBLN5 gene expression. FBLN5 degradation products of 52.8 and 41.3 kDa were increased substantially in EOC. We identified two candidate proteases (serine elastase and MMP-7, but not MMP-9) that cleave FBLN5. MMP-7, but not neutrophil elastase, gene expression was increased dramatically in EOC. Recombinant FBLN5 significantly inhibited adhesion of EOC cells to both laminin and collagen I. Finally, using immunohistochemistry, we found immunoreactive FBLN5 within tumor macrophages throughout human EOC tumors. This work indicates that FBLN5 is degraded in EOC most likely by proteases enriched in macrophages of the tumor microenvironment. Proteolysis of FBLN5 serves as a mechanism to promote cell adhesion and local metastasis of ovarian cancer cells. Promotion of a stable ECM with intact FBLN5 in the tumor matrix may serve as a novel therapeutic adjunct to prevent spread of ovarian cancer.
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Affiliation(s)
- Dustin B Manders
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Hari Annavarapu Kishore
- Department of Obstetrics and Gynecology, Green Center for Reproductive Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Patrick W Keller
- Department of Obstetrics and Gynecology, Green Center for Reproductive Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jun Tsunezumi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Hiromi Yanagisawa
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Current address: Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Jayanthi Lea
- Department of Obstetrics and Gynecology, Green Center for Reproductive Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ruth Ann Word
- Department of Obstetrics and Gynecology, Green Center for Reproductive Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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27
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Hariri H, Rogers S, Ugrankar R, Liu YL, Feathers JR, Henne WM. Lipid droplet biogenesis is spatially coordinated at ER-vacuole contacts under nutritional stress. EMBO Rep 2017; 19:57-72. [PMID: 29146766 DOI: 10.15252/embr.201744815] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic cells store lipids in cytosolic organelles known as lipid droplets (LDs). Lipid droplet bud from the endoplasmic reticulum (ER), and may be harvested by the vacuole for energy during prolonged periods of starvation. How cells spatially coordinate LD production is poorly understood. Here, we demonstrate that yeast ER-vacuole contact sites (NVJs) physically expand in response to metabolic stress, and serve as sites for LD production. NVJ tether Mdm1 demarcates sites of LD budding, and interacts with fatty acyl-CoA synthases at the NVJ periphery. Artificially expanding the NVJ through over-expressing Mdm1 is sufficient to drive NVJ-associated LD production, whereas ablating the NVJ induces defects in fatty acid-to-triglyceride production. Collectively, our data suggest a tight metabolic link between nutritional stress and LD biogenesis that is spatially coordinated at ER-vacuole contact sites.
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Affiliation(s)
- Hanaa Hariri
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sean Rogers
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rupali Ugrankar
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yang Lydia Liu
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - J Ryan Feathers
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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28
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Ray A, Schwartz N, de Souza Santos M, Zhang J, Orth K, Salomon D. Type VI secretion system MIX-effectors carry both antibacterial and anti-eukaryotic activities. EMBO Rep 2017; 18:1978-1990. [PMID: 28912123 PMCID: PMC5666596 DOI: 10.15252/embr.201744226] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022] Open
Abstract
Most type VI secretion systems (T6SSs) described to date are protein delivery apparatuses that mediate bactericidal activities. Several T6SSs were also reported to mediate virulence activities, although only few anti-eukaryotic effectors have been described. Here, we identify three T6SSs in the marine bacterium Vibrio proteolyticus and show that T6SS1 mediates bactericidal activities under warm marine-like conditions. Using comparative proteomics, we find nine potential T6SS1 effectors, five of which belong to the polymorphic MIX-effector class. Remarkably, in addition to six predicted bactericidal effectors, the T6SS1 secretome includes three putative anti-eukaryotic effectors. One of these is a MIX-effector containing a cytotoxic necrotizing factor 1 domain. We demonstrate that T6SS1 can use this MIX-effector to target phagocytic cells, resulting in morphological changes and actin cytoskeleton rearrangements. In conclusion, the V. proteolyticus T6SS1, a system homologous to one found in pathogenic vibrios, uses a suite of polymorphic effectors that target both bacteria and eukaryotic neighbors.
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Affiliation(s)
- Ann Ray
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nika Schwartz
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marcela de Souza Santos
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Junmei Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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29
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Khatamzas E, Hipp MM, Gaughan D, Pichulik T, Leslie A, Fernandes RA, Muraro D, Booth S, Zausmer K, Sun MY, Kessler B, Rowland-Jones S, Cerundolo V, Simmons A. Snapin promotes HIV-1 transmission from dendritic cells by dampening TLR8 signaling. EMBO J 2017; 36:2998-3011. [PMID: 28923824 PMCID: PMC5641917 DOI: 10.15252/embj.201695364] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/05/2017] [Accepted: 08/11/2017] [Indexed: 12/18/2022] Open
Abstract
HIV-1 traffics through dendritic cells (DCs) en route to establishing a productive infection in T lymphocytes but fails to induce an innate immune response. Within DC endosomes, HIV-1 somehow evades detection by the pattern-recognition receptor (PRR) Toll-like receptor 8 (TLR8). Using a phosphoproteomic approach, we identified a robust and diverse signaling cascade triggered by HIV-1 upon entry into human DCs. A secondary siRNA screen of the identified signaling factors revealed several new mediators of HIV-1 trans-infection of CD4+ T cells in DCs, including the dynein motor protein Snapin. Inhibition of Snapin enhanced localization of HIV-1 with TLR8+ early endosomes, triggered a pro-inflammatory response, and inhibited trans-infection of CD4+ T cells. Snapin inhibited TLR8 signaling in the absence of HIV-1 and is a general regulator of endosomal maturation. Thus, we identify a new mechanism of innate immune sensing by TLR8 in DCs, which is exploited by HIV-1 to promote transmission.
