bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020‒07‒19
twenty-nine papers selected by
John Silke
Walter and Eliza Hall Institute of Medical Research
  1. Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose.
  2. The Balance of TNF Mediated Pathways Regulates Inflammatory Cell Death Signaling in Healthy and Diseased Tissues.
  3. Cellular Mechanisms of NETosis.
  4. Mendelian diseases of dysregulated canonical NF-κB signaling: From immunodeficiency to inflammation.
  5. The pseudo-caspase FLIP(L) regulates cell fate following p53 activation.
  6. Recent Advances and Contradictions in the Study of the Individual Roles of Ubiquitin Ligases That Regulate RIG-I-Like Receptor-Mediated Antiviral Innate Immune Responses.
  7. Discovery of an Orally Active Small Molecule TNF-α Inhibitor.
  8. Discovery of simplified benzazole fragments derived from the marine benzosceptrin B as necroptosis inhibitors involving the receptor interacting protein Kinase-1.
  9. Snapshot of a Deadly Embrace: The Caspase-1-GSDMD Interface.
  10. In Vitro and Cellular Probes to Study PARP Enzyme Target Engagement.
  11. Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids.
  12. TNFα/TNFR2 signaling pathway: an active immune checkpoint for mesenchymal stem cell immunoregulatory function.
  13. Keratinocyte-Polyamines and Dendritic Cells: A Bad Duet for Psoriasis.
  14. Transmembrane TNF drives osteoproliferative joint inflammation reminiscent of human spondyloarthritis.
  15. Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation.
  16. HMGB1 amplifies ILC2-induced type-2 inflammation and airway smooth muscle remodelling.
  17. The commensal skin microbiota triggers type I IFN-dependent innate repair responses in injured skin.
  18. Tumor Necrosis Factor-α Trimer Disassembly and Inactivation via Peptide-Small Molecule Synergy.
  19. NOD1 and NOD2 in inflammatory and infectious diseases.
  20. Upregulated TNF/Eiger signaling mediates stem cell recovery and tissue homeostasis during nutrient resupply in Drosophila testis.
  21. The c-Rel-c-Myc axis controls metabolism and proliferation of human T leukemia cells.
  22. SUMO: From Bench to Bedside.
  23. HaloTag-targeted Sirtuin rearranging ligand (SirReal) for the development of proteolysis targeting chimeras (PROTACs) against the lysine deacetylase Sirtuin 2 (Sirt2).
  24. Chain reactions: molecular mechanisms of RBR ubiquitin ligases.
  25. Off and On Again: De- and Reubiquitination during Membrane Protein Degradation.
  26. Receptor-interacting protein kinase 1 (RIPK1) as a therapeutic target.
  27. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes.
  28. Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort.
  29. Poly(ADP-ribose) polymerase-2 is essential for endometrial receptivity and blastocyst implantation, and regulated by caspase-8.
  1. Int J Mol Sci. 2020 Jul 15. pii: E5004. [Epub ahead of print]21(14):
    Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose.
    Ekaterina O Serebrovskaya, Nadezda M Podvalnaya, Varvara V Dudenkova, Anna S Efremova, Nadya G Gurskaya, Dmitry A Gorbachev, Artem V Luzhin, Omar L Kantidze, Elena V Zagaynova, Stanislav I Shram, Konstantin A Lukyanov.
      Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays an important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed a fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster resonance energy transfer (FRET). The WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module. The sensor consisted of cyan Turquoise2 and yellow Venus fluorescent proteins, each in fusion with the WWE domain of RNF146 E3 ubiquitin ligase protein. This bipartite sensor named sPARroW (sensor for PAR relying on WWE) enabled monitoring of PAR accumulation and depletion in live mammalian cells in response to different stimuli, namely hydrogen peroxide treatment, UV irradiation and hyperthermia.
    Keywords:  DNA damage respose; FRET; PAR; WWE-domai; fluorescent protein; sensor
    DOI:  https://doi.org/10.3390/ijms21145004
  2. Front Cell Dev Biol. 2020 ;8 365
    The Balance of TNF Mediated Pathways Regulates Inflammatory Cell Death Signaling in Healthy and Diseased Tissues.
    Joshua D Webster, Domagoj Vucic.
      Tumor necrosis factor alpha (TNF; TNFα) is a critical regulator of immune responses in healthy organisms and in disease. TNF is involved in the development and proper functioning of the immune system by mediating cell survival and cell death inducing signaling. TNF stimulated signaling pathways are tightly regulated by a series of phosphorylation and ubiquitination events, which enable timely association of TNF receptors-associated intracellular signaling complexes. Disruption of these signaling events can disturb the balance and the composition of signaling complexes, potentially resulting in severe inflammatory diseases.
    Keywords:  NEMO; RIP1 (RIPK1); RIP3 kinase; RIPK1 inhibitors; TNF; apoptosis; necroptois
    DOI:  https://doi.org/10.3389/fcell.2020.00365
  3. Annu Rev Cell Dev Biol. 2020 Jul 14.
    Cellular Mechanisms of NETosis.
    Hawa Racine Thiam, Siu Ling Wong, Denisa D Wagner, Clare M Waterman.
