bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020‒08‒02
27 papers selected by
John Silke
Walter and Eliza Hall Institute of Medical Research
  1. Flexible Usage and Interconnectivity of Diverse Cell Death Pathways Protect against Intracellular Infection.
  2. Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms.
  3. Ubiquitination in the ERAD Process.
  4. Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy.
  5. RIPK protein kinase family: Atypical lives of typical kinases.
  6. STAT3 serine phosphorylation is required for TLR4 metabolic reprogramming and IL-1β expression.
  7. Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies.
  8. Pyroptotic and non-pyroptotic effector functions of caspase-11.
  9. JNK signaling contributes to skeletal muscle wasting and protein turnover in pancreatic cancer cachexia.
  10. An Apoptotic Caspase Network Safeguards Cell Death Induction in Pyroptotic Macrophages.
  11. The ups and downs of Poly(ADP-ribose) Polymerase-1 inhibitors in cancer therapy-Current progress and future direction.
  12. Lysosome-targeting chimaeras for degradation of extracellular proteins.
  13. Therapies targeting FLS and TNF can have synergistic effects.
  14. The ubiquitin-like modifier FAT10 - much more than a proteasome-targeting signal.
  15. SMAC mimetics induce autophagy-dependent apoptosis of HIV-1-infected macrophages.
  16. Fish TNF and TNF receptors.
  17. A bacteria-chemokine double act repairs the skin.
  18. An evolutionary approach to systematic discovery of novel deubiquitinases, applied to Legionella.
  19. Rational design to control the trade-off between receptor affinity and cooperativity.
  20. The Role of RNA Editing in the Immune Response.
  21. The regulation of the ZBP1-NLRP3 inflammasome and its implications in pyroptosis, apoptosis, and necroptosis (PANoptosis).
  22. A large-scale binding and functional map of human RNA-binding proteins.
  23. Deltex-1 is indispensible for the IL-6 and TGF-β treatment-triggered differentiation of Th17 cells.
  24. The function of the thymus and its impact on modern medicine.
  25. Multiple Roles for Chemokines in Neutrophil Biology.
  26. A programmable sequence of reporters for lineage analysis.
  27. RIP3-mediated necroptosis is regulated by inter-filament assembly of RIP homotypic interaction motif.
  1. Immunity. 2020 Jul 19. pii: S1074-7613(20)30284-3. [Epub ahead of print]
    Flexible Usage and Interconnectivity of Diverse Cell Death Pathways Protect against Intracellular Infection.
    Marcel Doerflinger, Yexuan Deng, Paul Whitney, Ranja Salvamoser, Sven Engel, Andrew J Kueh, Lin Tai, Annabell Bachem, Elise Gressier, Niall D Geoghegan, Stephen Wilcox, Kelly L Rogers, Alexandra L Garnham, Michael A Dengler, Stefanie M Bader, Gregor Ebert, Jaclyn S Pearson, Dominic De Nardo, Nancy Wang, Chenying Yang, Milton Pereira, Clare E Bryant, Richard A Strugnell, James E Vince, Marc Pellegrini, Andreas Strasser, Sammy Bedoui, Marco J Herold.
      Programmed cell death contributes to host defense against pathogens. To investigate the relative importance of pyroptosis, necroptosis, and apoptosis during Salmonella infection, we infected mice and macrophages deficient for diverse combinations of caspases-1, -11, -12, and -8 and receptor interacting serine/threonine kinase 3 (RIPK3). Loss of pyroptosis, caspase-8-driven apoptosis, or necroptosis had minor impact on Salmonella control. However, combined deficiency of these cell death pathways caused loss of bacterial control in mice and their macrophages, demonstrating that host defense can employ varying components of several cell death pathways to limit intracellular infections. This flexible use of distinct cell death pathways involved extensive cross-talk between initiators and effectors of pyroptosis and apoptosis, where initiator caspases-1 and -8 also functioned as executioners when all known effectors of cell death were absent. These findings uncover a highly coordinated and flexible cell death system with in-built fail-safe processes that protect the host from intracellular infections.
    Keywords:  Salmonella; apoptosis; caspase-1; caspase-11; caspase-8; cell death; effector caspases; gasdermin D; necroptosis; pyroptosis
    DOI:  https://doi.org/10.1016/j.immuni.2020.07.004
  2. Cell Chem Biol. 2020 Jul 27. pii: S2451-9456(20)30283-X. [Epub ahead of print]
    Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms.
    Timurs Maculins, Javier Garcia-Pardo, Anamarija Skenderovic, Jakob Gebel, Mateusz Putyrski, Andrew Vorobyov, Philipp Busse, Gabor Varga, Maria Kuzikov, Andrea Zaliani, Simin Rahighi, Veronique Schaeffer, Michael J Parnham, Sachdev S Sidhu, Andreas Ernst, Volker Dötsch, Masato Akutsu, Ivan Dikic.
      Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.
    Keywords:  LUBAC; NF-κB; cellular screening; high throughput; hit identification; inhibitor; protein engineering; protein-protein interaction; small molecule; ubiquitin
    DOI:  https://doi.org/10.1016/j.chembiol.2020.07.010
  3. Int J Mol Sci. 2020 Jul 28. pii: E5369. [Epub ahead of print]21(15):
    Ubiquitination in the ERAD Process.