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Affiliation(s)
- Elham Khatamzas
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Madeleine Maria Hipp
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Daniel Gaughan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Tica Pichulik
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for TB & HIV, Durban, South Africa
| | - Ricardo A Fernandes
- Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniele Muraro
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Sarah Booth
- Immunology & Immunotherapy, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kieran Zausmer
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Mei-Yi Sun
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Benedikt Kessler
- KwaZulu-Natal Research Institute for TB & HIV, Durban, South Africa
| | - Sarah Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford NDMRB, Oxford, UK
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine University of Oxford, Oxford, UK
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30
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Gao Q, Binns DD, Kinch LN, Grishin NV, Ortiz N, Chen X, Goodman JM. Pet10p is a yeast perilipin that stabilizes lipid droplets and promotes their assembly. J Cell Biol 2017; 216:3199-3217. [PMID: 28801319 PMCID: PMC5626530 DOI: 10.1083/jcb.201610013] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/28/2017] [Accepted: 07/11/2017] [Indexed: 11/22/2022] Open
Abstract
Pet10p is a yeast lipid droplet protein of unknown function. We show that it binds specifically to and is stabilized by droplets containing triacylglycerol (TG). Droplets isolated from cells with a PET10 deletion strongly aggregate, appear fragile, and fuse in vivo when cells are cultured in oleic acid. Pet10p binds early to nascent droplets, and their rate of appearance is decreased in pet10Δ Moreover, Pet10p functionally interacts with the endoplasmic reticulum droplet assembly factors seipin and Fit2 to maintain proper droplet morphology. The activity of Dga1p, a diacylglycerol acyltransferase, and TG accumulation were both 30-35% lower in the absence of Pet10p. Pet10p contains a PAT domain, a defining property of perilipins, which was not previously known to exist in yeast. We propose that the core functions of Pet10p and other perilipins extend beyond protection from lipases and include the preservation of droplet integrity as well as collaboration with seipin and Fit2 in droplet assembly and maintenance.
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Affiliation(s)
- Qiang Gao
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX
| | - Derk D Binns
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical School, Dallas, TX.,Department of Biophysics, University of Texas Southwestern Medical School, Dallas, TX
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical School, Dallas, TX.,Department of Biophysics, University of Texas Southwestern Medical School, Dallas, TX
| | - Natalie Ortiz
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX
| | - Xiao Chen
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX
| | - Joel M Goodman
- Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX
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31
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Lee R, Fischer R, Charles PD, Adlam D, Valli A, Di Gleria K, Kharbanda RK, Choudhury RP, Antoniades C, Kessler BM, Channon KM. A novel workflow combining plaque imaging, plaque and plasma proteomics identifies biomarkers of human coronary atherosclerotic plaque disruption. Clin Proteomics 2017. [PMID: 28642677 PMCID: PMC5477097 DOI: 10.1186/s12014-017-9157-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background
Atherosclerotic plaque rupture is the culprit event which underpins most acute vascular syndromes such as acute myocardial infarction. Novel biomarkers of plaque rupture could improve biological understanding and clinical management of patients presenting with possible acute vascular syndromes but such biomarker(s) remain elusive. Investigation of biomarkers in the context of de novo plaque rupture in humans is confounded by the inability to attribute the plaque rupture as the source of biomarker release, as plaque ruptures are typically associated with prompt down-stream events of myocardial necrosis and systemic inflammation. Methods We developed a novel approach to identify potential biomarkers of plaque rupture by integrating plaque imaging, using optical coherence tomography, with both plaque and plasma proteomic analysis in a human model of angioplasty-induced plaque disruption. Results We compared two pairs of coronary plaque debris, captured by a FilterWire Device, and their corresponding control samples and found matrix metalloproteinase 9 (MMP9) to be significantly enriched in plaque. Plaque contents, as defined by optical coherence tomography, affect the systemic changes of MMP9. Disruption of lipid-rich plaque led to prompt elevation of plasma MMP9, whereas disruption of non-lipid-rich plaque resulted in delayed elevation of plasma MMP9. Systemic MMP9 elevation is independent of the associated myocardial necrosis and systemic inflammation (measured by Troponin I and C-reactive protein, respectively). This information guided the selection of a subset of subjects of for further label free proteomics analysis by liquid chromatography tandem mass spectrometry (LC–MS/MS). We discovered five novel, plaque-enriched proteins (lipopolysaccharide binding protein, Annexin A5, eukaryotic translocation initiation factor, syntaxin 11, cytochrome B5 reductase 3) to be significantly elevated in systemic circulation at 5 min after plaque disruption. Conclusion This novel approach for biomarker discovery in human coronary artery plaque disruption can identify new biomarkers related to human coronary artery plaque composition and disruption. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9157-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regent Lee
- Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Adlam
- Division of Cardiovascular Medicine, University of Oxford, Oxford, UK
| | - Alessandro Valli
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katalin Di Gleria
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rajesh K Kharbanda
- Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Robin P Choudhury
- Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,Acute Vascular Imaging Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Charalambos Antoniades
- Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Keith M Channon
- Division of Cardiovascular Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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32
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Chen CC, Montalbano AP, Hussain I, Lee WR, Mendelson CR. The transcriptional repressor GATAD2B mediates progesterone receptor suppression of myometrial contractile gene expression. J Biol Chem 2017; 292:12560-12576. [PMID: 28576827 DOI: 10.1074/jbc.m117.791350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/31/2017] [Indexed: 01/05/2023] Open
Abstract
The mechanisms whereby progesterone (P4), acting via the progesterone receptor (PR), inhibits proinflammatory/contractile gene expression during pregnancy are incompletely defined. Using immortalized human myometrial (hTERT-HM) cells stably expressing wild-type PR-A or PR-B (PRWT), we found that P4 significantly inhibited IL-1β induction of the NF-κB target genes, COX-2 and IL-8 P4-PRWT transrepression occurred at the level of transcription initiation and was mediated by decreased recruitment of NF-κB p65 and RNA polymerase II to COX-2 and IL-8 promoters. However, in cells stably expressing a PR-A or PR-B DNA-binding domain mutant (PRmDBD), P4-mediated transrepression was significantly reduced, suggesting a critical role of the PR DBD. ChIP analysis of hTERT-HM cells stably expressing PRWT or PRmDBD revealed that P4 treatment caused equivalent recruitment of PRWT and PRmDBD to COX-2 and IL-8 promoters, suggesting that PR inhibitory effects were not mediated by its direct DNA binding. Using immunoprecipitation, followed by MS, we identified a transcriptional repressor, GATA zinc finger domain-containing 2B (GATAD2B), that interacted strongly with PRWT but poorly with PRmDBD P4 treatment of PRWT hTERT-HM cells caused enhanced recruitment of endogenous GATAD2B to COX-2 and IL-8 promoters. Further, siRNA knockdown of endogenous GATAD2B significantly reduced P4-PRWT transrepression of COX-2 and IL-8 Notably, GATAD2B expression was significantly decreased in pregnant mouse and human myometrium during labor. Our findings suggest that GATAD2B serves as an important mediator of P4-PR suppression of proinflammatory and contractile genes during pregnancy. Decreased GATAD2B expression near term may contribute to the decline in PR function, leading to labor.
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Affiliation(s)
- Chien-Cheng Chen
- Department of Biochemistry and the Department of Obstetrics and Gynecology, North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038
| | - Alina P Montalbano
- Department of Biochemistry and the Department of Obstetrics and Gynecology, North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038
| | - Imran Hussain
- Department of Biochemistry and the Department of Obstetrics and Gynecology, North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038
| | - Wan-Ru Lee
- Department of Biochemistry and the Department of Obstetrics and Gynecology, North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038
| | - Carole R Mendelson
- Department of Biochemistry and the Department of Obstetrics and Gynecology, North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038.
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Grieve AG, Xu H, Künzel U, Bambrough P, Sieber B, Freeman M. Phosphorylation of iRhom2 at the plasma membrane controls mammalian TACE-dependent inflammatory and growth factor signalling. eLife 2017; 6. [PMID: 28432785 PMCID: PMC5436907 DOI: 10.7554/elife.23968] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/20/2017] [Indexed: 12/21/2022] Open
Abstract
Proteolytic cleavage and release from the cell surface of membrane-tethered ligands is an important mechanism of regulating intercellular signalling. TACE is a major shedding protease, responsible for the liberation of the inflammatory cytokine TNFα and ligands of the epidermal growth factor receptor. iRhoms, catalytically inactive members of the rhomboid-like superfamily, have been shown to control the ER-to-Golgi transport and maturation of TACE. Here, we reveal that iRhom2 remains associated with TACE throughout the secretory pathway, and is stabilised at the cell surface by this interaction. At the plasma membrane, ERK1/2-mediated phosphorylation and 14-3-3 protein binding of the cytoplasmic amino-terminus of iRhom2 alter its interaction with mature TACE, thereby licensing its proteolytic activity. We show that this molecular mechanism is responsible for triggering inflammatory responses in primary mouse macrophages. Overall, iRhom2 binds to TACE throughout its lifecycle, implying that iRhom2 is a primary regulator of stimulated cytokine and growth factor signalling. DOI:http://dx.doi.org/10.7554/eLife.23968.001 Injury or infection can cause tissues in the body to become inflamed. The immune system triggers this inflammation to help repair the injury or fight the infection. A signal molecule known as TNF – which is produced by immune cells called macrophages – triggers inflammation. This protein is normally attached to the surface of the macrophage, and it only activates inflammation once it has been cut free. An enzyme called TACE cuts and releases TNF from the surface of macrophages. This enzyme is made inside the cell and is then transported to the surface. On the way, TACE matures from an inactive form to a fully functional enzyme. Previous work revealed that a protein called iRhom2 controls TACE maturation, but it has been unclear whether iRhom2 affects TACE in any additional ways. Grieve et al. studied the relationship between iRhom2 and TACE in more detail. The experiments show two new roles for iRhom2: in protecting TACE from being destroyed at the cell surface, and prompting TACE to release TNF to trigger inflammation. Injury or infection causes small molecules called phosphate groups to be attached to iRhom2 in macrophages, which causes TACE to release TNF. The findings of Grieve et al. provide the first evidence that iRhom2 influences the activity of TACE throughout the enzyme’s lifetime. Excessive inflammation, often triggered by the uncontrolled release of TNF, can lead to rheumatoid arthritis, cancer and many other diseases. Therefore, iRhom2 could be a promising new target for anti-inflammatory drugs that may help to treat these conditions. DOI:http://dx.doi.org/10.7554/eLife.23968.002
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Affiliation(s)
