bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020–08–30
thirteen papers selected by
John Silke, Walter and Eliza Hall Institute of Medical Research
  1. Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry.
  2. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.
  3. The diverse roles of RIP kinases in host-pathogen interactions.
  4. PhotoPROTACs: A Novel Biotechnology for Cancer Treatment.
  5. Role of RING-Type E3 Ubiquitin Ligases in Inflammatory Signalling and Inflammatory Bowel Disease.
  6. Tumor necrosis factors-α inhibition-induced paradoxical psoriasis: A case series and literature review.
  7. Sensing and clearance of apoptotic cells.
  8. SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1.
  9. Combining poly(ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors in breast cancer: rationale and preliminary clinical results.
  10. To cut or not to cut: New rules for proteolytic shedding of membrane proteins.
  11. RNAscope® and BaseScope™: In-situ RNA analysis for formalin-fixed paraffin-embedded tissues and beyond.
  12. Imaging mRNA trafficking in living cells using fluorogenic proteins.
  13. Common Sources of Inflammation and Their Impact on Hematopoietic Stem Cell Biology.
  1. Nat Commun. 2020 Aug 26. 11(1): 4268
    Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry.
    Wen-Hao Guo, Xiaoli Qi, Xin Yu, Yang Liu, Chan-I Chung, Fang Bai, Xingcheng Lin, Dong Lu, Lingfei Wang, Jianwei Chen, Lynn Hsiao Su, Krystle J Nomie, Feng Li, Meng C Wang, Xiaokun Shu, José N Onuchic, Jennifer A Woyach, Michael L Wang, Jin Wang.
      Current efforts in the proteolysis targeting chimera (PROTAC) field mostly focus on choosing an appropriate E3 ligase for the target protein, improving the binding affinities towards the target protein and the E3 ligase, and optimizing the PROTAC linker. However, due to the large molecular weights of PROTACs, their cellular uptake remains an issue. Through comparing how different warhead chemistry, reversible noncovalent (RNC), reversible covalent (RC), and irreversible covalent (IRC) binders, affects the degradation of Bruton's Tyrosine Kinase (BTK), we serendipitously discover that cyano-acrylamide-based reversible covalent chemistry can significantly enhance the intracellular accumulation and target engagement of PROTACs and develop RC-1 as a reversible covalent BTK PROTAC with a high target occupancy as its corresponding kinase inhibitor and effectiveness as a dual functional inhibitor and degrader, a different mechanism-of-action for PROTACs. Importantly, this reversible covalent strategy is generalizable to improve other PROTACs, opening a path to enhance PROTAC efficacy.
    DOI:  https://doi.org/10.1038/s41467-020-17997-6
  2. EMBO J. 2020 Aug 26. e106275
    Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.
    Theresa Klemm, Gregor Ebert, Dale J Calleja, Cody C Allison, Lachlan W Richardson, Jonathan P Bernardini, Bernadine Gc Lu, Nathan W Kuchel, Christoph Grohmann, Yuri Shibata, Zhong Yan Gan, James P Cooney, Marcel Doerflinger, Amanda E Au, Timothy R Blackmore, Gerbrand J van der Heden van Noort, Paul P Geurink, Huib Ovaa, Janet Newman, Alan Riboldi-Tunnicliffe, Peter E Czabotar, Jeffrey P Mitchell, Rebecca Feltham, Bernhard C Lechtenberg, Kym N Lowes, Grant Dewson, Marc Pellegrini, Guillaume Lessene, David Komander.
      The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.
    Keywords:  COVID-19; ISG15; papain-like protease; small molecule inhibitor; ubiquitin
    DOI:  https://doi.org/10.15252/embj.2020106275
  3. Semin Cell Dev Biol. 2020 Aug 25. pii: S1084-9521(20)30102-6. [Epub ahead of print]
    The diverse roles of RIP kinases in host-pathogen interactions.
    Vik Ven Eng, Madeleine A Wemyss, Jaclyn S Pearson.
      Receptor Interacting Protein Kinases (RIPKs) are cellular signaling molecules that are critical for homeostatic signaling in both communicable and non-communicable disease processes. In particular, RIPK1, RIPK2, RIPK3 and RIPK7 have emerged as key mediators of intracellular signal transduction including inflammation, autophagy and programmed cell death, and are thus essential for the early control of many diverse pathogenic organisms. In this review, we discuss the role of each RIPK in host responses to bacterial and viral pathogens, with a focus on studies that have used pathogen infection models rather than artificial stimulation with purified pathogen associated molecular patterns. We also discuss the intricate mechanisms of host evasion by pathogens that specifically target RIPKs for inactivation, and finally, we will touch on the controversial issue of drug development for kinase inhibitors to treat chronic inflammatory and neurological disorders, and the implications this may have on the outcome of pathogen infections.