    Anna Lopata, Andreas Kniss, Frank Löhr, Vladimir V Rogov, Volker Dötsch.
      In this review, we focus on the ubiquitination process within the endoplasmic reticulum associated protein degradation (ERAD) pathway. Approximately one third of all synthesized proteins in a cell are channeled into the endoplasmic reticulum (ER) lumen or are incorporated into the ER membrane. Since all newly synthesized proteins enter the ER in an unfolded manner, folding must occur within the ER lumen or co-translationally, rendering misfolding events a serious threat. To prevent the accumulation of misfolded protein in the ER, proteins that fail the quality control undergo retrotranslocation into the cytosol where they proceed with ubiquitination and degradation. The wide variety of misfolded targets requires on the one hand a promiscuity of the ubiquitination process and on the other hand a fast and highly processive mechanism. We present the various ERAD components involved in the ubiquitination process including the different E2 conjugating enzymes, E3 ligases, and E4 factors. The resulting K48-linked and K11-linked ubiquitin chains do not only represent a signal for degradation by the proteasome but are also recognized by the AAA+ ATPase Cdc48 and get in the process of retrotranslocation modified by enzymes bound to Cdc48. Lastly we discuss the conformations adopted in particular by K48-linked ubiquitin chains and their importance for degradation.
    Keywords:  CUE domain; ERAD; ubiquitin chain conformation; ubiquitination
    DOI:  https://doi.org/10.3390/ijms21155369
  4. ACS Cent Sci. 2020 Jul 22. 6(7): 1223-1230
    Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy.
    Rebecca Beveridge, Dirk Kessler, Klaus Rumpel, Peter Ettmayer, Anton Meinhart, Tim Clausen.
      Protein degraders, also known as proteolysis targeting chimeras (PROTACs), are bifunctional small molecules that promote cellular degradation of a protein of interest (POI). PROTACs act as molecular mediators, bringing an E3 ligase and a POI into proximity, thus promoting ubiquitination and degradation of the targeted POI. Despite their great promise as next-generation pharmaceutical drugs, the development of new PROTACs is challenged by the complexity of the system, which involves binary and ternary interactions between components. Here, we demonstrate the strength of native mass spectrometry (nMS), a label-free technique, to provide novel insight into PROTAC-mediated protein interactions. We show that nMS can monitor the formation of ternary E3-PROTAC-POI complexes and detect various intermediate species in a single experiment. A unique benefit of the method is its ability to reveal preferentially formed E3-PROTAC-POI combinations in competition experiments with multiple substrate proteins, thereby positioning it as an ideal high-throughput screening strategy during the development of new PROTACs.
    DOI:  https://doi.org/10.1021/acscentsci.0c00049
  5. Semin Cell Dev Biol. 2020 Jul 27. pii: S1084-9521(19)30244-7. [Epub ahead of print]
    RIPK protein kinase family: Atypical lives of typical kinases.
    Gregory D Cuny, Alexei Degterev.
      Receptor Interacting Protein Kinases (RIPKs) are a family of Ser/Thr/Tyr kinases whose functions, regulation and pathophysiologic roles have remained an enigma for a long time. In recent years, these proteins garnered significant interest due to their roles in regulating a variety of host defense functions including control of inflammatory gene expression, different forms of cell death, and cutaneous and intestinal barrier functions. In addition, there is accumulating evidence that while these kinases seemingly follow typical kinase blueprints, their functioning in cells can take forms that are atypical for protein kinases. Lastly, while these kinases generally belong to distinct areas of innate immune regulation, there are emerging overarching themes that may unify the functions of this kinase family. Our review seeks to discuss the biology of RIPKs, and how typical and atypical features of this family informs the activity of a rapidly growing repertoire of RIPK inhibitors.
    Keywords:  RIPK1; RIPK2; RIPK3; RIPK4; RIPK5; apoptosis; inflammation; kinase; necroptosis
    DOI:  https://doi.org/10.1016/j.semcdb.2020.06.014
  6. Nat Commun. 2020 Jul 30. 11(1): 3816
    STAT3 serine phosphorylation is required for TLR4 metabolic reprogramming and IL-1β expression.
    Jesse J Balic, Hassan Albargy, Kevin Luu, Francis J Kirby, W Samantha N Jayasekara, Finbar Mansell, Daniel J Garama, Dominic De Nardo, Nikola Baschuk, Cynthia Louis, Fiachra Humphries, Katherine Fitzgerald, Eicke Latz, Daniel J Gough, Ashley Mansell.
      Detection of microbial components such as lipopolysaccharide (LPS) by Toll-like receptor 4 (TLR4) on macrophages induces a robust pro-inflammatory response that is dependent on metabolic reprogramming. These innate metabolic changes have been compared to aerobic glycolysis in tumour cells. However, the mechanisms by which TLR4 activation leads to mitochondrial and glycolytic reprogramming are unknown. Here we show that TLR4 activation induces a signalling cascade recruiting TRAF6 and TBK-1, while TBK-1 phosphorylates STAT3 on S727. Using a genetically engineered mouse model incapable of undergoing STAT3 Ser727 phosphorylation, we show ex vivo and in vivo that STAT3 Ser727 phosphorylation is critical for LPS-induced glycolytic reprogramming, production of the central immune response metabolite succinate and inflammatory cytokine production in a model of LPS-induced inflammation. Our study identifies non-canonical STAT3 activation as the crucial signalling intermediary for TLR4-induced glycolysis, macrophage metabolic reprogramming and inflammation.