- Adam Graham Grieve
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Hongmei Xu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ulrike Künzel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Paul Bambrough
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Boris Sieber
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Matthew Freeman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Galgano D, Onnis A, Pappalardo E, Galvagni F, Acuto O, Baldari CT. The T cell IFT20 interactome reveals new players in immune synapse assembly. J Cell Sci 2017; 130:1110-1121. [PMID: 28154159 DOI: 10.1242/jcs.200006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/30/2017] [Indexed: 12/17/2022] Open
Abstract
Sustained signalling at the immune synapse (IS) requires the synaptic delivery of recycling endosome-associated T cell antigen receptors (TCRs). IFT20, a component of the intraflagellar transport system, controls TCR recycling to the IS as a complex with IFT57 and IFT88. Here, we used quantitative mass spectrometry to identify additional interaction partners of IFT20 in Jurkat T cells. In addition to IFT57 and IFT88, the analysis revealed new binding partners, including IFT54 (also known as TRAF3IP1), GMAP-210 (also known as TRIP11), Arp2/3 complex subunit-3 (ARPC3), COP9 signalosome subunit-1 (CSN1, also known as GPS1) and ERGIC-53 (also known as LMAN1). A direct interaction between IFT20 and both IFT54 and GMAP-210 was confirmed in pulldown assays. Confocal imaging of antigen-specific conjugates using T cells depleted of these proteins by RNA interference showed that TCR accumulation and phosphotyrosine signalling at the IS were impaired in the absence of IFT54, ARPC3 or ERGIC-53. Similar to in IFT20-deficient T cells, this defect resulted from a reduced ability of endosomal TCRs to polarize to the IS despite a correct translocation of the centrosome towards the antigen-presenting cell contact. Our data underscore the traffic-related role of an IFT20 complex that includes components of the intracellular trafficking machinery in IS assembly.
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Affiliation(s)
- Donatella Galgano
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Anna Onnis
- Department of Life Sciences, University of Siena, Siena 53100, Italy
| | - Elisa Pappalardo
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Cosima T Baldari
- Department of Life Sciences, University of Siena, Siena 53100, Italy
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Chan KW, Shone C, Hesp JR. Antibiotics and iron-limiting conditions and their effect on the production and composition of outer membrane vesicles secreted from clinical isolates of extraintestinal pathogenic E. coli. Proteomics Clin Appl 2016; 11. [PMID: 27666736 DOI: 10.1002/prca.201600091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/19/2016] [Accepted: 09/22/2016] [Indexed: 01/02/2023]
Abstract
PURPOSE The focus of this study was to characterize the effect of clinically relevant stress-inducing conditions on the production and composition of proinflammatory outer membrane vesicles (OMVs) produced from ST131 extraintestinal pathogenic Escherichia coli (ExPEC) clinical isolates. EXPERIMENTAL DESIGN A label-free method (relative normalized spectral index quantification, SINQ) was used to identify changes in the respective OMV proteomes following exposure of the ExPEC strains to antibiotics and low iron. Nanoparticle tracking analysis was used to quantify changes in abundance and size of OMVs produced by the gentamicin-resistant (GenR) and gentamicin-sensitive (GenS) ExPEC strains. RESULTS Up to a 13.1-fold increase in abundance of particles were detected when the gentamicin-sensitive strain was exposed to a range of gentamicin concentrations. In contrast, no increase was observed for the gentamicin-resistant strain. Iron-limiting conditions had minimal effect on OMV production for either strain. Marked changes in the OMV proteome were observed for both strains including increases in Hsp100/Clp proteins, ATP-dependent ClpP protease, and regulatory proteins. CONCLUSION These data provide information on changes in the composition of OMV particles derived from ExPEC strains generated in response to clinically relevant conditions. We show that the levels of the proinflammatory OMVs increase for gentamicin-sensitive ExPEC exposed to the antibiotic.
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Affiliation(s)
- Kin W Chan
- Public Health England, Porton, Salisbury, UK
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Akinci B, Sankella S, Gilpin C, Ozono K, Garg A, Agarwal AK. Progeroid syndrome patients with ZMPSTE24 deficiency could benefit when treated with rapamycin and dimethylsulfoxide. Cold Spring Harb Mol Case Stud 2016; 3:a001339. [PMID: 28050601 PMCID: PMC5171694 DOI: 10.1101/mcs.a001339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Patients with progeroid syndromes such as mandibuloacral dysplasia, type B (MADB) and restrictive dermopathy (RD) harbor mutations in zinc metalloproteinase (ZMPSTE24), an enzyme essential for posttranslational proteolysis of prelamin A to form mature lamin A. Dermal fibroblasts from these patients show increased nuclear dysmorphology and reduced proliferation; however, the efficacy of various pharmacological agents in reversing these cellular phenotypes remains unknown. In this study, fibroblasts from MADB patients exhibited marked nuclear abnormalities and reduced proliferation that improved upon treatment with rapamycin and dimethylsulfoxide but not with other agents, including farnesyl transferase inhibitors. Surprisingly, fibroblasts from an RD patient with a homozygous null mutation in ZMPSTE24, resulting in exclusive accumulation of prelamin A with no lamin A on immunoblotting of cellular lysate, exhibited few nuclear abnormalities and near-normal cellular proliferation. An unbiased proteomic analysis of the cellular lysate from RD fibroblasts revealed a lack of processing of vimentin, a cytoskeletal protein. Interestingly, the assembly of the vimentin microfibrils in MADB fibroblasts improved with rapamycin and dimethylsulfoxide. We conclude that rapamycin and dimethylsulfoxide are beneficial for improving nuclear morphology and cell proliferation of MADB fibroblasts. Data from a single RD patient's fibroblasts also suggest that prelamin A accumulation by itself might not be detrimental and requires additional alterations at the cellular level to manifest the phenotype.