    Keywords:  Bacterial infection; Cell death; Inflammation; Pathogen; RIP kinase; Viral infection
    DOI:  https://doi.org/10.1016/j.semcdb.2020.08.005
  4. Trends Cell Biol. 2020 Aug 24. pii: S0962-8924(20)30150-1. [Epub ahead of print]
    PhotoPROTACs: A Novel Biotechnology for Cancer Treatment.
    Zhi-Wei Wang, Yi Liu, Xueqiong Zhu.
      PROteolysis-TArgeting Chimeras (PROTACs) have been developed for targeting specific protein destruction. Two recent studies in Science Advances by Liu et al. and Reynders et al. reported a novel technology, PHOtochemically TArgeting Chimeras (PHOTACs) or opto-PROTAC, which is light-induced control of protein degradation. This new approach might lead to precision therapeutics in patients with cancer.
    Keywords:  E3 ligases; PROTACs; degradation; therapy; ubiquitination
    DOI:  https://doi.org/10.1016/j.tcb.2020.08.003
  5. Mediators Inflamm. 2020 ;2020 5310180
    Role of RING-Type E3 Ubiquitin Ligases in Inflammatory Signalling and Inflammatory Bowel Disease.
    Liguo Zhu, Ying Li, Longyuan Zhou, Guang Yang, Ying Wang, Jing Han, Li Li, Shenghong Zhang.
      Ubiquitination is a three-step enzymatic cascade for posttranslational protein modification. It includes the ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3). RING-type E3 ubiquitin ligases catalyse the posttranslational proteolytic and nonproteolytic functions in various physiological and pathological processes, such as inflammation-associated signal transduction. Resulting from the diversity of substrates and functional mechanisms, RING-type ligases regulate microbe recognition and inflammation by being involved in multiple inflammatory signalling pathways. These processes also occur in autoimmune diseases, especially inflammatory bowel disease (IBD). To understand the importance of RING-type ligases in inflammation, we have discussed their functional mechanisms in multiple inflammation-associated pathways and correlation between RING-type ligases and IBD. Owing to the limited data on the biology of RING-type ligases, there is an urgent need to analyse their potential as biomarkers and therapeutic targets in IBD in the future.
    DOI:  https://doi.org/10.1155/2020/5310180
  6. Dermatol Ther. 2020 Aug 26. e14225
    Tumor necrosis factors-α inhibition-induced paradoxical psoriasis: A case series and literature review.
    Ni Lian, Li Zhang, Min Chen.
      Today, anti-12/IL23, anti-IL17, and anti-IL23 provide more efficacious and/or safer treatment options for psoriasis. Though, anti-TNF remains a gold standard in the therapy of chronic inflammatory diseases. Paradoxical psoriasis has been reported to occur in patients treated with TNF-α inhibitors. According to the existing literature, including case reports, most patients with paradoxical psoriasis chose to stop the treatment immediately. This article presents a case series involving 150 patients with psoriasis who received treatments with TNF-α inhibitors. We observed 10 (6.7%) patients developing paradoxical psoriasis, and they rejected the recommendation of immediate discontinuation and decided to continue the original treatment. Surprisingly, 80% of them achieved remission again after the aggravation of symptoms and did not have any other serious adverse event. However, there is currently little research that has clarified the mechanism of paradoxical psoriasis. Therefore, we also presented a review of the literature to determine the pathogenesis of paradoxical psoriasis and speculated on the possible causes of the observed transient exacerbation cases. Investigation of the pathogenesis of this paradoxical adverse reaction not only is helpful to guide clinicians to better manage patients, but also may contribute to the discovery of new therapeutic targets in the future. This article is protected by copyright. All rights reserved.
    Keywords:  exacerbation; paradoxical; psoriasis; tumor necrosis factor-α inhibition
    DOI:  https://doi.org/10.1111/dth.14225
  7. Curr Opin Immunol. 2020 Aug 24. pii: S0952-7915(20)30076-5. [Epub ahead of print]68 1-8
    Sensing and clearance of apoptotic cells.
    Shigekazu Nagata, Katsumori Segawa.
