bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020–10–04
eleven papers selected by
John Silke, Walter and Eliza Hall Institute of Medical Research
  1. RIPK1 ubiquitination: Evidence, correlations and the undefined.
  2. Impaired RIPK1 ubiquitination sensitizes mice to TNF toxicity and inflammatory cell death.
  3. A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2.
  4. TWEAK/Fn14 axis is an important player in fibrosis.
  5. Genetic inactivation of RIP1 kinase does not ameliorate disease in a mouse model of ALS.
  6. YB-1 Interferes with TNFα-TNFR Binding and Modulates Progranulin-Mediated Inhibition of TNFα Signaling.
  7. High-fat diet intensifies MLL-AF9-induced acute myeloid leukemia through activation of the FLT3 signaling in mouse primitive hematopoietic cells.
  8. Unfolding transmembrane TNFα dynamics in cancer therapeutics.
  9. The rapid "teabag" method for high-end purification of membrane proteins.
  10. ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins.
  11. Glymphatic failure as a final common pathway to dementia.
  1. Semin Cell Dev Biol. 2020 Sep 23. pii: S1084-9521(19)30241-1. [Epub ahead of print]
    RIPK1 ubiquitination: Evidence, correlations and the undefined.
    Daniel S Simpson, Anna Gabrielyan, Rebecca Feltham.
      Over the last two decades the mechanisms that underpin cell survival and cell death have been intensively studied. One molecule in particular, Receptor Interacting Protein Kinase 1 (RIPK1), has gained interest due to the ability to function upstream of both NF-κB signaling and caspase-dependent and -independent cell death. RIPK1 is critical in determining cell fate downstream of cytokine signaling receptors such as the Tumour Necrosis Factor Receptor Super Family (TNFRSF) and the innate immune Toll-like receptors. Various studies have attempted to untangle how ubiquitination of RIPK1 dictates signaling outcomes; however, due to the complex nature of ubiquitin signaling it has been difficult to prove that ubiquitination of RIPK1 does in fact influence signaling outcomes. Therefore, we ask the question: What do we really know about RIPK1 ubiquitination, and, to what extent can we conclude that ubiquitination of RIPK1 impacts RIPK1-mediated signaling events?
    Keywords:  RIPK1; Ubiquitination
    DOI:  https://doi.org/10.1016/j.semcdb.2020.08.008
  2. Cell Death Differ. 2020 Sep 30.
    Impaired RIPK1 ubiquitination sensitizes mice to TNF toxicity and inflammatory cell death.
    Matthias Kist, László G Kőműves, Tatiana Goncharov, Debra L Dugger, Charles Yu, Merone Roose-Girma, Kim Newton, Joshua D Webster, Domagoj Vucic.
      Receptor-interacting protein 1 (RIP1; RIPK1) is a key regulator of multiple signaling pathways that mediate inflammatory responses and cell death. TNF-TNFR1 triggered signaling complex formation, subsequent NF-κB and MAPK activation and induction of cell death involve RIPK1 ubiquitination at several lysine residues including Lys376 and Lys115. Here we show that mutating the ubiquitination site K376 of RIPK1 (K376R) in mice activates cell death resulting in embryonic lethality. In contrast to Ripk1K376R/K376R mice, Ripk1K115R/K115R mice reached adulthood and showed slightly higher responsiveness to TNF-induced death. Cell death observed in Ripk1K376R/K376R embryos relied on RIPK1 kinase activity as administration of RIPK1 inhibitor GNE684 to pregnant heterozygous mice effectively blocked cell death and prolonged survival. Embryonic lethality of Ripk1K376R/K376R mice was prevented by the loss of TNFR1, or by simultaneous deletion of caspase-8 and RIPK3. Interestingly, elimination of the wild-type allele from adult Ripk1K376R/cko mice was tolerated. However, adult Ripk1K376R/cko mice were exquisitely sensitive to TNF-induced hypothermia and associated lethality. Absence of the K376 ubiquitination site diminished K11-linked, K63-linked, and linear ubiquitination of RIPK1, and promoted the assembly of death-inducing cellular complexes, suggesting that multiple ubiquitin linkages contribute to the stability of the RIPK1 signaling complex that stimulates NF-κB and MAPK activation. In contrast, mutating K115 did not affect RIPK1 ubiquitination or TNF stimulated NF-κB and MAPK signaling. Overall, our data indicate that selective impairment of RIPK1 ubiquitination can lower the threshold for RIPK1 activation by TNF resulting in cell death and embryonic lethality.