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Affiliation(s)
- Baris Akinci
- Division of Nutrition and Metabolic Diseases, Center for Human Nutrition, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Shireesha Sankella
- Division of Nutrition and Metabolic Diseases, Center for Human Nutrition, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Christopher Gilpin
- Molecular and Cellular Imaging, Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Center for Human Nutrition, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Anil K Agarwal
- Division of Nutrition and Metabolic Diseases, Center for Human Nutrition, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Kalantari R, Hicks JA, Li L, Gagnon KT, Sridhara V, Lemoff A, Mirzaei H, Corey DR. Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (NEW YORK, N.Y.) 2016; 22:1085-98. [PMID: 27198507 PMCID: PMC4911916 DOI: 10.1261/rna.056499.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 05/25/2023]
Abstract
Argonaute 2 (AGO2), the catalytic engine of RNAi, is typically associated with inhibition of translation in the cytoplasm. AGO2 has also been implicated in nuclear processes including transcription and splicing. There has been little insight into AGO2's nuclear interactions or how they might differ relative to cytoplasm. Here we investigate the interactions of cytoplasmic and nuclear AGO2 using semi-quantitative mass spectrometry. Mass spectrometry often reveals long lists of candidate proteins, complicating efforts to rigorously discriminate true interacting partners from artifacts. We prioritized candidates using orthogonal analytical strategies that compare replicate mass spectra of proteins associated with Flag-tagged and endogenous AGO2. Interactions with TRNC6A, TRNC6B, TNRC6C, and AGO3 are conserved between nuclei and cytoplasm. TAR binding protein interacted stably with cytoplasmic AGO2 but not nuclear AGO2, consistent with strand loading in the cytoplasm. Our data suggest that interactions between functionally important components of RNAi machinery are conserved between the nucleus and cytoplasm but that accessory proteins differ. Orthogonal analysis of mass spectra is a powerful approach to streamlining identification of protein partners.
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Affiliation(s)
- Roya Kalantari
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Hicks
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liande Li
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Viswanadham Sridhara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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McCombs JE, Kohler JJ. Pneumococcal Neuraminidase Substrates Identified through Comparative Proteomics Enabled by Chemoselective Labeling. Bioconjug Chem 2016; 27:1013-22. [PMID: 26954852 DOI: 10.1021/acs.bioconjchem.6b00050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Neuraminidases (sialidases) are enzymes that hydrolytically remove sialic acid from sialylated proteins and lipids. Neuraminidases are encoded by a range of human pathogens, including bacteria, viruses, fungi, and protozoa. Many pathogen neuraminidases are virulence factors, indicating that desialylation of host glycoconjugates can be a critical step in infection. Specifically, desialylation of host cell surface glycoproteins can enable these molecules to function as pathogen receptors or can alter signaling through the plasma membrane. Despite these critical effects, no unbiased approaches exist to identify glycoprotein substrates of neuraminidases. Here, we combine previously reported glycoproteomics methods with quantitative proteomics analysis to identify glycoproteins whose sialylation changes in response to neuraminidase treatment. The two glycoproteomics methods-periodate oxidation and aniline-catalyzed oxime ligation (PAL) and galactose oxidase and aniline-catalyzed oxime ligation (GAL)-rely on chemoselective labeling of sialylated and nonsialylated glycoproteins, respectively. We demonstrated the utility of the combined approaches by identifying substrates of two pneumococcal neuraminidases in a human cell line that models the blood-brain barrier. The methods deliver complementary lists of neuraminidase substrates, with GAL identifying a larger number of substrates than PAL (77 versus 17). Putative neuraminidase substrates were confirmed by other methods, establishing the validity of the approach. Among the identified substrates were host glycoproteins known to function in bacteria adherence and infection. Functional assays suggest that multiple desialylated cell surface glycoproteins may act together as pneumococcus receptors. Overall, this method will provide a powerful approach to identify glycoproteins that are desialylated by both purified neuraminidases and intact pathogens.
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Affiliation(s)
- Janet E McCombs
- Department of Biochemistry, The University of Texas Southwestern Medical Center , Dallas, Texas 75390-9038, United States
| | - Jennifer J Kohler
- Department of Biochemistry, The University of Texas Southwestern Medical Center , Dallas, Texas 75390-9038, United States
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Melnik S, Caudron-Herger M, Brant L, Carr IM, Rippe K, Cook PR, Papantonis A. Isolation of the protein and RNA content of active sites of transcription from mammalian cells. Nat Protoc 2016; 11:553-65. [DOI: 10.1038/nprot.2016.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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40
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Discovery of tumor-specific irreversible inhibitors of stearoyl CoA desaturase. Nat Chem Biol 2016; 12:218-25. [PMID: 26829472 PMCID: PMC4798879 DOI: 10.1038/nchembio.2016] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 12/09/2015] [Indexed: 01/09/2023]
Abstract
A hallmark of targeted cancer therapies is selective toxicity among cancer cell lines. We evaluated results from a viability screen of over 200,000 small molecules to identify two chemical series, oxalamides and benzothiazoles, that were selectively toxic to the same four of 12 human lung cancer cell lines at low nanomolar concentrations. Sensitive cell lines expressed cytochrome P450 (CYP) 4F11, which metabolized the compounds into irreversible stearoyl CoA desaturase (SCD) inhibitors. SCD is recognized as a promising biological target in cancer and metabolic disease. However, SCD is essential to sebocytes, and accordingly SCD inhibitors cause skin toxicity. Mouse sebocytes were unable to activate the benzothiazoles or oxalamides into SCD inhibitors, providing a therapeutic window for inhibiting SCD in vivo. We thus offer a strategy to target SCD in cancer by taking advantage of high CYP expression in a subset of tumors.