      Macrophages specifically engulf apoptotic cells but not healthy cells. Phosphatidylserine (PtdSer) is localized at the inner leaflet of plasma membranes as a result of the action of flippases (ATP11A and 11C). When cells undergo apoptosis, caspase 3 cleaves and inactivates the flippases, while simultaneously cleaving XKR8 to activate its phospholipid scramblase activity. PtdSer is thus swiftly and irreversibly exposed to the cell surface as an 'eat me' signal. Tissue resident macrophages recognize the apoptotic cells using a PtdSer-receptor TIM4 and engulf them with TAM tyrosine-kinase receptors, and integrins. The PtdSer 'eat me' signal appears to override 'don't eat me' signals in most cases.
    DOI:  https://doi.org/10.1016/j.coi.2020.07.007
  8. Sci Adv. 2020 Jul;6(30): eaaz2590
    SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1.
    Nicolás G Simonet, Joshua K Thackray, Berta N Vazquez, Alessandro Ianni, Maria Espinosa-Alcantud, Julia Morales-Sanfrutos, Sarah Hurtado-Bagès, Eduard Sabidó, Marcus Buschbeck, Jay Tischfield, Carolina De La Torre, Manel Esteller, Thomas Braun, Mireia Olivella, Lourdes Serrano, Alejandro Vaquero.
      Sirtuins are key players of metabolic stress response. Originally described as deacetylases, some sirtuins also exhibit poorly understood mono-adenosine 5'-diphosphate (ADP)-ribosyltransferase (mADPRT) activity. We report that the deacetylase SirT7 is a dual sirtuin, as it also features auto-mADPRT activity. SirT7 mADPRT occurs at a previously undefined active site, and its abrogation alters SirT7 chromatin distribution. We identify an epigenetic pathway by which ADP-ribosyl-SirT7 is recognized by the ADP-ribose reader mH2A1.1 under glucose starvation, inducing SirT7 relocalization to intergenic regions. SirT7 promotes mH2A1 enrichment in a subset of nearby genes, many of them involved in second messenger signaling, resulting in their specific up- or down-regulation. The expression profile of these genes under calorie restriction is consistently abrogated in SirT7-deficient mice, resulting in impaired activation of autophagy. Our work provides a novel perspective on sirtuin duality and suggests a role for SirT7/mH2A1.1 axis in glucose homeostasis and aging.
    DOI:  https://doi.org/10.1126/sciadv.aaz2590
  9. Curr Opin Oncol. 2020 Aug 26.
    Combining poly(ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors in breast cancer: rationale and preliminary clinical results.
    Anthony Goncalves, Essia Mezni, François Bertucci.
       PURPOSE OF REVIEW: Recently, both immune checkpoint inhibitors and poly(ADP-ribose) polymerase inhibitors have demonstrated clinical benefit in some subsets of HER2-negative breast cancer patients. A biological rationale exists supporting a potential synergism between these compounds, which may further increase their antitumor activity in the clinic.
    RECENT FINDINGS: PARP inhibitors were shown to activate type I interferon pathway, thus eliciting local and general immune response, while inducing programmed cell death-ligand 1 (PD-L1) up-regulation. In addition, the DNA damages created by PARP inhibition may increase tumor mutational burden and neo-antigens, thereby favoring efficacy of immune checkpoint inhibitors. Accordingly, clinical trials combining PARP inhibitors and agents targeting the PD-1/PD-L1 axis have been initiated in breast cancer in both advanced and early stages, enrolling patients with germline BRCA1/2 mutation, homologous recombination deficiency and/or with triple negative phenotype. Preliminary safety and efficacy results are encouraging, but it is still unclear whether the combination adds benefit compared with each therapeutic administered as single agent.
    SUMMARY: Although a strong rationale exists to support the combination of PARP inhibitors with immune checkpoint inhibitors, future clinical trials will have to demonstrate whether it improves outcome and to identify which patients are the most likely to benefit from.
    DOI:  https://doi.org/10.1097/CCO.0000000000000680
  10. J Biol Chem. 2020 Aug 28. 295(35): 12353-12354
    To cut or not to cut: New rules for proteolytic shedding of membrane proteins.
    Stefan F Lichtenthaler, Edgar Meinl.
      Sheddases are specialized proteases that control the abundance and function of membrane proteins by cleaving their substrate's extracellular domain (ectodomain), a process known as shedding. Hundreds of shedding substrates have been identified, but little is known about the mechanisms that govern ectodomain shedding. Iwagishi et al. now report that negatively charged amino acids in the membrane-proximal juxtamembrane domain of substrates make them resistant to shedding by the metalloprotease ADAM17. These findings will help researchers better understand the regulation of shedding and may aid in the development of drugs targeting sheddases.
