bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020–10–25
twelve papers selected by
John Silke, Walter and Eliza Hall Institute of Medical Research
  1. Global view of human protein glycosylation pathways and functions.
  2. Ubiquitomics: An Overview and Future.
  3. Temporal Analysis of Brd4 Displacement in the Control of B Cell Survival, Proliferation, and Differentiation.
  4. Clinical MDR1 inhibitors enhance Smac-mimetic bioavailability to kill murine LSCs and improve survival in AML models.
  5. The therapeutic potential of PROTACs.
  6. Kinase inhibition in autoimmunity and inflammation.
  7. TNF Receptor 1 Promotes Early-Life Immunity and Protects against Colitis in Mice.
  8. C-tag TNF: a reporter system to study TNF shedding.
  9. First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α.
  10. Cell-cell interfaces as specialized compartments directing cell function.
  11. Budding of a Retrovirus: Some Assemblies Required.
  12. The timestamp that can tell an RNA molecule's age - to the hour.
  1. Nat Rev Mol Cell Biol. 2020 Oct 21.
    Global view of human protein glycosylation pathways and functions.
    Katrine T Schjoldager, Yoshiki Narimatsu, Hiren J Joshi, Henrik Clausen.
      Glycosylation is the most abundant and diverse form of post-translational modification of proteins that is common to all eukaryotic cells. Enzymatic glycosylation of proteins involves a complex metabolic network and different types of glycosylation pathways that orchestrate enormous amplification of the proteome in producing diversity of proteoforms and its biological functions. The tremendous structural diversity of glycans attached to proteins poses analytical challenges that limit exploration of specific functions of glycosylation. Major advances in quantitative transcriptomics, proteomics and nuclease-based gene editing are now opening new global ways to explore protein glycosylation through analysing and targeting enzymes involved in glycosylation processes. In silico models predicting cellular glycosylation capacities and glycosylation outcomes are emerging, and refined maps of the glycosylation pathways facilitate genetic approaches to address functions of the vast glycoproteome. These approaches apply commonly available cell biology tools, and we predict that use of (single-cell) transcriptomics, genetic screens, genetic engineering of cellular glycosylation capacities and custom design of glycoprotein therapeutics are advancements that will ignite wider integration of glycosylation in general cell biology.
    DOI:  https://doi.org/10.1038/s41580-020-00294-x
  2. Biomolecules. 2020 Oct 17. pii: E1453. [Epub ahead of print]10(10):
    Ubiquitomics: An Overview and Future.
    George Vere, Rachel Kealy, Benedikt M Kessler, Adan Pinto-Fernandez.
      Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
    Keywords:  mass spectrometry; proteomics; ubiquitin; ubiquitome; ubiquitomics
    DOI:  https://doi.org/10.3390/biom10101453
  3. Cell Rep. 2020 Oct 20. pii: S2211-1247(20)31279-1. [Epub ahead of print]33(3): 108290
    Temporal Analysis of Brd4 Displacement in the Control of B Cell Survival, Proliferation, and Differentiation.
    Isabella Y Kong, Joel S Rimes, Amanda Light, Izabela Todorovski, Sarah Jones, Eric Morand, Deborah A Knight, Ylva E Bergman, Simon J Hogg, Hendrik Falk, Brendon J Monahan, Paul A Stupple, Ian P Street, Susanne Heinzel, Philippe Bouillet, Ricky W Johnstone, Philip D Hodgkin, Stephin J Vervoort, Edwin D Hawkins.
      JQ1 is a BET-bromodomain inhibitor that has immunomodulatory effects. However, the precise molecular mechanism that JQ1 targets to elicit changes in antibody production is not understood. Our results show that JQ1 induces apoptosis, reduces cell proliferation, and as a consequence, inhibits antibody-secreting cell differentiation. ChIP-sequencing reveals a selective displacement of Brd4 in response to acute JQ1 treatment (<2 h), resulting in specific transcriptional repression. After 8 h, subsequent alterations in gene expression arise as a result of the global loss of Brd4 occupancy. We demonstrate that apoptosis induced by JQ1 is solely attributed to the pro-apoptotic protein Bim (Bcl2l11). Conversely, cell-cycle regulation by JQ1 is associated with multiple Myc-associated gene targets. Our results demonstrate that JQ1 drives temporal changes in Brd4 displacement that results in a specific transcriptional profile that directly affects B cell survival and proliferation to modulate the humoral immune response.