    DOI:  https://doi.org/10.1038/s41467-020-17669-5
  7. J Hematol Oncol. 2020 Jul 27. 13(1): 103
    Proteolysis targeting chimeras (PROTACs) are emerging therapeutics for hematologic malignancies.
    Yonghan He, Sajid Khan, Zhiguang Huo, Dongwen Lv, Xuan Zhang, Xingui Liu, Yaxia Yuan, Robert Hromas, Mingjiang Xu, Guangrong Zheng, Daohong Zhou.
      Proteolysis targeting chimeras (PROTACs) are heterobifunctional small molecules that utilize the ubiquitin proteasome system (UPS) to degrade proteins of interest (POI). PROTACs are potentially superior to conventional small molecule inhibitors (SMIs) because of their unique mechanism of action (MOA, i.e., degrading POI in a sub-stoichiometric manner), ability to target "undruggable" and mutant proteins, and improved target selectivity. Therefore, PROTACs have become an emerging technology for the development of novel targeted anticancer therapeutics. In fact, some of these reported PROTACs exhibit unprecedented efficacy and specificity in degrading various oncogenic proteins and have advanced to various stages of preclinical and clinical development for the treatment of cancer and hematologic malignancy. In this review, we systematically summarize the known PROTACs that have the potential to be used to treat various hematologic malignancies and discuss strategies to improve the safety of PROTACs for clinical application. Particularly, we propose to use the latest human pan-tissue single-cell RNA sequencing data to identify hematopoietic cell type-specific/selective E3 ligases to generate tumor-specific/selective PROTACs. These PROTACs have the potential to become safer therapeutics for hematologic malignancies because they can overcome some of the on-target toxicities of SMIs and PROTACs.
    Keywords:  Cell-specific E3 ligases; Hematologic malignancy; PROTAC; Small molecule inhibitor
    DOI:  https://doi.org/10.1186/s13045-020-00924-z
  8. Immunol Rev. 2020 Aug 01. e12910
    Pyroptotic and non-pyroptotic effector functions of caspase-11.
    Arwa Abu Khweek, Amal O Amer.
      Innate immune cells, epithelial cells, and many other cell types are capable of detecting infection or tissue injury, thus mounting regulated immune response. Inflammasomes are highly sophisticated and effective orchestrators of innate immunity. These oligomerized multiprotein complexes are at the center of various innate immune pathways, including modulation of the cytoskeleton, production and maturation of cytokines, and control of bacterial growth and cell death. Inflammasome assembly often results in caspase-1 activation, which is an inflammatory caspase that is involved in pyroptotic cell death and release of inflammatory cytokines in response to pathogen patterns and endogenous danger stimuli. However, the nature of stimuli and inflammasome components are diverse. Caspase-1 activation mediated release of mature IL-1β and IL-18 in response to canonical stimuli initiated by NOD-like receptor (NLR), and apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC). On the other hand, caspase-11 delineates a non-canonical inflammasome that promotes pyroptotic cell death and non-pyroptotic functions in response to non-canonical stimuli. Caspase-11 in mice and its homologues in humans (caspase-4/5) belong to caspase-1 family of cysteine proteases, and play a role in inflammation. Knockout mice provided new genetic tools to study inflammatory caspases and revealed the role of caspase-11 in mediating septic shock in response to lethal doses of lipopolysaccharide (LPS). Recognition of LPS mediates caspase-11 activation, which promotes a myriad of downstream effects that include pyroptotic and non-pyroptotic effector functions. Therefore, the physiological functions of caspase-11 are much broader than its previously established roles in apoptosis and cytokine maturation. Inflammation induced by exogenous or endogenous agents can be detrimental and, if excessive, can result in organ and tissue damage. Consequently, the existence of sophisticated mechanisms that tightly regulate the specificity and sensitivity of inflammasome pathways provides a fine-tuning balance between adequate immune response and minimal tissue damage. In this review, we summarize effector functions of caspase-11.
    Keywords:   Burkholderia ; Legionella ; Salmonella ; caspase-1; caspase-11; danger-associated molecular patterns; gasdermin; pathogen-associated molecular patterns; pyroptosis
    DOI:  https://doi.org/10.1111/imr.12910
  9. Cancer Lett. 2020 Jul 28. pii: S0304-3835(20)30381-5. [Epub ahead of print]
    JNK signaling contributes to skeletal muscle wasting and protein turnover in pancreatic cancer cachexia.
    Scott E Mulder, Aneesha Dasgupta, Ryan J King, Jaime Abrego, Kuldeep S Attri, Divya Murthy, Surendra K Shukla, Pankaj K Singh.