    DOI:  https://doi.org/10.1038/s41418-020-00629-3
  3. Bioinformatics. 2020 Sep 29. pii: btaa844. [Epub ahead of print]
    A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2.
    Juan Pablo Prada, Gaby Wangorsch, Kirstin Kucka, Isabell Lang, Thomas Dandekar, Harald Wajant.
       MOTIVATION: Clustering enables TNF receptors to stimulate intracellular signaling. The differential soluble ligand-induced clustering behavior of TNF receptor 1 (TNFR1) and TNFR2 was modeled.
    METHODS: A structured, rule-based model implemented ligand-independent pre-ligand binding assembly domain (PLAD)-mediated homotypic low affinity interactions of unliganded and liganded TNF receptors.
    RESULTS: Soluble TNF initiates TNFR1 signaling but not TNFR2 signaling despite receptor binding unless it is secondarily oligomerized. We consider high affinity binding of TNF to signaling-incompetent pre-assembled dimeric TNFR1 and TNFR2 molecules and secondary clustering of liganded dimers to signaling competent ligand-receptor clusters. Published receptor numbers, affinities and measured different activities of clustered receptors validated model simulations for a large range of receptor and ligand concentrations. Different PLAD-PLAD affinities and different activities of receptor clusters explain the observed differences in the TNF receptor stimulating activities of soluble TNF.
    AVAILABILITY: All scripts and data are in manuscript and supplement at Bioinformatics online.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa844
  4. J Cell Physiol. 2020 Sep 30.
    TWEAK/Fn14 axis is an important player in fibrosis.
    Yitian Zhang, Weihui Zeng, Yumin Xia.
      Fibrosis is a common pathological condition associated with abnormal repair after tissue injury. However, the etiology and molecular mechanisms of fibrosis are still not well-understood. Tumor necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) belongs to the TNF superfamily and acts by binding to its receptor, fibroblast growth factor-inducible 14 (Fn14), thereby activating a variety of intracellular signal transduction pathways in various types of cells. Besides promoting the expression of growth factors, activation of TWEAK/Fn14 signaling after tissue injury can promote the expression of pro-inflammatory cytokines, which trigger the immune response, thereby exacerbating the injury. Severe or repetitive injury leads to a dysregulated tissue repair process, in which the TWEAK/Fn14 axis promotes the activation and proliferation of myofibroblasts, induces the secretion of the extracellular matrix, and regulates profibrotic mediators to further perpetuate and sustain the fibrotic process. In this review, we summarize the available experimental evidence on the underlying molecular mechanisms by which the TWEAK/Fn14 pathway mediates the development and progression of fibrosis. In addition, we discuss the therapeutic potential of the TWEAK/Fn14 pathway in fibrosis-associated diseases based on evidence derived from multiple models and cells from injured tissue and fibrotic tissue.
    Keywords:  Fn14; TWEAK; fibrosis; injury; tumor necrosis factor
    DOI:  https://doi.org/10.1002/jcp.30089
  5. Cell Death Differ. 2020 Sep 29.
    Genetic inactivation of RIP1 kinase does not ameliorate disease in a mouse model of ALS.
    Sara Dominguez, Eugene Varfolomeev, Robert Brendza, Kim Stark, Joy Tea, Jose Imperio, Hai Ngu, Timothy Earr, Oded Foreman, Joshua D Webster, Amy Easton, Domagoj Vucic, Baris Bingol.
      RIP1 kinase is proposed to play a critical role in driving necroptosis and inflammation in neurodegenerative disorders, including Amyotrophic Lateral Sclerosis (ALS). Preclinical studies indicated that while pharmacological inhibition of RIP1 kinase can ameliorate axonal pathology and delay disease onset in the mutant SOD1 transgenic (SOD1-Tg) mice, genetic blockade of necroptosis does not provide benefit in this mouse model. To clarify the role of RIP1 kinase activity in driving pathology in SOD1-Tg mice, we crossed SOD1-Tgs to RIP1 kinase-dead knock-in mice, and measured disease progression using functional and histopathological endpoints. Genetic inactivation of the RIP1 kinase activity in the SOD1-Tgs did not benefit the declining muscle strength or nerve function, motor neuron degeneration or neuroinflammation. In addition, we did not find evidence of phosphorylated RIP1 accumulation in the spinal cords of ALS patients. On the other hand, genetic inactivation of RIP1 kinase activity ameliorated the depletion of the neurotransmitter dopamine in a toxin model of dopaminergic neurodegeneration. These findings indicate that RIP1 kinase activity is dispensable for disease pathogenesis in the SOD1-Tg mice while inhibition of kinase activity may provide benefit in acute injury models.