    Keywords:  B cells; cellular immunology; epigenetics
    DOI:  https://doi.org/10.1016/j.celrep.2020.108290
  4. Blood Adv. 2020 Oct 27. 4(20): 5062-5077
    Clinical MDR1 inhibitors enhance Smac-mimetic bioavailability to kill murine LSCs and improve survival in AML models.
    Emma Morrish, Anthony Copeland, Donia M Moujalled, Jason A Powell, Natasha Silke, Ann Lin, Kate E Jarman, Jarrod J Sandow, Gregor Ebert, Liana Mackiewicz, Jessica A Beach, Elizabeth L Christie, Alexander C Lewis, Giovanna Pomilio, Karla C Fischer, Laura MacPherson, David D L Bowtell, Andrew I Webb, Marc Pellegrini, Mark A Dawson, Stuart M Pitson, Andrew H Wei, John Silke, Gabriela Brumatti.
      The specific targeting of inhibitor of apoptosis (IAP) proteins by Smac-mimetic (SM) drugs, such as birinapant, has been tested in clinical trials of acute myeloid leukemia (AML) and certain solid cancers. Despite their promising safety profile, SMs have had variable and limited success. Using a library of more than 5700 bioactive compounds, we screened for approaches that could sensitize AML cells to birinapant and identified multidrug resistance protein 1 inhibitors (MDR1i) as a class of clinically approved drugs that can enhance the efficacy of SM therapy. Genetic or pharmacological inhibition of MDR1 increased intracellular levels of birinapant and sensitized AML cells from leukemia murine models, human leukemia cell lines, and primary AML samples to killing by birinapant. The combination of clinical MDR1 and IAP inhibitors was well tolerated in vivo and more effective against leukemic cells, compared with normal hematopoietic progenitors. Importantly, birinapant combined with third-generation MDR1i effectively killed murine leukemic stem cells (LSCs) and prolonged survival of AML-burdened mice, suggesting a therapeutic opportunity for AML. This study identified a drug combination strategy that, by efficiently killing LSCs, may have the potential to improve outcomes in patients with AML.
    DOI:  https://doi.org/10.1182/bloodadvances.2020001576
  5. Expert Opin Ther Pat. 2020 Oct 20.
    The therapeutic potential of PROTACs.
    Andrew B Benowitz, Katherine L Jones, John D Harling.
       INTRODUCTION: PROTACs represent a novel class of heterobifunctional molecules that simultaneously bind to a target protein and to an E3 ligase complex, resulting in the transfer of ubiquitin and initiating a process ultimately causing the proteasomal degradation of the target protein. This mechanism of action imbues PROTACs with the ability to modulate target biology in unique ways compared to inhibitors, and the development of PROTACs as therapeutic agents is expected to result in new medicines to treat multiple diseases.
    AREAS COVERED: This review includes published PCT (WO) patent applications covering January 2013 through June 2020. Only English language patent applications with exemplified PROTACs reported to degrade a target protein(s) were deemed in scope, and the definition of 'PROTAC' was restricted to a bifunctional molecule which contains a discrete binding element for a specific degradation target(s), as well as a separate discrete E3 ligase-binding moiety.
    EXPERT OPINION: Delivering on the enormous potential of PROTACs will require the development of PROTAC medicines that are differentiated from traditional small-molecule inhibitors. The modular composition of PROTACs affords both opportunities and challenges in securing robust intellectual property, and we envision that requirements for novelty are likely to evolve as this area matures.
    Keywords:  PROTAC; bifunctional molecules; protein degradation; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1080/13543776.2021.1840553
  6. Nat Rev Drug Discov. 2020 Oct 19.
    Kinase inhibition in autoimmunity and inflammation.
    Ali A Zarrin, Katherine Bao, Patrick Lupardus, Domagoj Vucic.