      Cancer cachexia patients experience significant muscle wasting, which impairs the quality of life and treatment efficacy for patients. Skeletal muscle protein turnover is imparted by increased expression of ubiquitin-proteasome pathway components. Mitogen-activated protein kinases p38 and ERK have been shown to augment E3 ubiquitin ligase expression. Utilizing reverse phase protein arrays, we identified pancreatic cancer cell-conditioned media-induced activation of JNK signaling in myotubes differentiated from C2C12 myoblasts. Inhibition of JNK signaling with SP600125 reduced cancer cell-conditioned media-induced myotube atrophy, myosin heavy chain 2 protein turnover, and mRNA expression of cachexia-specific ubiquitin ligases Trim63 and Fbxo32. Furthermore, utilizing an orthotopic pancreatic cancer cachexia mouse model, we demonstrated that treatment of tumor-bearing mice with SP600125 improved longitudinal measurements forelimb grip strength. Post-necropsy measurements demonstrated that SP600125 treatment rescued body weight, carcass weight, and gastrocnemius muscle weight without impacting tumor growth. JNK inhibitor treatment also rescued myofiber degeneration and reduced the muscle expression of Trim63 and Fbxo32. These data demonstrate that JNK signaling contributes to muscle wasting in cancer cachexia and its inhibition has the potential to be utilized as an anti-cachectic therapy.
    Keywords:  Cancer cachexia; JNK signaling; Muscle wasting; Ubiquitin ligases
    DOI:  https://doi.org/10.1016/j.canlet.2020.07.025
  10. Cell Rep. 2020 Jul 28. pii: S2211-1247(20)30940-2. [Epub ahead of print]32(4): 107959
    An Apoptotic Caspase Network Safeguards Cell Death Induction in Pyroptotic Macrophages.
    Nathalia Moraes de Vasconcelos, Nina Van Opdenbosch, Hanne Van Gorp, Rosa Martín-Pérez, Annalisa Zecchin, Peter Vandenabeele, Mohamed Lamkanfi.
      Pyroptosis has emerged as a key mechanism by which inflammasomes promote host defense against microbial pathogens and sterile inflammation. Gasdermin D (GSDMD)-mediated cell lysis is a hallmark of pyroptosis, but our understanding of cell death signaling during pyroptosis is fragmented. Here, we show that independently of GSDMD-mediated plasma membrane permeabilization, inflammasome receptors engage caspase-1 and caspase-8, both of which redundantly promote activation of apoptotic executioner caspase-3 and caspase-7 in pyroptotic macrophages. Impaired GSDMD pore formation downstream of caspase-1 and caspase-8 activation suffices to unmask the apoptotic phenotype of pyroptotic macrophages. Combined inactivation of initiator caspase-1 and caspase-8, or executioner caspase-3 and caspase-7, is required to abolish inflammasome-induced DEVDase activity during pyroptosis and in apoptotic Gsdmd-/- cells. Collectively, these results unveil a robust apoptotic caspase network that is activated in parallel to GSDMD-mediated plasma membrane permeabilization and safeguards cell death induction in pyroptotic macrophages.
    Keywords:  GSDMD; apoptosis; caspase-1; caspase-3; caspase-7; caspase-8; inflammasome; pyroptosis
    DOI:  https://doi.org/10.1016/j.celrep.2020.107959
  11. Eur J Med Chem. 2020 Jul 15. pii: S0223-5234(20)30542-0. [Epub ahead of print]203 112570
    The ups and downs of Poly(ADP-ribose) Polymerase-1 inhibitors in cancer therapy-Current progress and future direction.
    Yue Zhao, Liu-Xia Zhang, Ting Jiang, Jing Long, Zhong-Ye Ma, Ai-Ping Lu, Yan Cheng, Dong-Sheng Cao.
      Poly(ADP-ribose) Polymerase 1 (PARP1), one of the most investigated 18 membered PARP family enzymes, is involved in a variety of cellular functions including DNA damage repair, gene transcription and cell apoptosis. PARP1 can form a PARP1(ADP-ribose) polymers, then bind to the DNA damage gap to recruit DNA repair proteins, and repair the break to maintain genomic stability. PARP1 is highly expressed in tumor cells, so the inhibition of PARP1 can block DNA repair, promote tumor cell apoptosis, and exert antitumor activity. To date, four PARP1 inhibitors namely olaparib, rucaparib, niraparib and talazoparib, have been approved by Food and Drug Administration (FDA) for treating ovarian cancer and breast cancer with BRCA1/2 mutation. These drugs have showed super advantages over conventional chemotherapeutic drugs with low hematological toxicity and slowly developed drug resistance. In this article, we summarize and analyze the structure features of PARP1, the biological functions and antitumor mechanisms of PARP1 inhibitors. Importantly, we suggest that establishing a new structure-activity relationship of developed PARP1 inhibitors via substructural searching and the matched molecular pair analysis would accelerate the process in finding more potent and safer PARP1 inhibitors.
    Keywords:  Cancer; DNA damage repair; Matched molecular pair; PARP1; PARP1 inhibitors; Structure-activity relationship
    DOI:  https://doi.org/10.1016/j.ejmech.2020.112570
  12. Nature. 2020 Jul 29.
    Lysosome-targeting chimaeras for degradation of extracellular proteins.
    Steven M Banik, Kayvon Pedram, Simon Wisnovsky, Green Ahn, Nicholas M Riley, Carolyn R Bertozzi.