      Neutrophils are critical to innate immunity, including host defense against bacterial and fungal infections. They achieve their host defense role by phagocytosing pathogens, secreting their granules full of cytotoxic enzymes, or expelling neutrophil extracellular traps (NETs) during the process of NETosis. NETs are weblike DNA structures decorated with histones and antimicrobial proteins released by activated neutrophils. Initially described as a means for neutrophils to neutralize pathogens, NET release also occurs in sterile inflammation, promotes thrombosis, and can mediate tissue damage. To effectively manipulate this double-edged sword to fight a particular disease, researchers must work toward understanding the mechanisms driving NETosis. Such understanding would allow the generation of new drugs to promote or prevent NETosis as needed. While knowledge regarding the (patho)physiological roles of NETosis is accumulating, little is known about the cellular and biophysical bases of this process. In this review, we describe and discuss our current knowledge of the molecular, cellular, and biophysical mechanisms mediating NET release as well as open questions in the field. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 36 is October 6, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-cellbio-020520-111016
  4. J Leukoc Biol. 2020 Jul 17.
    Mendelian diseases of dysregulated canonical NF-κB signaling: From immunodeficiency to inflammation.
    Oskar Schnappauf, Ivona Aksentijevich.
      NF-κB is a master transcription factor that activates the expression of target genes in response to various stimulatory signals. Activated NF-κB mediates a plethora of diverse functions including innate and adaptive immune responses, inflammation, cell proliferation, and NF-κB is regulated through interactions with IκB inhibitory proteins, which are in turn regulated by the inhibitor of κB kinase (IKK) complex. Together, these 3 components form the core of the NF-κB signalosomes that have cell-specific functions which are dependent on the interactions with other signaling molecules and pathways. The activity of NF-κB pathway is also regulated by a variety of post-translational modifications including phosphorylation and ubiquitination by Lys63, Met1, and Lys48 ubiquitin chains. The physiologic role of NF-κB is best studied in the immune system due to discovery of many human diseases caused by pathogenic variants in various proteins that constitute the NF-κB pathway. These disease-causing variants can act either as gain-of-function (GoF) or loss-of-function (LoF) and depending on the function of mutated protein, can cause either immunodeficiency or systemic inflammation. Typically, pathogenic missense variants act as GoF and they lead to increased activity in the pathway. LoF variants can be inherited as recessive or dominant alleles and can cause either a decrease or an increase in pathway activity. Dominantly inherited LoF variants often result in haploinsufficiency of inhibitory proteins. Here, we review human Mendelian immunologic diseases, which results from mutations in different molecules in the canonical NF-κB pathway and surprisingly present with a continuum of clinical features including immunodeficiency, atopy, autoimmunity, and autoinflammation.
    Keywords:  NF-κB; atopy; autoimmunity; autoinflammation; immunodeficiency; ubiquitination
    DOI:  https://doi.org/10.1002/JLB.2MR0520-166R
  5. Proc Natl Acad Sci U S A. 2020 Jul 13. pii: 202001520. [Epub ahead of print]
    The pseudo-caspase FLIP(L) regulates cell fate following p53 activation.
    Andrea Lees, Alexander J McIntyre, Nyree T Crawford, Fiammetta Falcone, Christopher McCann, Caitriona Holohan, Gerard P Quinn, Jamie Z Roberts, Tamas Sessler, Peter F Gallagher, Gemma M A Gregg, Katherine McAllister, Kirsty M McLaughlin, Wendy L Allen, Laurence J Egan, Aideen E Ryan, Melissa J Labonte-Wilson, Philip D Dunne, Mark Wappett, Vicky M Coyle, Patrick G Johnston, Emma M Kerr, Daniel B Longley, Simon S McDade.
      p53 is the most frequently mutated, well-studied tumor-suppressor gene, yet the molecular basis of the switch from p53-induced cell-cycle arrest to apoptosis remains poorly understood. Using a combination of transcriptomics and functional genomics, we unexpectedly identified a nodal role for the caspase-8 paralog and only human pseudo-caspase, FLIP(L), in regulating this switch. Moreover, we identify FLIP(L) as a direct p53 transcriptional target gene that is rapidly up-regulated in response to Nutlin-3A, an MDM2 inhibitor that potently activates p53. Genetically or pharmacologically inhibiting expression of FLIP(L) using siRNA or entinostat (a clinically relevant class-I HDAC inhibitor) efficiently promoted apoptosis in colorectal cancer cells in response to Nutlin-3A, which otherwise predominantly induced cell-cycle arrest. Enhanced apoptosis was also observed when entinostat was combined with clinically relevant, p53-activating chemotherapy in vitro, and this translated into enhanced in vivo efficacy. Mechanistically, FLIP(L) inhibited p53-induced apoptosis by blocking activation of caspase-8 by the TRAIL-R2/DR5 death receptor; notably, this activation was not dependent on receptor engagement by its ligand, TRAIL. In the absence of caspase-8, another of its paralogs, caspase-10 (also transcriptionally up-regulated by p53), induced apoptosis in Nutlin-3A-treated, FLIP(L)-depleted cells, albeit to a lesser extent than in caspase-8-proficient cells. FLIP(L) depletion also modulated transcription of canonical p53 target genes, suppressing p53-induced expression of the cell-cycle regulator p21 and enhancing p53-induced up-regulation of proapoptotic PUMA. Thus, even in the absence of caspase-8/10, FLIP(L) silencing promoted p53-induced apoptosis by enhancing PUMA expression. Thus, we report unexpected, therapeutically relevant roles for FLIP(L) in determining cell fate following p53 activation.