      Despite recent advances in the treatment of autoimmune and inflammatory diseases, unmet medical needs in some areas still exist. One of the main therapeutic approaches to alleviate dysregulated inflammation has been to target the activity of kinases that regulate production of inflammatory mediators. Small-molecule kinase inhibitors have the potential for broad efficacy, convenience and tissue penetrance, and thus often offer important advantages over biologics. However, designing kinase inhibitors with target selectivity and minimal off-target effects can be challenging. Nevertheless, immense progress has been made in advancing kinase inhibitors with desirable drug-like properties into the clinic, including inhibitors of JAKs, IRAK4, RIPKs, BTK, SYK and TPL2. This Review will address the latest discoveries around kinase inhibitors with an emphasis on clinically validated autoimmunity and inflammatory pathways.
    DOI:  https://doi.org/10.1038/s41573-020-0082-8
  7. Cell Rep. 2020 Oct 20. pii: S2211-1247(20)31264-X. [Epub ahead of print]33(3): 108275
    TNF Receptor 1 Promotes Early-Life Immunity and Protects against Colitis in Mice.
    Cambrian Y Liu, Sharon S Tam, Ying Huang, Philip E Dubé, Rabea Alhosh, Nandini Girish, Shivesh Punit, Shirin Nataneli, Fan Li, Jeffrey M Bender, M Kay Washington, D Brent Polk.
      Neutralization of tumor necrosis factor (TNF) represents a widely used therapeutic strategy for autoimmune diseases including inflammatory bowel disease (IBD). However, the fact that many patients with IBD are non-responsive to anti-TNF therapies suggests the need for a better understanding of TNF signaling in IBD. Here, we show that co-deletion of TNF receptor 1 (TNFR1, Tnfrsf1a) in the Il10-/- spontaneous colitis model exacerbates disease, resulting in very-early-onset inflammation after weaning. The disease can be interrupted by treatment with antibiotics. The single deletion of TNFR1 induces subclinical colonic epithelial dysfunction and mucosal immune abnormalities, including accumulation of neutrophils and depletion of B cells. During the pre-disease period (before weaning), both Tnfr1-/- and Il10-/-Tnfr1-/- animals exhibit impaired expression of pro-inflammatory cytokines compared with wild-type and Il10-/- controls, respectively. Collectively, these results demonstrate the net anti-inflammatory functions of TNF/TNFR1 signaling through the regulation of colonic immune homeostasis in early life.
    Keywords:  IBD; antibiotics; barrier; microbiome; mucosa; tolerance; weaning reaction
    DOI:  https://doi.org/10.1016/j.celrep.2020.108275
  8. J Biol Chem. 2020 Oct 20. pii: jbc.RA120.015248. [Epub ahead of print]
    C-tag TNF: a reporter system to study TNF shedding.
    Francesca Pinci, Moritz M Gaidt, Christophe Jung, Gunnar Kuut, Margaret A Jackson, Stefan Bauernfried, Veit Hornung.
      TNF is a highly pro-inflammatory cytokine that contributes not only to the regulation of immune responses but also to the development of severe inflammatory diseases. TNF is synthesized as a transmembrane protein, which is further matured via proteolytic cleavage by metalloproteases such as ADAM17, a process known as shedding. At present, TNF is mainly detected by measuring the precursor or the mature cytokine of bulk cell populations by techniques such as ELISA or immunoblotting. However, these methods do not provide information on the exact timing and extent of TNF cleavage at single-cell resolution and they do not allow the live visualization of shedding events. Here, we generated C-tag TNF as a genetically encoded reporter to study TNF shedding at the single-cell level. The functionality of the C-tag TNF reporter is based on the exposure of a cryptic epitope on the C-terminus of the transmembrane portion of pro-TNF upon cleavage. In both denatured and non-denatured samples, this epitope can be detected by a nanobody in a highly sensitive and specific manner only upon TNF shedding. As such, C-tag TNF can successfully be used for the detection of TNF cleavage in flow cytometry and live-cell imaging applications. We furthermore demonstrate its applicability in a forward genetic screen geared toward the identification of genetic regulators of TNF maturation. In summary, the C-tag TNF reporter can be employed to gain novel insights into the complex regulation of ADAM-dependent TNF shedding.
    Keywords:  ADAM; CRISPR/Cas; cell surface enzyme; flow cytometry; microscopy; reporter; shedding; tumor necrosis factor (TNF)
    DOI:  https://doi.org/10.1074/jbc.RA120.015248
  9. iScience. 2020 Sep 25. 23(9): 101529
    First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α.