      The majority of therapies that target individual proteins rely on specific activity-modulating interactions with the target protein-for example, enzyme inhibition or ligand blocking. However, several major classes of therapeutically relevant proteins have unknown or inaccessible activity profiles and so cannot be targeted by such strategies. Protein-degradation platforms such as proteolysis-targeting chimaeras (PROTACs)1,2 and others (for example, dTAGs3, Trim-Away4, chaperone-mediated autophagy targeting5 and SNIPERs6) have been developed for proteins that are typically difficult to target; however, these methods involve the manipulation of intracellular protein degradation machinery and are therefore fundamentally limited to proteins that contain cytosolic domains to which ligands can bind and recruit the requisite cellular components. Extracellular and membrane-associated proteins-the products of 40% of all protein-encoding genes7-are key agents in cancer, ageing-related diseases and autoimmune disorders8, and so a general strategy to selectively degrade these proteins has the potential to improve human health. Here we establish the targeted degradation of extracellular and membrane-associated proteins using conjugates that bind both a cell-surface lysosome-shuttling receptor and the extracellular domain of a target protein. These initial lysosome-targeting chimaeras, which we term LYTACs, consist of a small molecule or antibody fused to chemically synthesized glycopeptide ligands that are agonists of the cation-independent mannose-6-phosphate receptor (CI-M6PR). We use LYTACs to develop a CRISPR interference screen that reveals the biochemical pathway for CI-M6PR-mediated cargo internalization in cell lines, and uncover the exocyst complex as a previously unidentified-but essential-component of this pathway. We demonstrate the scope of this platform through the degradation of therapeutically relevant proteins, including apolipoprotein E4, epidermal growth factor receptor, CD71 and programmed death-ligand 1. Our results establish a modular strategy for directing secreted and membrane proteins for lysosomal degradation, with broad implications for biochemical research and for therapeutics.
    DOI:  https://doi.org/10.1038/s41586-020-2545-9
  13. Nat Rev Rheumatol. 2020 Jul 31.
    Therapies targeting FLS and TNF can have synergistic effects.
    Sarah Onuora.
      
    DOI:  https://doi.org/10.1038/s41584-020-0487-0
  14. J Cell Sci. 2020 Jul 21. pii: jcs246041. [Epub ahead of print]133(14):
    The ubiquitin-like modifier FAT10 - much more than a proteasome-targeting signal.
    Annette Aichem, Marcus Groettrup.
      Human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10) also called ubiquitin D (UBD) is a member of the ubiquitin-like modifier (ULM) family. The FAT10 gene is localized in the MHC class I locus and FAT10 protein expression is mainly restricted to cells and organs of the immune system. In all other cell types and tissues, FAT10 expression is highly inducible by the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF). Besides ubiquitin, FAT10 is the only ULM which directly targets its substrates for degradation by the 26S proteasome. This poses the question as to why two ULMs sharing the proteasome-targeting function have evolved and how they differ from each other. This Review summarizes the current knowledge of the special structure of FAT10 and highlights its differences from ubiquitin. We discuss how these differences might result in differential outcomes concerning proteasomal degradation mechanisms and non-covalent target interactions. Moreover, recent insights about the structural and functional impact of FAT10 interacting with specific non-covalent interaction partners are reviewed.
    Keywords:  Autophagy; FAT10; Proteasome; Proteostasis; Ubiquitin; Ubiquitin-like modifier; VCP
    DOI:  https://doi.org/10.1242/jcs.246041
  15. Cell Death Dis. 2020 Jul 27. 11(7): 590
    SMAC mimetics induce autophagy-dependent apoptosis of HIV-1-infected macrophages.
    Grant R Campbell, Rachel K To, Gang Zhang, Stephen A Spector.
      Human immunodeficiency type 1 (HIV)-infected macrophages (HIV-Mφ) are a reservoir for latent HIV infection and a barrier to HIV eradication. In contrast to CD4+ T cells, HIV-Mφ are resistant to the cytopathic effects of acute HIV infection and have increased expression of cell survival factors, including X-linked inhibitor of apoptosis (XIAP), baculoviral IAP repeat containing (BIRC) 2/cIAP1, beclin-1, BCL2, BCL-xl, triggering receptor expressed on myeloid cells 1, mitofusin (MFN) 1, and MFN2. DIABLO/SMAC mimetics are therapeutic agents that affect cancer cell survival and induce cell death. We found that DIABLO/SMAC mimetics (LCL-161, AT-406 (also known as SM-406 or Debio 1143), and birinapant) selectively kill HIV-Mφ without increasing bystander cell death. DIABLO/SMAC mimetic treatment of HIV-Mφ-induced XIAP and BIRC2 degradation, leading to the induction of autophagy and the formation of a death-inducing signaling complex on phagophore membranes that includes both pro-apoptotic or necroptotic (FADD, receptor-interacting protein kinase (RIPK) 1, RIPK3, caspase 8, and MLKL) and autophagy (ATG5, ATG7, and SQSTM1) proteins. Genetic or pharmacologic inhibition of early stages of autophagy, but not late stages of autophagy, ablated this interaction and inhibited apoptosis. Furthermore, DIABLO/SMAC mimetic-mediated apoptosis of HIV-Mφ is dependent upon tumor necrosis factor signaling. Our findings thus demonstrate that DIABLO/SMAC mimetics selectively induce autophagy-dependent apoptosis in HIV-Mφ.