    DOI:  https://doi.org/10.1074/jbc.H120.015304
  11. J Biomol Tech. 2020 Aug;31(Suppl): S32
    RNAscope® and BaseScope™: In-situ RNA analysis for formalin-fixed paraffin-embedded tissues and beyond.
    Shanmugapriya Selvaraj, Valeria Mezzano, Cynthia Loomis, Douglass Hanniford, Cynthia Loomis.
      In-situ hybridization (ISH) analysis is a highly desirable, versatile approach for assessing biomarker expression status in a spatial context. Most researchers rely on immunostaining (protein targets) or qPCR (mRNA). However, not all proteins can be immunolabeled due to a lack of well-validated antibodies. The qPCR approach, although highly specific, cannot provide spatial information. RNAscope® employs a unique double Z probe that has to bind to the target RNA in tandem in order to be recognized by the preamplifiers and amplifiers. A fluorescent/chromogenic labeled probe then binds to the multiple binding sites of the amplifiers, which improves detection of low expressing RNA and reduces non-specific binding. RNAscope® replaces cumbersome radioactive and chromogenic ISH with more hassle-free chromogen and fluorescence-labelled probes. At the NYULMC Experimental Pathology Core we have integrated RNAscope® with Polaris multispectral imaging and quantitative analysis using different software platforms. About 21 laboratories have used this workflow to address their specific questions. We have also established and validated the newer BaseScope™ assay. In contrast to RNAscope®, which targets lncRNA and mRNA sequences greater than 300nt, BaseScope™ enables detection of short RNA target sequences between 50-300nt. It can be used to detect exon junctions/splice variants, circular RNA, pre-miRNA, and point mutations. We adapted BaseScope™ to co-detect circular RNA and its linear counterpart in a differentiating cell population, which could not be established on glass chamber slides and had to be stained on a plastic petri dish. In conclusion, RNAscope® and BaseScope™ RNA-ISH are powerful alternative strategies for assessing the spatial distribution of critical biomarkers within intact tissues and cells. This approach coupled with sophisticated imaging modalities and downstream analysis support provides new collaborative opportunities for Core aboratories.
  12. Curr Opin Chem Biol. 2020 Aug 20. pii: S1367-5931(20)30103-4. [Epub ahead of print]57 177-183
    Imaging mRNA trafficking in living cells using fluorogenic proteins.
    Jiahui Wu, Samie R Jaffrey.
      mRNAs play key roles in regulating diverse cellular functions. In many cases, mRNAs exhibit distinct intracellular localizations that are necessary for the spatiotemporal control of protein expression in cells. Therefore, imaging the localization and dynamics of these mRNAs is crucial for understanding diverse aspects of cellular function. In this review, we summarize how mRNA imaging can be achieved using tethered fluorescent proteins and fluorogenic aptamers. We discuss 'fluorogenic proteins' and describe how these recently developed RNA-regulated fluorescent proteins simplify mRNA imaging experiments.
    Keywords:  Aptamers; Fluorescent proteins; Fluorogenic proteins; Imaging; RNA
    DOI:  https://doi.org/10.1016/j.cbpa.2020.07.007
  13. Curr Stem Cell Rep. 2020 Aug 17. 1-12
    Common Sources of Inflammation and Their Impact on Hematopoietic Stem Cell Biology.
    Daniel Hormaechea-Agulla, Duy T Le, Katherine Y King.
       Purpose of Review: Inflammatory signals have emerged as critical regulators of hematopoietic stem cell (HSC) function. Specifically, HSCs are highly responsive to acute changes in systemic inflammation and this influences not only their division rate but also their lineage fate. Identifying how inflammation regulates HSCs and shapes the blood system is crucial to understanding the mechanisms underpinning these processes, as well as potential links between them.
    Recent Findings: A widening array of physiologic and pathologic processes involving heightened inflammation are now recognized to critically affect HSC biology and blood lineage production. Conditions documented to affect HSC function include not only acute and chronic infections but also autoinflammatory conditions, irradiation injury, and physiologic states such as aging and obesity.
    Summary: Recognizing the contexts during which inflammation affects primitive hematopoiesis is essential to improving our understanding of HSC biology and informing new therapeutic interventions against maladaptive hematopoiesis that occurs during inflammatory diseases, infections, and cancer-related disorders.
    Keywords:  Bone marrow; Hematopoiesis; Infectious diseases; Inflammatory conditions; Pro-inflammatory cytokines
    DOI:  https://doi.org/10.1007/s40778-020-00177-z
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