    Samuel Zambrano, Alessia Loffreda, Elena Carelli, Giacomo Stefanelli, Federica Colombo, Edouard Bertrand, Carlo Tacchetti, Alessandra Agresti, Marco E Bianchi, Nacho Molina, Davide Mazza.
      Nuclear factor (NF)-κB controls the transcriptional response to inflammatory signals by translocating into the nucleus, but we lack a single-cell characterization of the resulting transcription dynamics. Here we show that upon tumor necrosis factor (TNF)-α transcription of NF-κB target genes is heterogeneous in individual cells but results in an average nascent transcription profile that is prompt (i.e., occurs almost immediately) and sharp (i.e., increases and decreases rapidly) compared with NF-κB nuclear localization. Using an NF-κB-controlled MS2 reporter we show that the single-cell nascent transcription is more heterogeneous than NF-κB translocation dynamics, with a fraction of synchronized "first responders" that shape the average transcriptional profile and are more prone to respond to multiple TNF-α stimulations. A mathematical model combining NF-κB-mediated gene activation and a gene refractory state is able to reproduce these features. Our work shows how the expression of target genes induced by transcriptional activators can be heterogeneous across single cells and yet time resolved on average.
    Keywords:  Biological Sciences; Biophysics; Immunology; Molecular Biology; Systems Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101529
  10. Nat Rev Mol Cell Biol. 2020 Oct 22.
    Cell-cell interfaces as specialized compartments directing cell function.
    Brian Belardi, Sungmin Son, James H Felce, Michael L Dustin, Daniel A Fletcher.
      Cell-cell interfaces are found throughout multicellular organisms, from transient interactions between motile immune cells to long-lived cell-cell contacts in epithelia. Studies of immune cell interactions, epithelial cell barriers, neuronal contacts and sites of cell-cell fusion have identified a core set of features shared by cell-cell interfaces that critically control their function. Data from diverse cell types also show that cells actively and passively regulate the localization, strength, duration and cytoskeletal coupling of receptor interactions governing cell-cell signalling and physical connections between cells, indicating that cell-cell interfaces have a unique membrane organization that emerges from local molecular and cellular mechanics. In this Review, we discuss recent findings that support the emerging view of cell-cell interfaces as specialized compartments that biophysically constrain the arrangement and activity of their protein, lipid and glycan components. We also review how these biophysical features of cell-cell interfaces allow cells to respond with high selectivity and sensitivity to multiple inputs, serving as the basis for wide-ranging cellular functions. Finally, we consider how the unique properties of cell-cell interfaces present opportunities for therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41580-020-00298-7
  11. Viruses. 2020 Oct 20. pii: E1188. [Epub ahead of print]12(10):
    Budding of a Retrovirus: Some Assemblies Required.
    Kevin M Rose, Vanessa M Hirsch, Fadila Bouamr.
      One of the most important steps in any viral lifecycle is the production of progeny virions. For retroviruses as well as other viruses, this step is a highly organized process that occurs with exquisite spatial and temporal specificity on the cellular plasma membrane. To facilitate this process, retroviruses encode short peptide motifs, or L domains, that hijack host factors to ensure completion of this critical step. One such cellular machinery targeted by viruses is known as the Endosomal Sorting Complex Required for Transport (ESCRTs). Typically responsible for vesicular trafficking within the cell, ESCRTs are co-opted by the retroviral Gag polyprotein to assist in viral particle assembly and release of infectious virions. This review in the Viruses Special Issue "The 11th International Retroviral Nucleocapsid and Assembly Symposium", details recent findings that shed light on the molecular details of how ESCRTs and the ESCRT adaptor protein ALIX, facilitate retroviral dissemination at sites of viral assembly.
    Keywords:  ALIX; ESCRT-I; HIV-1 budding; maturation; nucleocapsid; ribonucleoprotein
    DOI:  https://doi.org/10.3390/v12101188
  12. Nature. 2020 Oct 19.
    The timestamp that can tell an RNA molecule's age - to the hour.
      
    Keywords:  Biotechnology
    DOI:  https://doi.org/10.1038/d41586-020-02954-6
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