    Keywords:  FLIP; TRAIL-R2; apoptosis; entinostat; p53
    DOI:  https://doi.org/10.1073/pnas.2001520117
  6. Front Immunol. 2020 ;11 1296
    Recent Advances and Contradictions in the Study of the Individual Roles of Ubiquitin Ligases That Regulate RIG-I-Like Receptor-Mediated Antiviral Innate Immune Responses.
    Hiroyuki Oshiumi.
      RIG-I and MDA5 are cytoplasmic viral RNA sensors and are essential for antiviral innate immune responses, such as type I interferon production. Post-translational modification is critical for the activation and inactivation of RIG-I and MDA5. At least seven ubiquitin ligases have been reported to be involved in either K63- or K48-linked polyubiquitination of RIG-I and MDA5, and these ubiquitin ligases are further regulated by other factors. TRIM25 is an E3 ubiquitin ligase that delivers a K63-linked polyubiquitin moiety to the caspase activation and recruitment domains (CARDs) of RIG-I, thereby activating the antiviral innate immune response. Recent studies have shown that NDR2, ZCCHC3, and Lnczc3h7a promote TRIM25-mediated RIG-I activation. Riplet is another ubiquitin ligase that mediates the K63-linked polyubiquitination of the C-terminal domain (CTD) of RIG-I; however, it was also reported that Riplet delivers the K63-linked polyubiquitin moiety to the CARDs of RIG-I as well as to the CTD, thereby activating RIG-I. Further, there are several factors that attenuate the activation of RIG-I and MDA5. RNF125, TRIM40, and c-Cbl mediate K48-linked polyubiquitination and induce degradation of RIG-I and/or MDA5. USP21 and CYLD remove the K63-linked polyubiquitin chain from RIG-I, and NLRP12 inhibits polyubiquitin-mediated RIG-I activation. Although these new regulators have been reported, their distinctive roles and functional differences remain elusive, and in some cases, studies on the topic are contradictory to each other. In the present review, recent studies related to post-translational modifications of RIG-I and MDA5 are summarized, and several controversies and unanswered questions in this field are discussed.
    Keywords:  MDA5; RIG-I; innate immunity; type I interferon; ubiquitin; virus
    DOI:  https://doi.org/10.3389/fimmu.2020.01296
  7. J Med Chem. 2020 Jul 15.
    Discovery of an Orally Active Small Molecule TNF-α Inhibitor.
    Weiguang Sun, Yanli Wu, Mengzhu Zheng, Yueying Yang, Yang Liu, Canrong Wu, Yirong Zhou, Yonghui Zhang, Lixia Chen, Hua Li.
      Tumor necrosis factor α (TNF-α) is an important therapeutic target for rheumatoid arthritis, inflammatory bowel disease and septic hepatitis. In this study, structure-based virtual ligand screening combined with in vitro and in vivo assays was applied. A lead compound, benpyrine, could directly bind to TNF-α and block TNF-α-trigged signaling activation. Furthermore, endotoxemia murine model showed that benpyrine could attenuate TNF-α-induced inflammation, thereby reducing liver and lung injury. Meanwhile, administration of benpyrine by gavage significantly relieved the symptoms of collagen-induced arthritis and imiquimod-induced psoriasiform inflammation in mice. Thus, our study discovered a novel, highly specific and orally active small molecule TNF-α inhibitor that is potentially useful for treating TNF-α mediated inflammatory and autoimmune disease.
    DOI:  https://doi.org/10.1021/acs.jmedchem.0c00377
  8. Eur J Med Chem. 2020 Jun 25. pii: S0223-5234(20)30306-8. [Epub ahead of print]201 112337
    Discovery of simplified benzazole fragments derived from the marine benzosceptrin B as necroptosis inhibitors involving the receptor interacting protein Kinase-1.
    Mohamed Benchekroun, Ludmila Ermolenko, Minh Quan Tran, Agathe Vagneux, Hristo Nedev, Claire Delehouzé, Mohamed Souab, Blandine Baratte, Béatrice Josselin, Bogdan I Iorga, Sandrine Ruchaud, Stéphane Bach, Ali Al-Mourabit.
      With the aim to develop new chemical tools based on simplified natural metabolites to help deciphering the molecular mechanism of necroptosis, simplified benzazole fragments including 2-aminobenzimidazole and the 2-aminobenzothiazole analogs were prepared during the synthesis of the marine benzosceptrin B. Conpounds inhibiting the RIPK1 protein kinase were discovered. A library of 54 synthetic analogs were prepared and evaluated through a phenotypic screen using the inhibition of the necrotic cell death induced by TNF-α in human Jurkat T cells deficient for the FADD protein. This article reports the design, synthesis and biological evaluation of a series of 2-aminobenzazoles on the necroptotic cell death through the inhibition of RIPK1 protein kinase. The 2-aminobenzimidazole and 2-aminobenzothiazole platforms presented herein can serve as novel chemical tools to study the molecular regulation of necroptosis and further develop lead drug candidates for chronic pathologies involving necroptosis.
    Keywords:  Aminobenzimidazole; Kinase inhibitors; Necroptosis; Synthesis
    DOI:  https://doi.org/10.1016/j.ejmech.2020.112337
  9. Immunity. 2020 Jul 14. pii: S1074-7613(20)30274-0. [Epub ahead of print]53(1): 6-8
    Snapshot of a Deadly Embrace: The Caspase-1-GSDMD Interface.
    Lieselotte Vande Walle, Mohamed Lamkanfi.