    DOI:  https://doi.org/10.1038/s41418-020-00625-7
  6. Int J Mol Sci. 2020 Sep 25. pii: E7076. [Epub ahead of print]21(19):
    YB-1 Interferes with TNFα-TNFR Binding and Modulates Progranulin-Mediated Inhibition of TNFα Signaling.
    Christopher L Hessman, Josephine Hildebrandt, Aneri Shah, Sabine Brandt, Antonia Bock, Björn C Frye, Ute Raffetseder, Robert Geffers, Monika C Brunner-Weinzierl, Berend Isermann, Peter R Mertens, Jonathan A Lindquist.
      Inflammation and an influx of macrophages are common elements in many diseases. Among pro-inflammatory cytokines, tumor necrosis factor α (TNFα) plays a central role by amplifying the cytokine network. Progranulin (PGRN) is a growth factor that binds to TNF receptors and interferes with TNFα-mediated signaling. Extracellular PGRN is processed into granulins by proteases released from immune cells. PGRN exerts anti-inflammatory effects, whereas granulins are pro-inflammatory. The factors coordinating these ambivalent functions remain unclear. In our study, we identify Y-box binding protein-1 (YB-1) as a candidate for this immune-modulating activity. Using a yeast-2-hybrid assay with YB-1 protein as bait, clones encoding for progranulin were selected using stringent criteria for strong interaction. We demonstrate that at physiological concentrations, YB-1 interferes with the binding of TNFα to its receptors in a dose-dependent manner using a flow cytometry-based binding assay. We show that YB-1 in combination with progranulin interferes with TNFα-mediated signaling, supporting the functionality with an NF-κB luciferase reporter assay. Together, we show that YB-1 displays immunomodulating functions by affecting the binding of TNFα to its receptors and influencing TNFα-mediated signaling via its interaction with progranulin.
    Keywords:  DNA binding protein-B (DbpB); Y-box binding protein-1 (YB-1); immune modulation; inflammation; macrophage; progranulin; signaling; tumor necrosis factor alpha (TNFα)
    DOI:  https://doi.org/10.3390/ijms21197076
  7. Sci Rep. 2020 Sep 30. 10(1): 16187
    High-fat diet intensifies MLL-AF9-induced acute myeloid leukemia through activation of the FLT3 signaling in mouse primitive hematopoietic cells.
    François Hermetet, Rony Mshaik, John Simonet, Patrick Callier, Laurent Delva, Ronan Quéré.
      Using a MLL-AF9 knock-in mouse model, we discovered that consumption of a high-fat diet (HFD) accelerates the risk of developing acute myeloid leukemia (AML). This regimen increases the clusterization of FLT3 within lipid rafts on the cell surface of primitive hematopoietic cells, which overactivates this receptor as well as the downstream JAK/STAT signaling known to enhance the transformation of MLL-AF9 knock-in cells. Treatment of mice on a HFD with Quizartinib, a potent inhibitor of FLT3 phosphorylation, inhibits the JAK3/STAT3, signaling and finally antagonizes the accelerated development of AML that occurred following the HFD regimen. We can therefore conclude that, on a mouse model of AML, a HFD enforces the FLT3 signaling pathway on primitive hematopoietic cells and, in turn, improves the oncogenic transformation of MLL-AF9 knock-in cells and the leukemia initiation.
    DOI:  https://doi.org/10.1038/s41598-020-73020-4
  8. Cytokine. 2020 Sep 28. pii: S1043-4666(20)30319-7. [Epub ahead of print]137 155303
    Unfolding transmembrane TNFα dynamics in cancer therapeutics.
    Srirupa Bhattacharyya, Siddhartha Sankar Ghosh.
      Cytokines are a group of glycoprotein signaling mediators, which play essential roles in maintaining several complex physiological functions of our body. TNFα is such a pleiotropic cytokine, which involves maintaining a plethora of immune responses. Initially, TNFα is synthesized as a 26 kDa full-length transmembrane form, which is enzymatically cleaved to produce the soluble circulating 17 kDa TNFα. Although the anti-cancer potential of soluble TNFα was discovered more than a century back, its dual ability to promote tumor, posed a major hindrance in finding its acceptance as a proper anti-cancer molecule. In contrast, the membrane-tethered tmTNFα holds the potential of tumor regression without initiating cell proliferation. The membrane-tethered form of TNFα is the physiological precursor of soluble TNFα that remains biologically active and is capable of initiating signaling cascades after binding with the TNFα receptors- TNFR I and TNFR II. In this review, we emphasize on the basic biology and molecular aspects of tmTNFα for its anti-cancer potential.