    DOI:  https://doi.org/10.1038/s41419-020-02761-x
  16. Sci China Life Sci. 2020 Jul 24.
    Fish TNF and TNF receptors.
    Yaoguo Li, Tiaoyi Xiao, Jun Zou.
      Tumor necrosis factors (TNFs) are a group of cytokines that play critical roles in regulating a diverse range of physiological processes in vertebrates. TNFs function by activating a large number of structurally related receptors, leading to TNF mediated biological processes which are evolutionarily conserved. Fish have a much diversified TNF family, partly due to the whole genome duplication events which have occurred in this lineage, providing an excellent model to investigate the neo- and sub-functionalised properties of TNF superfamily. Fish possess most of the TNFs and receptors found in mammals and also some homologues exclusively present in fish. It seems that TNFSF4 (OX40), TNFSF7 (CD27) and TNFSF8 (CD30) and their cognate receptors are absent in teleosts. It has been shown that fish viruses are able to produce TNFR homologues to establish infection by manipulating the host immune system. Understanding the roles of TNFSFs in fish immune defence and the pathogenesis of fish diseases will provide insights into the functions of TNFSFs from an evolutionary perspective and better strategies for improving fish health and welfare in aquaculture. This review summarises recent advances in the study offish TNF biology and focuses on the molecular properties and immunological functions of the TNF and TNFR superfamily.
    Keywords:  TNF receptor; cytokine; evolution; fish; tumor necrosis factor superfamily
    DOI:  https://doi.org/10.1007/s11427-020-1712-4
  17. Nat Immunol. 2020 Jul 27.
    A bacteria-chemokine double act repairs the skin.
    Vinod Nadella, Keisuke Nagao.
      
    DOI:  https://doi.org/10.1038/s41590-020-0755-9
  18. Life Sci Alliance. 2020 Sep;pii: e202000838. [Epub ahead of print]3(9):
    An evolutionary approach to systematic discovery of novel deubiquitinases, applied to Legionella.
    Thomas Hermanns, Ilka Woiwode, Ricardo Fm Guerreiro, Robert Vogt, Michael Lammers, Kay Hofmann.
      Deubiquitinating enzymes (DUBs) are important regulators of the posttranslational protein ubiquitination system. Mammalian genomes encode about 100 different DUBs, which can be grouped into seven different classes. Members of other DUB classes are found in pathogenic bacteria, which use them to target the host defense. By combining bioinformatical and experimental approaches, we address the question if the known DUB families have a common evolutionary ancestry and share conserved features that set them apart from other proteases. By systematically comparing family-specific hidden Markov models, we uncovered distant relationships between established DUBs and other cysteine protease families. Most DUB families share a conserved aromatic residue linked to the active site, which restricts the cleavage of substrates with side chains at the S2 position, corresponding to Gly-75 in ubiquitin. By applying these criteria to Legionella pneumophila ORFs, we identified lpg1621 and lpg1148 as deubiquitinases, characterized their cleavage specificities, and confirmed the importance of the aromatic gatekeeper motif for substrate selection.
    DOI:  https://doi.org/10.26508/lsa.202000838
  19. Proc Natl Acad Sci U S A. 2020 Jul 29. pii: 202006254. [Epub ahead of print]
    Rational design to control the trade-off between receptor affinity and cooperativity.
    Gabriel Ortega, Davide Mariottini, Alessandra Troina, Frederick W Dahlquist, Francesco Ricci, Kevin W Plaxco.
      Cooperativity enhances the responsiveness of biomolecular receptors to small changes in the concentration of their target ligand, albeit with a concomitant reduction in affinity. The binding midpoint of a two-site receptor with a Hill coefficient of 1.9, for example, must be at least 19 times higher than the dissociation constant of the higher affinity of its two binding sites. This trade-off can be overcome, however, by the extra binding energy provided by the addition of more binding sites, which can be used to achieve highly cooperative receptors that still retain high affinity. Exploring this experimentally, we have employed an "intrinsic disorder" mechanism to design two cooperative, three-binding-site receptors starting from a single-site-and thus noncooperative-doxorubicin-binding aptamer. The first receptor follows a binding energy landscape that partitions the energy provided by the additional binding event to favor affinity, achieving a Hill coefficient of 1.9 but affinity within a factor of 2 of the parent aptamer. The binding energy landscape of the second receptor, in contrast, partitions more of this energy toward cooperativity, achieving a Hill coefficient of 2.3, but at the cost of 4-fold poorer affinity than that of the parent aptamer. The switch between these two behaviors is driven primarily by the affinity of the receptors' second binding event, which serves as an allosteric "gatekeeper" defining the extent to which the system is weighted toward higher cooperativity or higher affinity.
    Keywords:  allostery; aptamers; biosensors; cooperativity; intrinsic disorder
    DOI:  https://doi.org/10.1073/pnas.2006254117
  20. Methods Mol Biol. 2021 ;2181 287-307
    The Role of RNA Editing in the Immune Response.
    Sadeem Ahmad, Xin Mu, Sun Hur.