      Proteolytic maturation of the pore-forming protein gasdermin D (GSDMD) by inflammasome-activated caspase-1 is crucial for initiating pyroptosis, a lytic form of cell death. In this issue of Immunity, Lui et al. report the X-ray structure of the caspase-1-GSDMD complex, mapping the interaction interfaces that determine recognition and cleavage of GSDMD by inflammatory caspases.
    DOI:  https://doi.org/10.1016/j.immuni.2020.06.019
  10. Cell Chem Biol. 2020 Jul 16. pii: S2451-9456(20)30232-4. [Epub ahead of print]27(7): 877-887.e14
    In Vitro and Cellular Probes to Study PARP Enzyme Target Engagement.
    Tim J Wigle, Danielle J Blackwell, Laurie B Schenkel, Yue Ren, W David Church, Hetvi J Desai, Kerren K Swinger, Andrew G Santospago, Christina R Majer, Alvin Z Lu, Mario Niepel, Nicholas R Perl, Melissa M Vasbinder, Heike Keilhack, Kevin W Kuntz.
      Poly(ADP-ribose) polymerase (PARP) enzymes use nicotinamide adenine dinucleotide (NAD+) to modify up to seven different amino acids with a single mono(ADP-ribose) unit (MARylation deposited by PARP monoenzymes) or branched poly(ADP-ribose) polymers (PARylation deposited by PARP polyenzymes). To enable the development of tool compounds for PARP monoenzymes and polyenzymes, we have developed active site probes for use in in vitro and cellular biophysical assays to characterize active site-directed inhibitors that compete for NAD+ binding. These assays are agnostic of the protein substrate for each PARP, overcoming a general lack of knowledge around the substrates for these enzymes. The in vitro assays use less enzyme than previously described activity assays, enabling discrimination of inhibitor potencies in the single-digit nanomolar range, and the cell-based assays can differentiate compounds with sub-nanomolar potencies and measure inhibitor residence time in live cells.
    Keywords:  NanoBRET; PARP7; TIPARP; bioluminescence resonance energy transfer (BRET); cellular biophysics; mono(ADP-ribosylation) (MARylation); nicotinamide adenine dinucleotide (NAD(+)); poly(ADP-ribose) polymerase (PARP); probe displacement; time-resolved fluorescence energy transfer (TR-FRET)
    DOI:  https://doi.org/10.1016/j.chembiol.2020.06.009
  11. Immunity. 2020 Jul 14. pii: S1074-7613(20)30269-7. [Epub ahead of print]53(1): 54-77
    Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids.
    Eva Bartok, Gunther Hartmann.
      All lifeforms have developed highly sophisticated systems equipped to detect altered self and non-self nucleic acids (NA). In vertebrates, NA-sensing receptors safeguard the integrity of the organism by detecting pathogens, dyshomeostasis and damage, and inducing appropriate responses to eliminate pathogens and reconstitute homeostasis. Effector mechanisms include i) immune signaling, ii) restriction of NA functions such as inhibition of mRNA translation, and iii) cell death pathways. An appropriate effector response is necessary for host defense, but dysregulated NA-sensing can lead to devastating autoimmune and autoinflammatory disease. Their inherent biochemical similarity renders the reliable distinction between self NA under homeostatic conditions and altered or exogenous NA particularly challenging. In this review, we provide an overview of recent progress in our understanding of the closely coordinated and regulated network of innate immune receptors, restriction factors, and nucleases to effectively respond to pathogens and maintain host integrity.
    DOI:  https://doi.org/10.1016/j.immuni.2020.06.014
  12. Stem Cell Res Ther. 2020 Jul 16. 11(1): 281
    TNFα/TNFR2 signaling pathway: an active immune checkpoint for mesenchymal stem cell immunoregulatory function.
    Ghada Beldi, Maryam Khosravi, Mohamed Essameldin Abdelgawad, Benoît L Salomon, Georges Uzan, Houda Haouas, Sina Naserian.
      BACKGROUND: In addition to their multilineage potential, mesenchymal stem cells (MSCs) have a broad range of functions from tissue regeneration to immunomodulation. MSCs have the ability to modulate the immune response and change the progression of different inflammatory and autoimmune disorders. However, there are still many challenges to overcome before their widespread clinical administration including the mechanisms behind their immunoregulatory function. MSCs inhibit effector T cells and other immune cells, while inducing regulatory T cells (T regs), thus, reducing directly and indirectly the production of pro-inflammatory cytokines. TNF/TNFR signaling plays a dual role: while the interaction of TNFα with TNFR1 mediates pro-inflammatory effects and cell death, its interaction with TNFR2 mediates anti-inflammatory effects and cell survival. Many immunosuppressive cells like T regs, regulatory B cells (B regs), endothelial progenitor cells (EPCs), and myeloid-derived suppressor cells (MDSCs) express TNFR2, and this is directly related to their immunosuppression efficiency. In this article, we investigated the role of the TNFα/TNFR2 immune checkpoint signaling pathway in the immunomodulatory capacities of MSCs.METHODS: Co-cultures of MSCs from wild-type (WT) and TNFR2 knocked-out (TNFR2 KO) mice with T cells (WT and TNFα KO) were performed under various experimental conditions.
    RESULTS: We demonstrate that TNFR2 is a key regulatory molecule which is strongly involved in the immunomodulatory properties of MSCs. This includes their ability to suppress T cell proliferation, activation, and pro-inflammatory cytokine production, in addition to their capacity to induce active T regs.