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41
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Costello I, Nowotschin S, Sun X, Mould AW, Hadjantonakis AK, Bikoff EK, Robertson EJ. Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development. Genes Dev 2016; 29:2108-22. [PMID: 26494787 PMCID: PMC4617976 DOI: 10.1101/gad.268979.115] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Costello et al. demonstrate that Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. In proteomic experiments, they characterize a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. Gene regulatory networks controlling functional activities of spatially and temporally distinct endodermal cell populations in the early mouse embryo remain ill defined. The T-box transcription factor Eomes, acting downstream from Nodal/Smad signals, directly activates the LIM domain homeobox transcription factor Lhx1 in the visceral endoderm. Here we demonstrate Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. Conditional inactivation of Lhx1 disrupts anterior definitive endoderm development and impedes node and midline morphogenesis in part due to severe disturbances in visceral endoderm displacement. Transcriptional profiling and ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) experiments identified Lhx1 target genes, including numerous anterior definitive endoderm markers and components of the Wnt signaling pathway. Interestingly, Lhx1-binding sites were enriched at enhancers, including the Nodal-proximal epiblast enhancer element and enhancer regions controlling Otx2 and Foxa2 expression. Moreover, in proteomic experiments, we characterized a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. These partnerships cooperatively regulate development of the anterior mesendoderm, node, and midline cell populations responsible for establishment of the left–right body axis and head formation.
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Affiliation(s)
- Ita Costello
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Xin Sun
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Arne W Mould
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | - Elizabeth K Bikoff
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Elizabeth J Robertson
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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42
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Patidar PL, Motea EA, Fattah FJ, Zhou Y, Morales JC, Xie Y, Garner HR, Boothman DA. The Kub5-Hera/RPRD1B interactome: a novel role in preserving genetic stability by regulating DNA mismatch repair. Nucleic Acids Res 2016; 44:1718-31. [PMID: 26819409 PMCID: PMC4770225 DOI: 10.1093/nar/gkv1492] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 12/09/2015] [Indexed: 12/29/2022] Open
Abstract
Ku70-binding protein 5 (Kub5)-Hera (K-H)/RPRD1B maintains genetic integrity by concomitantly minimizing persistent R-loops and promoting repair of DNA double strand breaks (DSBs). We used tandem affinity purification-mass spectrometry, co-immunoprecipitation and gel-filtration chromatography to define higher-order protein complexes containing K-H scaffolding protein to gain insight into its cellular functions. We confirmed known protein partners (Ku70, RNA Pol II, p15RS) and discovered several novel associated proteins that function in RNA metabolism (Topoisomerase 1 and RNA helicases), DNA repair/replication processes (PARP1, MSH2, Ku, DNA-PKcs, MCM proteins, PCNA and DNA Pol δ) and in protein metabolic processes, including translation. Notably, this approach directed us to investigate an unpredicted involvement of K-H in DNA mismatch repair (MMR) where K-H depletion led to concomitant MMR deficiency and compromised global microsatellite stability. Mechanistically, MMR deficiency in K-H-depleted cells was a consequence of reduced stability of the core MMR proteins (MLH1 and PMS2) caused by elevated basal caspase-dependent proteolysis. Pan-caspase inhibitor treatment restored MMR protein loss. These findings represent a novel mechanism to acquire MMR deficiency/microsatellite alterations. A significant proportion of colon, endometrial and ovarian cancers exhibit k-h expression/copy number loss and may have severe mutator phenotypes with enhanced malignancies that are currently overlooked based on sporadic MSI+ screening.
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Affiliation(s)
- Praveen L Patidar
- Departments of Pharmacology and Radiation Oncology, Program in Cell Stress and Cancer Nanomedicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Edward A Motea
- Departments of Pharmacology and Radiation Oncology, Program in Cell Stress and Cancer Nanomedicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Farjana J Fattah
- Departments of Pharmacology and Radiation Oncology, Program in Cell Stress and Cancer Nanomedicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yunyun Zhou
- Quantitative Biomedical Center, Department of Clinical Science, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, USA
| | - Julio C Morales
- Department of Neurosurgery, University of Oklahoma Heath Science Center, Oklahoma City, OK, USA
| | - Yang Xie
- Quantitative Biomedical Center, Department of Clinical Science, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, USA
| | - Harold R Garner
- Edward Via College of Osteopathic Medicine and the MITTE Office, Virginia Tech, Blacksburg, VA, USA
| | - David A Boothman
- Departments of Pharmacology and Radiation Oncology, Program in Cell Stress and Cancer Nanomedicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Codrea MC, Nahnsen S. Platforms and Pipelines for Proteomics Data Analysis and Management. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:203-215. [PMID: 27975218 DOI: 10.1007/978-3-319-41448-5_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Since mass spectrometry was introduced as the core technology for large-scale analysis of the proteome, the speed of data acquisition, dynamic ranges of measurements, and data quality are continuously improving. These improvements are triggered by regular launches of new methodologies and instruments.
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Affiliation(s)
- Marius Cosmin Codrea
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.