      The innate immune receptors in higher organisms have evolved to detect molecular signatures associated with pathogenic infection and trigger appropriate immune response. One common class of molecules utilized by the innate immune system for self vs. nonself discrimination is RNA, which is ironically present in all forms of life. To avoid self-RNA recognition, the innate immune sensors have evolved sophisticated discriminatory mechanisms that involve cellular RNA metabolic machineries. Posttranscriptional RNA modification and editing represent one such mechanism that allows cells to chemically tag the host RNAs as "self" and thus tolerate the abundant self-RNA molecules. In this chapter, we discuss recent advances in our understanding of the role of RNA editing/modification in the modulation of immune signaling pathways, and application of RNA editing/modification in RNA-based therapeutics and cancer immunotherapies.
    Keywords:  ADAR; APOBEC; Editing; Innate immunity; PKR; RIG-I-like receptors; RNA modification; Toll-like receptors
    DOI:  https://doi.org/10.1007/978-1-0716-0787-9_17
  21. Immunol Rev. 2020 Jul 29.
    The regulation of the ZBP1-NLRP3 inflammasome and its implications in pyroptosis, apoptosis, and necroptosis (PANoptosis).
    Min Zheng, Thirumala-Devi Kanneganti.
      ZBP1 has been characterized as a critical innate immune sensor of not only viral RNA products but also endogenous nucleic acid ligands. ZBP1 sensing of the Z-RNA produced during influenza virus infection induces cell death in the form of pyroptosis, apoptosis, and necroptosis (PANoptosis). PANoptosis is a coordinated cell death pathway that is driven through a multiprotein complex called the PANoptosome and enables crosstalk and co-regulation among these processes. During influenza virus infection, a key step in PANoptosis and PANoptosome assembly is the formation of the ZBP1-NLRP3 inflammasome. When Z-RNA is sensed, ZBP1 recruits RIPK3 and caspase-8 to activate the ZBP1-NLRP3 inflammasome. Several other host factors have been found to be important for ZBP1-NLRP3 inflammasome assembly, including molecules involved in the type I interferon signaling pathway and caspase-6. Additionally, influenza viral proteins, such as M2, NS1, and PB1-F2, have also been shown to regulate the ZBP1-NLRP3 inflammasome. This review explains the functions of ZBP1 and the mechanistic details underlying the activation of the ZBP1-NLRP3 inflammasome and the formation of the PANoptosome. Improved understanding of the ZBP1-NLRP3 inflammasome will direct the development of therapeutic strategies to target infectious and inflammatory diseases.
    Keywords:  NLRP3; PANoptosis; PANoptosome; ZBP1; apoptosis; inflammasome; influenza A virus; innate immunity; necroptosis; pyroptosis; virus infection
    DOI:  https://doi.org/10.1111/imr.12909
  22. Nature. 2020 Jul;583(7818): 711-719
    A large-scale binding and functional map of human RNA-binding proteins.
    Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M Blue, Jia-Yu Chen, Neal A L Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O Duff, Keri E Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Michael P McGurk, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A Yee, Bing Zhou, Ashley L Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lécuyer, Christopher B Burge, Brenton R Graveley, Gene W Yeo.
      Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.
    DOI:  https://doi.org/10.1038/s41586-020-2077-3
  23. Cell Immunol. 2020 Jul 22. pii: S0008-8749(20)30336-1. [Epub ahead of print]356 104176
    Deltex-1 is indispensible for the IL-6 and TGF-β treatment-triggered differentiation of Th17 cells.
    Zhengle Tang, Yuan Wang, Rui Xing, Shan Zeng, Jingfang Di, Feiyue Xing.
      CSL(CBF1, Su(H) and LAG-1)-dependent Hes-1 signaling plays an important part in regulating Th17 cell differentiation. However, little is known about influence of CSL-independent Deltex-1 signaling on this subset. The current focus is on roles of the Deltex-1 signaling in the Th17 cell differentiation. IL-17-producing CD4+ T cell subpopulation could be induced in vitro by treatment of both IL-6 and TGF-β. This could be reversed by knockdown of the deltex-1 gene, following the attenuation of retinoic acid-related orphan receptor γt (RORγt) and its DNA-binding activity in nuclei. Subsequently, Th17-associated cytokines generated by the treated cells were also diminished by the inhibition of Deltex-1 signaling, but the production of IL-10 was enhanced. Contrary to the alteration of RORγt, both zinc-finger transcription factor-3 (GATA3) and transcription factor Forkhead box P3 (Foxp3) were augmented at their mRNA and protein levels as well as DNA-binding activities with the emerging phenotypes of the corresponding cellular subpopulation and T-bet (encoded by TBX21) was not changed. These results reveal for the first time that Deltex-1 is indispensible for the IL-6 and TGF-β treatment-triggered differentiation of Th17 cells, indicating that CSL-independent Deltex-1 signaling favors naïve CD4+ T cells to deviate into Th17 cells via the enhancement of RORγt/IL-17A.
    Keywords:  Deltex-1; Differentiation; RORγt; Regulation; Th17
    DOI:  https://doi.org/10.1016/j.cellimm.2020.104176
  24. Science. 2020 Jul 31. pii: eaba2429. [Epub ahead of print]369(6503):
    The function of the thymus and its impact on modern medicine.