    CONCLUSIONS: Our results reveal for the first time the importance of the TNFα/TNFR2 axis as an active immune checkpoint regulating MSC immunological functions.
    Keywords:  Immune checkpoint; Immune regulation; Mesenchymal stem cells; Regulatory T cells; TNFα/TNFR2 signaling pathway; Tolerance induction
    DOI:  https://doi.org/10.1186/s13287-020-01740-5
  13. Immunity. 2020 Jul 14. pii: S1074-7613(20)30270-3. [Epub ahead of print]53(1): 16-18
    Keratinocyte-Polyamines and Dendritic Cells: A Bad Duet for Psoriasis.
    Mohna Bandyopadhyay, Adriana T Larregina.
      The role of keratinocyte metabolism in psoriasis is not fully elucidated. In this issue of Immunity, Lou et al. describe that interleukin-17 (IL-17) re-programs the urea cycle in keratinocytes increasing polyamines that stabilize RNA-Ag-complexes that upon cellular turnover activate dendritic cells, which amplify psoriasis inflammation.
    DOI:  https://doi.org/10.1016/j.immuni.2020.06.015
  14. J Exp Med. 2020 Oct 05. pii: e20200288. [Epub ahead of print]217(10):
    Transmembrane TNF drives osteoproliferative joint inflammation reminiscent of human spondyloarthritis.
    Merlijn H Kaaij, Melissa N van Tok, Iris C Blijdorp, Carmen A Ambarus, Michael Stock, Désiree Pots, Véronique L Knaup, Marietta Armaka, Eleni Christodoulou-Vafeiadou, Tessa K van Melsen, Huriatul Masdar, Harry J P P Eskes, Nataliya G Yeremenko, George Kollias, Georg Schett, Sander W Tas, Leonie M van Duivenvoorde, Dominique L P Baeten.
      TNF plays a key role in immune-mediated inflammatory diseases including rheumatoid arthritis (RA) and spondyloarthritis (SpA). It remains incompletely understood how TNF can lead to different disease phenotypes such as destructive peripheral polysynovitis in RA versus axial and peripheral osteoproliferative inflammation in SpA. We observed a marked increase of transmembrane (tm) versus soluble (s) TNF in SpA versus RA together with a decrease in the enzymatic activity of ADAM17. In contrast with the destructive polysynovitis observed in classical TNF overexpression models, mice overexpressing tmTNF developed axial and peripheral joint disease with synovitis, enthesitis, and osteitis. Histological and radiological assessment evidenced marked endochondral new bone formation leading to joint ankylosis over time. SpA-like inflammation, but not osteoproliferation, was dependent on TNF-receptor I and mediated by stromal tmTNF overexpression. Collectively, these data indicate that TNF can drive distinct inflammatory pathologies. We propose that tmTNF is responsible for the key pathological features of SpA.
    DOI:  https://doi.org/10.1084/jem.20200288
  15. Nat Immunol. 2020 Jul 13.
    Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation.
    Andrew S Mendiola, Jae Kyu Ryu, Sophia Bardehle, Anke Meyer-Franke, Kenny Kean-Hooi Ang, Chris Wilson, Kim M Baeten, Kristina Hanspers, Mario Merlini, Sean Thomas, Mark A Petersen, Alexander Williams, Reuben Thomas, Victoria A Rafalski, Rosa Meza-Acevedo, Reshmi Tognatta, Zhaoqi Yan, Samuel J Pfaff, Michael R Machado, Catherine Bedard, Pamela E Rios Coronado, Xiqian Jiang, Jin Wang, Michael A Pleiss, Ari J Green, Scott S Zamvil, Alexander R Pico, Benoit G Bruneau, Michelle R Arkin, Katerina Akassoglou.
      An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    DOI:  https://doi.org/10.1038/s41590-020-0754-x
  16. PLoS Pathog. 2020 Jul 13. 16(7): e1008651
    HMGB1 amplifies ILC2-induced type-2 inflammation and airway smooth muscle remodelling.
    Zhixuan Loh, Jennifer Simpson, Ashik Ullah, Vivian Zhang, Wan J Gan, Jason P Lynch, Rhiannon B Werder, Al Amin Sikder, Katie Lane, Choon Boon Sim, Enzo Porrello, Stuart B Mazzone, Peter D Sly, Raymond J Steptoe, Kirsten M Spann, Maria B Sukkar, John W Upham, Simon Phipps.
      Type-2 immunity elicits tissue repair and homeostasis, however dysregulated type-2 responses cause aberrant tissue remodelling, as observed in asthma. Severe respiratory viral infections in infancy predispose to later asthma, however, the processes that mediate tissue damage-induced type-2 inflammation and the origins of airway remodelling remain ill-defined. Here, using a preclinical mouse model of viral bronchiolitis, we find that increased epithelial and mesenchymal high-mobility group box 1 (HMGB1) expression is associated with increased numbers of IL-13-producing type-2 innate lymphoid cell (ILC2s) and the expansion of the airway smooth muscle (ASM) layer. Anti-HMGB1 ablated lung ILC2 numbers and ASM growth in vivo, and inhibited ILC2-mediated ASM cell proliferation in a co-culture model. Furthermore, we identified that HMGB1/RAGE (receptor for advanced glycation endproducts) signalling mediates an ILC2-intrinsic IL-13 auto-amplification loop. In summary, therapeutic targeting of the HMGB1/RAGE signalling axis may act as a novel asthma preventative by dampening ILC2-mediated type-2 inflammation and associated ASM remodelling.