    Keywords:  Apoptosis; Cancer; Cytotoxicity; Transmembrane tumor necrosis factor α (tmTNFα)
    DOI:  https://doi.org/10.1016/j.cyto.2020.155303
  9. Sci Rep. 2020 Sep 30. 10(1): 16167
    The rapid "teabag" method for high-end purification of membrane proteins.
    Jenny Hering, Julie Winkel Missel, Liying Zhang, Anders Gunnarsson, Marie Castaldo, Per Amstrup Pedersen, Margareta Ek, Pontus Gourdon, Harm Jan Snijder.
      Overproduction and purification of membrane proteins are generally challenging and time-consuming procedures due to low expression levels, misfolding, and low stability once extracted from the membrane. Reducing processing steps and shortening the timespan for purification represent attractive approaches to overcome some of these challenges. We have therefore compared a fast "teabag" purification method with conventional purification for five different membrane proteins (MraY, AQP10, ClC-1, PAR2 and KCC2). Notably, this new approach reduces the purification time significantly, and the quality of the purified membrane proteins is equal to or exceeds conventional methods as assessed by size exclusion chromatography, SDS-PAGE and downstream applications such as ITC, crystallization and cryo-EM. Furthermore, the method is scalable, applicable to a range of affinity resins and allows for parallelization. Consequently, the technique has the potential to substantially simplify purification efforts of membrane proteins in basic and applied sciences.
    DOI:  https://doi.org/10.1038/s41598-020-73285-9
  10. bioRxiv. 2020 Sep 25. pii: 2020.09.24.298851. [Epub ahead of print]
    ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins.
    Vinay Ayyappan, Ricky Wat, Calvin Barber, Christina A Vivelo, Kathryn Gauch, Pat Visanpattanasin, Garth Cook, Christos Sazeides, Anthony K L Leung.
      ADP-ribosylation is a protein modification responsible for biological processes such as DNA repair, RNA regulation, cell cycle, and biomolecular condensate formation. Dysregulation of ADP-ribosylation is implicated in cancer, neurodegeneration, and viral infection. We developed ADPriboDB (adpribodb.leunglab.org) to facilitate studies in uncovering insights into the mechanisms and biological significance of ADP-ribosylation. ADPriboDB 2.0 serves as a one-stop repository comprising 48,346 entries and 9,097 ADP-ribosylated proteins, of which 6,708 were newly identified since the original database release. In this updated version, we provide information regarding the sites of ADP-ribosylation in 32,946 entries. The wealth of information allows us to interrogate existing databases or newly available data. For example, we found that ADP-ribosylated substrates are significantly associated with the recently identified human protein interaction networks associated with SARS-CoV-2, which encodes a conserved protein domain called macrodomain that binds and removes ADP-ribosylation. In addition, we create a new interactive tool to visualize the local context of ADP-ribosylation, such as structural and functional features as well as other post-translational modifications (e.g., phosphorylation, methylation and ubiquitination). This information provides opportunities to explore the biology of ADP-ribosylation and generate new hypotheses for experimental testing.
    DOI:  https://doi.org/10.1101/2020.09.24.298851
  11. Science. 2020 Oct 02. 370(6512): 50-56
    Glymphatic failure as a final common pathway to dementia.
    Maiken Nedergaard, Steven A Goldman.
      Sleep is evolutionarily conserved across all species, and impaired sleep is a common trait of the diseased brain. Sleep quality decreases as we age, and disruption of the regular sleep architecture is a frequent antecedent to the onset of dementia in neurodegenerative diseases. The glymphatic system, which clears the brain of protein waste products, is mostly active during sleep. Yet the glymphatic system degrades with age, suggesting a causal relationship between sleep disturbance and symptomatic progression in the neurodegenerative dementias. The ties that bind sleep, aging, glymphatic clearance, and protein aggregation have shed new light on the pathogenesis of a broad range of neurodegenerative diseases, for which glymphatic failure may constitute a therapeutically targetable final common pathway.
    DOI:  https://doi.org/10.1126/science.abb8739
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