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Yamashiro Y, Papke CL, Kim J, Ringuette LJ, Zhang QJ, Liu ZP, Mirzaei H, Wagenseil JE, Davis EC, Yanagisawa H. Abnormal mechanosensing and cofilin activation promote the progression of ascending aortic aneurysms in mice. Sci Signal 2015; 8:ra105. [PMID: 26486174 DOI: 10.1126/scisignal.aab3141] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Smooth muscle cells (SMCs) and the extracellular matrix (ECM) are intimately associated in the aortic wall. Fbln4(SMKO) mice with an SMC-specific deletion of the Fbln4 gene, which encodes the vascular ECM component fibulin-4, develop ascending aortic aneurysms that have increased abundance of angiotensin-converting enzyme (ACE); inhibiting angiotensin II signaling within the first month of life prevents aneurysm development. We used comparative proteomics analysis of Fbln4(SMKO) aortas from postnatal day (P) 1 to P30 mice to identify key molecules involved in aneurysm initiation and expansion. At P14, the actin depolymerizing factor cofilin was dephosphorylated and thus activated, and at P7, the abundance of slingshot-1 (SSH1) phosphatase, an activator of cofilin, was increased, leading to actin cytoskeletal remodeling. Also, by P7, biomechanical changes and underdeveloped elastic lamina-SMC connections were evident, and the abundance of early growth response 1 (Egr1), a mechanosensitive transcription factor that stimulates ACE expression, was increased, which was before the increases in ACE abundance and cofilin activation. Postnatal deletion of Fbln4 in SMCs at P7 prevented cofilin activation and aneurysm formation, suggesting that these processes required disruption of elastic lamina-SMC connections. Phosphoinositide 3-kinase (PI3K) is involved in the angiotensin II-mediated activation of SSH1, and administration of PI3K inhibitors from P7 to P30 decreased SSH1 abundance and prevented aneurysms. These results suggest that aneurysm formation arises from abnormal mechanosensing of SMCs resulting from the loss of elastic lamina-SMC connections and from increased SSH1 and cofilin activity, which may be potential therapeutic targets for treating ascending aortic aneurysms.
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Affiliation(s)
- Yoshito Yamashiro
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christina L Papke
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jungsil Kim
- Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, MO 63130, USA
| | - Lea-Jeanne Ringuette
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Qing-Jun Zhang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhi-Ping Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry and Proteomics Core Unit, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessica E Wagenseil
- Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, MO 63130, USA
| | - Elaine C Davis
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Hiromi Yanagisawa
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan.
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Serve A, Pieler MM, Benndorf D, Rapp E, Wolff MW, Reichl U. Comparison of Influenza Virus Particle Purification Using Magnetic Sulfated Cellulose Particles with an Established Centrifugation Method for Analytics. Anal Chem 2015; 87:10708-11. [DOI: 10.1021/acs.analchem.5b02681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anja Serve
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Michael Martin Pieler
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Michael Werner Wolff
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
- Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
- Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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46
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Fiebig M, Kelly S, Gluenz E. Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates. PLoS Pathog 2015; 11:e1005186. [PMID: 26452044 PMCID: PMC4599935 DOI: 10.1371/journal.ppat.1005186] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/03/2015] [Indexed: 02/07/2023] Open
Abstract
Leishmania spp. are protozoan parasites that have two principal life cycle stages: the motile promastigote forms that live in the alimentary tract of the sandfly and the amastigote forms, which are adapted to survive and replicate in the harsh conditions of the phagolysosome of mammalian macrophages. Here, we used Illumina sequencing of poly-A selected RNA to characterise and compare the transcriptomes of L. mexicana promastigotes, axenic amastigotes and intracellular amastigotes. These data allowed the production of the first transcriptome evidence-based annotation of gene models for this species, including genome-wide mapping of trans-splice sites and poly-A addition sites. The revised genome annotation encompassed 9,169 protein-coding genes including 936 novel genes as well as modifications to previously existing gene models. Comparative analysis of gene expression across promastigote and amastigote forms revealed that 3,832 genes are differentially expressed between promastigotes and intracellular amastigotes. A large proportion of genes that were downregulated during differentiation to amastigotes were associated with the function of the motile flagellum. In contrast, those genes that were upregulated included cell surface proteins, transporters, peptidases and many uncharacterized genes, including 293 of the 936 novel genes. Genome-wide distribution analysis of the differentially expressed genes revealed that the tetraploid chromosome 30 is highly enriched for genes that were upregulated in amastigotes, providing the first evidence of a link between this whole chromosome duplication event and adaptation to the vertebrate host in this group. Peptide evidence for 42 proteins encoded by novel transcripts supports the idea of an as yet uncharacterised set of small proteins in Leishmania spp. with possible implications for host-pathogen interactions.