    Jacques F A P Miller.
      The lymphoid system is intimately involved in immunological processes. The small lymphocyte that circulates through blood into lymphoid tissues, then through the lymph and back to the blood through the thoracic duct, is able to initiate immune responses after appropriate stimulation by antigen. However, the lymphocytes found in the thymus are deficient in this ability despite the fact that the thymus plays a central role in lymphocyte production and in ensuring the normal development of immunological faculty. During embryogenesis, lymphocytes are present in the thymus before they can be identified in the circulation and in other lymphoid tissues. They become "educated" in the thymus to recognize a great diversity of peptide antigens bound to the body's own marker antigen, the major histocompatibility complex, but they are purged if they strongly react against their own self-components. Lymphocytes differentiate to become various T cell subsets and then exit through the bloodstream to populate certain areas of the lymphoid system as peripheral T lymphocytes with distinct markers and immune functions.
    DOI:  https://doi.org/10.1126/science.aba2429
  25. Front Immunol. 2020 ;11 1259
    Multiple Roles for Chemokines in Neutrophil Biology.
    Arianna Capucetti, Francesca Albano, Raffaella Bonecchi.
      Chemokines are recognized as the most critical mediators for selective neutrophil recruitment during inflammatory conditions. Furthermore, they are considered fundamental regulators of neutrophil mobilization from the bone marrow (BM) to the bloodstream and for their homing back at the end of their life for apoptosis and clearance. However, chemokines are also important mediators of neutrophil effector functions including oxidative burst, degranulation, neutrophil extracellular trap (NET)osis, and production of inflammatory mediators. Neutrophils have been historically considered as a homogeneous population. In recent years, several maturation stages and subsets with different phenotypic profiles and effector functions were described both in physiological and pathological conditions such as infections, autoimmunity, and cancer. The aim of this review is to give an overview of the current evidence regarding the role of chemokines and chemokine receptors in neutrophil biology, including their possible role in neutrophil maturation, differentiation, and in defining emerging neutrophil subsets.
    Keywords:  atypical chemokine receptors; chemokine receptors; chemokines; neutrophil subpopulations; neutrophils
    DOI:  https://doi.org/10.3389/fimmu.2020.01259
  26. Nat Neurosci. 2020 Jul 27.
    A programmable sequence of reporters for lineage analysis.
    Jorge Garcia-Marques, Isabel Espinosa-Medina, Kai-Yuan Ku, Ching-Po Yang, Minoru Koyama, Hung-Hsiang Yu, Tzumin Lee.
      We present CLADES (cell lineage access driven by an edition sequence), a technology for cell lineage studies based on CRISPR-Cas9 techniques. CLADES relies on a system of genetic switches to activate and inactivate reporter genes in a predetermined order. Targeting CLADES to progenitor cells allows the progeny to inherit a sequential cascade of reporters, thereby coupling birth order to reporter expression. This system, which can also be temporally induced by heat shock, enables the temporal resolution of lineage development and can therefore be used to deconstruct an extended cell lineage by tracking the reporters expressed in the progeny. When targeted to the germ line, the same cascade progresses across animal generations, predominantly marking each generation with the corresponding combination of reporters. CLADES therefore offers an innovative strategy for making programmable cascades of genes that can be used for genetic manipulation or to record serial biological events.
    DOI:  https://doi.org/10.1038/s41593-020-0676-9
  27. Cell Death Differ. 2020 Jul 31.
    RIP3-mediated necroptosis is regulated by inter-filament assembly of RIP homotypic interaction motif.
    Hong Hu, Xialian Wu, Guoxiang Wu, Ning Nan, Jing Zhang, Xinxin Zhu, Yu Zhang, Zhaoqian Shu, Jia Liu, Xiaoyan Liu, Junxia Lu, Huayi Wang.
      Necroptosis is mediated by signaling complexes called necrosomes, which contain receptor-interacting protein 3 (RIP3) and upstream effectors, such as RIP1. In necrosomes, the RIP homotypic interaction motif (RHIM) of RIP3 and RIP1 forms amyloidal complex. But how the amyloidal necrosomes control RIP3 activation and cell necroptosis has not been determined. Here, we showed that RIP3 amyloid fibrils could further assemble into large fibrillar networks which presents as cellular puncta during necroptosis. A viral RHIM-containing necroptosis inhibitor M45 could form heteroamyloid with RIP3 in cells and prevent RIP3 puncta formation and cell necroptosis. We characterized mutual antagonism between RIP3-RHIM and M45-RHIM in necroptosis regulation, which was caused by distinct inter-filament interactions in RIP3, M45 amyloids revealed with atomic force microscopy. Moreover, double mutations Asn464 and Met468 in RIP3-RHIM to Asp disrupted RIP3 kinase-dependent necroptosis. While the mutant RIP3(N464D/M468D) could form amyloid as wild type upon necroptosis induction. Based on these results, we propose that RIP3 amyloid formation is required but not sufficient in necroptosis signaling, the ordered inter-filament assembly of RIP3 is critical in RIP3 amyloid mediated kinase activation and cell necroptosis.
    DOI:  https://doi.org/10.1038/s41418-020-0598-9
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