    DOI:  https://doi.org/10.1371/journal.ppat.1008651
  17. Nat Immunol. 2020 Jul 13.
    The commensal skin microbiota triggers type I IFN-dependent innate repair responses in injured skin.
    Jeremy Di Domizio, Cyrine Belkhodja, Pauline Chenuet, Anissa Fries, Timothy Murray, Paula Marcos Mondéjar, Olivier Demaria, Curdin Conrad, Bernhard Homey, Sabine Werner, Daniel E Speiser, Bernhard Ryffel, Michel Gilliet.
      Skin wounds heal by coordinated induction of inflammation and tissue repair, but the initiating events are poorly defined. Here we uncover a fundamental role of commensal skin microbiota in this process and show that it is mediated by the recruitment and the activation of type I interferon (IFN)-producing plasmacytoid DC (pDC). Commensal bacteria colonizing skin wounds trigger activation of neutrophils to express the chemokine CXCL10, which recruits pDC and acts as an antimicrobial protein to kill exposed microbiota, leading to the formation of CXCL10-bacterial DNA complexes. These complexes and not complexes with host-derived DNA activate pDC to produce type I IFNs, which accelerate wound closure by triggering skin inflammation and early T cell-independent wound repair responses, mediated by macrophages and fibroblasts that produce major growth factors required for healing. These findings identify a key function of commensal microbiota in driving a central innate wound healing response of the skin.
    DOI:  https://doi.org/10.1038/s41590-020-0721-6
  18. ACS Chem Biol. 2020 Jul 14.
    Tumor Necrosis Factor-α Trimer Disassembly and Inactivation via Peptide-Small Molecule Synergy.
    James W Checco, Geoffrey A Eddinger, Nicholas J Rettko, Alexander R Chartier, Samuel H Gellman.
      Aberrant signaling by tumor necrosis factor-α (TNFα) is associated with inflammatory diseases that can be treated with engineered proteins that inhibit binding of this cytokine to cell-surface receptors. Despite these clinical successes, there is considerable interest in the development of smaller antagonists of TNFα-receptor interactions. We describe a new 29-residue α/β-peptide, a molecule that contains three β-amino acid residues and three α-aminoisobutryic acid (Aib) residues, that displays potent inhibition of TNFα binding to TNFα receptor 1 (TNFR1) and rescues cells from TNFα-induced death. The complement of nonproteinogenic residues renders this α/β-peptide highly resistant to proteolysis, relative to all-α analogues. The mechanism of inhibitory action of the new 29-mer involves disruption of the trimeric TNFα quaternary structure, which prevents productive binding to TNFα receptors. Unexpectedly, we discovered that peptide-induced trimer disruption can be promoted by structurally diverse small molecules, including a detergent commonly used during selection procedures. The discovery of this synergistic effect provides a new context for understanding previous reports on peptidic antagonists of TNFα-receptor interactions and suggests new avenues for future efforts to block signaling via proteins with an active form that is oligomeric, including other members of the TNFα family.
    DOI:  https://doi.org/10.1021/acschembio.0c00313
  19. Immunol Rev. 2020 Jul 17.
    NOD1 and NOD2 in inflammatory and infectious diseases.
    Bruno C Trindade, Grace Y Chen.
      It has been long recognized that NOD1 and NOD2 are critical players in the host immune response, primarily by their sensing bacterial peptidoglycan-conserved motifs. Significant advances have been made from efforts that characterize their upstream activators, assembly of signaling complexes, and activation of downstream signaling pathways. Disruption in NOD1 and NOD2 signaling has also been associated with impaired host defense and resistance to the development of inflammatory diseases. In this review, we will describe how NOD1 and NOD2 sense microbes and cellular stress to regulate host responses that can affect disease pathogenesis and outcomes.
    Keywords:  NOD1; NOD2; Nod-like receptor; immunity; inflammation; innate
    DOI:  https://doi.org/10.1111/imr.12902
  20. Sci Rep. 2020 Jul 15. 10(1): 11674
    Upregulated TNF/Eiger signaling mediates stem cell recovery and tissue homeostasis during nutrient resupply in Drosophila testis.
    Yi Chieh Chang, Hsin Tu, To-Wei Huang, Bo-Wen Xu, Haiwei Pi.
      Stem cell activity and cell differentiation is robustly influenced by the nutrient availability in the gonads. The signal that connects nutrient availability to gonadal stem cell activity remains largely unknown. In this study, we show that tumor necrosis factor Eiger (Egr) is upregulated in testicular smooth muscles as a response to prolonged protein starvation in Drosophila testis. While Egr is not essential for starvation-induced changes in germline and somatic stem cell numbers, Egr and its receptor Grindelwald influence the recovery dynamics of somatic cyst stem cells (CySCs) upon protein refeeding. Moreover, Egr is also involved in the refeeding-induced, ectopic expression of the CySC self-renewal protein and the accumulation of early germ cells. Egr primarily acts through the Jun N-terminal kinase (JNK) signaling in Drosophila. We show that inhibition of JNK signaling in cyst cells suppresses the refeeding-induced abnormality in both somatic and germ cells. In conclusion, our study reveals both beneficial and detrimental effects of Egr upregulation in the recovery of stem cells and spermatogenesis from prolonged protein starvation.
    DOI:  https://doi.org/10.1038/s41598-020-68313-7
  21. Mol Immunol. 2020 Jul 10. pii: S0161-5890(20)30413-2. [Epub ahead of print]125 115-122
    The c-Rel-c-Myc axis controls metabolism and proliferation of human T leukemia cells.