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Affiliation(s)
- Michael Fiebig
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, United Kingdom
- * E-mail: (SK); (EG)
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
- * E-mail: (SK); (EG)
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47
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Salomon D, Klimko JA, Trudgian DC, Kinch LN, Grishin NV, Mirzaei H, Orth K. Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria. PLoS Pathog 2015; 11:e1005128. [PMID: 26305100 PMCID: PMC4549250 DOI: 10.1371/journal.ppat.1005128] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread protein secretion apparatus used by Gram-negative bacteria to deliver toxic effector proteins into adjacent bacterial or host cells. Here, we uncovered a role in interbacterial competition for the two T6SSs encoded by the marine pathogen Vibrio alginolyticus. Using comparative proteomics and genetics, we identified their effector repertoires. In addition to the previously described effector V12G01_02265, we identified three new effectors secreted by T6SS1, indicating that the T6SS1 secretes at least four antibacterial effectors, of which three are members of the MIX-effector class. We also showed that the T6SS2 secretes at least three antibacterial effectors. Our findings revealed that many MIX-effectors belonging to clan V are “orphan” effectors that neighbor mobile elements and are shared between marine bacteria via horizontal gene transfer. We demonstrated that a MIX V-effector from V. alginolyticus is a functional T6SS effector when ectopically expressed in another Vibrio species. We propose that mobile MIX V-effectors serve as an environmental reservoir of T6SS effectors that are shared and used to diversify antibacterial toxin repertoires in marine bacteria, resulting in enhanced competitive fitness. The bacterial type VI secretion system (T6SS) is a contact-dependent protein secretion apparatus that is emerging as a major component of interbacterial competition in the environment. The bacterium Vibrio alginolyticus is a pathogen of marine animals and a causal agent of wound infections, otitis, and gastroenteritis in humans. In this study, we provide a comprehensive characterization of the environmental regulation, antibacterial activities, and secreted effector repertoires of the two T6SSs found in this pathogen. We also identify a subset of T6SS effectors that appear to be mobile and shared between marine bacteria that can interact with each other in aquatic environments. Our findings suggest that bacteria can incorporate T6SS effectors from competitors in the environment. These newly acquired toxins may be used to expand and diversify T6SS effector repertoires and enhance bacterial fitness.
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Affiliation(s)
- Dor Salomon
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (DS); (KO)
| | - John A. Klimko
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - David C. Trudgian
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (DS); (KO)
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48
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Nilse L, Sigloch FC, Biniossek ML, Schilling O. Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling. Proteomics Clin Appl 2015; 9:706-14. [DOI: 10.1002/prca.201400173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/23/2015] [Accepted: 04/28/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Lars Nilse
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Florian Christoph Sigloch
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- Faculty of Biology; University of Freiburg; Freiburg Germany
| | - Martin L. Biniossek
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research; University of Freiburg; Freiburg Germany
- BIOSS Centre for Biological Signalling Studies; University of Freiburg; Freiburg Germany
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49
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Katafuchi T, Esterházy D, Lemoff A, Ding X, Sondhi V, Kliewer SA, Mirzaei H, Mangelsdorf DJ. Detection of FGF15 in plasma by stable isotope standards and capture by anti-peptide antibodies and targeted mass spectrometry. Cell Metab 2015; 21:898-904. [PMID: 26039452 PMCID: PMC4454892 DOI: 10.1016/j.cmet.2015.05.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/18/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
Abstract
Fibroblast growth factor 15 (FGF15) has been proposed as a postprandial hormone that signals from intestine to liver to regulate bile acid and carbohydrate homeostasis. However, detecting FGF15 in blood using conventional techniques has proven difficult. Here, we describe a stable isotope standards and capture by anti-peptide antibodies (SISCAPA) assay that combines immuno-enrichment with selected reaction monitoring (SRM) mass spectrometry to overcome this issue. Using this assay, we show that FGF15 circulates in plasma in an FXR and circadian rhythm-dependent manner at concentrations that activate its receptor. Consistent with the proposed endocrine role for FGF15 in liver, mice lacking hepatocyte expression of the obligate FGF15 co-receptor, β-Klotho, have increased bile acid synthesis and reduced glycogen storage despite having supraphysiological plasma FGF15 concentrations. Collectively, these data demonstrate that FGF15 functions as a hormone and highlight the utility of SISCAPA-SRM as a sensitive assay for detecting low-abundance proteins in plasma.
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Affiliation(s)
- Takeshi Katafuchi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daria Esterházy
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xunshan Ding
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Varun Sondhi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Steven A Kliewer
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - David J Mangelsdorf
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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50
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Geoghegan V, Guo A, Trudgian D, Thomas B, Acuto O. Comprehensive identification of arginine methylation in primary T cells reveals regulatory roles in cell signalling. Nat Commun 2015; 6:6758. [PMID: 25849564 PMCID: PMC4396391 DOI: 10.1038/ncomms7758] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/25/2015] [Indexed: 12/11/2022] Open
Abstract
The impact of protein arginine methylation on the regulation of immune functions is virtually unknown. Here, we apply a novel method—isomethionine methyl-SILAC—coupled with antibody-mediated arginine-methylated peptide enrichment to identify methylated peptides in human T cells by mass spectrometry. This approach allowed the identification of 2,502 arginine methylation sites from 1,257 tissue-specific and housekeeping proteins. We find that components of T cell antigen receptor signal machinery and several key transcription factors that regulate T cell fate determination are methylated on arginine. Moreover, we demonstrate changes in arginine methylation stoichiometry during cellular stimulation in a subset of proteins critical to T cell differentiation. Our data suggest that protein arginine methyltransferases exert key regulatory roles in T cell activation and differentiation, opening a new field of investigation in T cell biology. Arginine methylation is an important regulatory post-translational modification. Here, the authors present a new SILAC-based method—iMethyl-SILAC—that allows unambiguous identification of arginine-methylated peptide pairs by mass spectrometry and apply it to greatly expand the known T-cell arginine methylome.
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Affiliation(s)
- Vincent Geoghegan
- Laboratory of T cell signalling, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ailan Guo
- Cell Signaling Technology Inc., Trask Lane, Danvers, Massachusetts 01923, USA
| | - David Trudgian
- Central Proteomics Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Oreste Acuto
- Laboratory of T cell signalling, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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