    Xinyuan Li, George Luo, Ting Li, Honghong Sun, Wei Wang, Emily Eiler, Jason R Goldsmith, Youhai H Chen.
      Genome-wide association studies have established that human REL is a susceptibility gene for lymphoid cancers and inflammatory diseases. REL is the hematopoietic member of the nuclear factor-κB (NF-κB) family and is frequently amplified in human lymphomas. However, the mechanism through which REL and its encoded protein c-Rel affect human lymphoma is largely unknown. Using both loss-of-function and gain-of-function approaches, we studied the roles of REL gene in human Jurkat leukemia cells. Compared with control Jurkat cells, REL knockout cells exhibited significant defects in cell growth and mitochondrial respiration. Genome-wide transcriptome analyses revealed that T cells lacking c-Rel had selective defects in the expression of inflammatory and metabolic genes including c-Myc. We found that c-Rel controlled the expression of c-Myc through its promotor, and expressing c-Myc in c-Rel-deficient lymphoma cells rescued their proliferative and metabolic defects. Thus, the human c-Rel-c-Myc axis controls lymphoma growth and metabolism and could be a therapeutic target for lymphomas.
    Keywords:  CRISPR-Cas9; Immunometabolism; Lymphoma; Mitochondria; NF-κB
    DOI:  https://doi.org/10.1016/j.molimm.2020.06.029
  22. Physiol Rev. 2020 Oct 01. 100(4): 1599-1619
    SUMO: From Bench to Bedside.
    Hui-Ming Chang, Edward T H Yeh.
      Sentrin/small ubiquitin-like modifier (SUMO) is protein modification pathway that regulates multiple biological processes, including cell division, DNA replication/repair, signal transduction, and cellular metabolism. In this review, we will focus on recent advances in the mechanisms of disease pathogenesis, such as cancer, diabetes, seizure, and heart failure, which have been linked to the SUMO pathway. SUMO is conjugated to lysine residues in target proteins through an isopeptide linkage catalyzed by SUMO-specific activating (E1), conjugating (E2), and ligating (E3) enzymes. In steady state, the quantity of SUMO-modified substrates is usually a small fraction of unmodified substrates due to the deconjugation activity of the family Sentrin/SUMO-specific proteases (SENPs). In contrast to the complexity of the ubiquitination/deubiquitination machinery, the biochemistry of SUMOylation and de-SUMOylation is relatively modest. Specificity of the SUMO pathway is achieved through redox regulation, acetylation, phosphorylation, or other posttranslational protein modification of the SUMOylation and de-SUMOylation enzymes. There are three major SUMOs. SUMO-1 usually modifies a substrate as a monomer; however, SUMO-2/3 can form poly-SUMO chains. The monomeric SUMO-1 or poly-SUMO chains can interact with other proteins through SUMO-interactive motif (SIM). Thus SUMO modification provides a platform to enhance protein-protein interaction. The consequence of SUMOylation includes changes in cellular localization, protein activity, or protein stability. Furthermore, SUMO may join force with ubiquitin to degrade proteins through SUMO-targeted ubiquitin ligases (STUbL). After 20 yr of research, SUMO has been shown to play critical roles in most, if not all, biological pathways. Thus the SUMO enzymes could be targets for drug development to treat human diseases.
    Keywords:  SUMO; Sentrin; biochemistry; cancer; heart; physiology
    DOI:  https://doi.org/10.1152/physrev.00025.2019
  23. Chembiochem. 2020 Jul 16.
    HaloTag-targeted Sirtuin rearranging ligand (SirReal) for the development of proteolysis targeting chimeras (PROTACs) against the lysine deacetylase Sirtuin 2 (Sirt2).
    Matthias Schiedel, Attila Lehotzky, Sandor Szunyogh, Judit Oláh, Sören Hammelmann, Nathalie Wössner, Dina Robaa, Oliver Einsle, Wolfgang Sippl, Judit Ovádi, Manfred Jung.
      We have discovered the sirtuin rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis targeting chimera (PROTAC), enabled small molecule-induced degradation of Sirt2. Here, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that also other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can be harnessed for small molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be utilized as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular.
    Keywords:  Epigenetics; Halotag; PROTACs; Sirtuins; tubulin
    DOI:  https://doi.org/10.1002/cbic.202000351
  24. Biochem Soc Trans. 2020 Jul 17. pii: BST20200237. [Epub ahead of print]
    Chain reactions: molecular mechanisms of RBR ubiquitin ligases.
    Thomas R Cotton, Bernhard C Lechtenberg.
      Ubiquitination is a fundamental post-translational modification that regulates almost all aspects of cellular signalling and is ultimately catalysed by the action of E3 ubiquitin ligases. The RING-between-RING (RBR) family of E3 ligases encompasses 14 distinct human enzymes that are defined by a unique domain organisation and catalytic mechanism. Detailed characterisation of several RBR ligase family members in the last decade has revealed common structural and mechanistic features. At the same time these studies have highlighted critical differences with respect to autoinhibition, activation and catalysis. Importantly, the majority of RBR E3 ligases remain poorly studied, and thus the extent of diversity within the family remains unknown. In this mini-review we outline the current understanding of the RBR E3 mechanism, structure and regulation with a particular focus on recent findings and developments that will shape the field in coming years.
    Keywords:  RBR ubiquitin ligases; enzyme activity; post-translational modification; ubiquitin ligases; ubiquitin signalling
    DOI:  https://doi.org/10.1042/BST20200237
  25. Mol Cell. 2020 Jul 16. pii: S1097-2765(20)30465-2. [Epub ahead of print]79(2): 203-204
    Off and On Again: De- and Reubiquitination during Membrane Protein Degradation.
    Claudia C Schmidt, Alexander Stein.
      In this issue of Molecular Cell, Hu et al. (2020) show that the cytosolic E3 ligase RNF126 reubiquitinates membrane proteins after their extraction from the membrane of the endoplasmic reticulum to target them for proteasomal degradation.
    DOI:  https://doi.org/10.1016/j.molcel.2020.06.036
  26. Nat Rev Drug Discov. 2020 Jul 15.
    Receptor-interacting protein kinase 1 (RIPK1) as a therapeutic target.
    Lauren Mifflin, Dimitry Ofengeim, Junying Yuan.
      Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is a key mediator of cell death and inflammation. The unique hydrophobic pocket in the allosteric regulatory domain of RIPK1 has enabled the development of highly selective small-molecule inhibitors of its kinase activity, which have demonstrated safety in preclinical models and clinical trials. Potential applications of these RIPK1 inhibitors for the treatment of monogenic and polygenic autoimmune, inflammatory, neurodegenerative, ischaemic and acute conditions, such as sepsis, are emerging. This article reviews RIPK1 biology and disease-associated mutations in RIPK1 signalling pathways, highlighting clinical trials of RIPK1 inhibitors and potential strategies to mitigate development challenges.
    DOI:  https://doi.org/10.1038/s41573-020-0071-y
  27. Nat Commun. 2020 Jul 16. 11(1): 3563
    Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes.
    Martin Mehnert, Rodolfo Ciuffa, Fabian Frommelt, Federico Uliana, Audrey van Drogen, Kilian Ruminski, Matthias Gstaiger, Ruedi Aebersold.
      Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.
    DOI:  https://doi.org/10.1038/s41467-020-17387-y
  28. Nature. 2020 Jul 17.
    Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort.
    James E D Thaventhiran, Hana Lango Allen, Oliver S Burren, William Rae, Daniel Greene, Emily Staples, Zinan Zhang, James H R Farmery, Ilenia Simeoni, Elizabeth Rivers, Jesmeen Maimaris, Christopher J Penkett, Jonathan Stephens, Sri V V Deevi, Alba Sanchis-Juan, Nicholas S Gleadall, Moira J Thomas, Ravishankar B Sargur, Pavels Gordins, Helen E Baxendale, Matthew Brown, Paul Tuijnenburg, Austen Worth, Steven Hanson, Rachel J Linger, Matthew S Buckland, Paula J Rayner-Matthews, Kimberly C Gilmour, Crina Samarghitean, Suranjith L Seneviratne, David M Sansom, Andy G Lynch, Karyn Megy, Eva Ellinghaus, David Ellinghaus, Silje F Jorgensen, Tom H Karlsen, Kathleen E Stirrups, Antony J Cutler, Dinakantha S Kumararatne, Anita Chandra, J David M Edgar, Archana Herwadkar, Nichola Cooper, Sofia Grigoriadou, Aarnoud P Huissoon, Sarah Goddard, Stephen Jolles, Catharina Schuetz, Felix Boschann, , Paul A Lyons, Matthew E Hurles, Sinisa Savic, Siobhan O Burns, Taco W Kuijpers, Ernest Turro, Willem H Ouwehand, Adrian J Thrasher, Kenneth G C Smith.
      An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    DOI:  https://doi.org/10.1038/s41586-020-2556-6
  29. Mol Cell Endocrinol. 2020 Jul 14. pii: S0303-7207(20)30246-X. [Epub ahead of print] 110946
    Poly(ADP-ribose) polymerase-2 is essential for endometrial receptivity and blastocyst implantation, and regulated by caspase-8.
    Upendra Kumar Soni, Sangappa Basanna Chadchan, Anubha Joshi, Vijay Kumar, Vineet Kumar Maurya, Raj Kumar Verma, Rajesh Kumar Jha.
      Embryo implantation is a very complex process and several factors play important roles. Using a mouse model, we investigated the functions of PARP-2 and caspase-8 during endometrial receptivity for blastocyst implantation. We found that PARP-2 was upregulated at the receptive stage's implantation region and predominantly expressed in the endometrial stromal region, but downregulated during pregnancy failure and pseudopregnancy. To reinforce the necessity of PARP-2 for embryo implantation, we pharmacologically inhibited PARP-2 'before' & 'after' embryo arrival and observed a reduction in blastocyst implantation. Conversely, elevated caspase-8 expression and activity during pseudopregnancy, delayed implantation, and embryo implantation failure conditions and decreased levels in the decidualization exhibited an inverse pattern with PARP-2, suggesting caspase-8 as a negative regulator for embryo implantation. In vitro caspase-8 downregulates the PARP-2 activity in the mouse endometrial epithelial and stromal cells. These data suggest that PARP-2 and its negative regulation by caspase-8 constitute a crucial step in embryo implantation.
    Keywords:  Caspase-8; Decidualization; Delayed implantation; Embryo implantation; Endometrial receptivity; Implantation failure; Poly(ADP-Ribose) polymerase-2 (PARP-2)
    DOI:  https://doi.org/10.1016/j.mce.2020.110946
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