bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020‒11‒15
eight papers selected by
John Silke
Walter and Eliza Hall Institute of Medical Research


  1. Curr Opin Immunol. 2020 Nov 04. pii: S0952-7915(20)30093-5. [Epub ahead of print]68 83-97
    Weir A, Hughes S, Rashidi M, Hildebrand JM, Vince JE.
      The necroptotic cell death pathway has received significant attention for its ability to trigger inflammatory responses and its potential involvement in related conditions. Recent insights into the essential membrane damaging necroptotic pseudokinase effector, Mixed lineage kinase domain like (MLKL), have revealed a growing number of diverse MLKL functions that contribute to the inflammatory nature of necroptosis. Here we review distinct MLKL signalling roles and document the immunogenic molecules released by necroptosis. We discuss specific in vivo MLKL-driven responses, the activation of inflammasome complexes and innate lymphoid cells that have been documented to drive disease. Finally, we list necroptotic competent cell types and their involvement in MLKL-driven cell death-associated and inflammatory-associated conditions.
    DOI:  https://doi.org/10.1016/j.coi.2020.09.008
  2. Methods Mol Biol. 2021 ;2248 73-80
    Choksi S, Choudhary G, Liu ZG.
      Tumor necrosis factor (TNF) plays a key role in inflammatory responses and in various cellular events such as apoptosis and necroptosis. The interaction of TNF with its receptor, TNFR1, drives the initiation of complex molecular pathways leading to inflammation and cell death. RARγ is released from the nucleus to orchestrate the formation of the cytosolic death complexes, and it is cytosolic RARγ that plays a pivotal role in switching TNF-induced inflammatory responses to RIPK1-initiated cell death. Thus, RARγ provides a checkpoint for the transition from inflammatory signaling to death machinery of RIPK1-initiated cell death in response to TNF. Here, we use techniques to identify RARγ as a downstream mediator of TNFR1 signaling complex. We use confocal imaging to show the localization of RARγ upon activation of cell death. Immunoprecipitation of RARγ identified the interacting proteins.
    Keywords:  Immunoprecipitation; RARγ; RIPK1; TRADD
    DOI:  https://doi.org/10.1007/978-1-0716-1130-2_5
  3. Methods Mol Biol. 2021 ;2248 185-200
    Kucka K, Medler J, Wajant H.
      Quantitative analysis of the binding of tumor necrosis factor (TNF) superfamily ligands (TNFLs) to TNF receptor superfamily receptors (TNFRs) is of crucial relevance for the understanding of the mechanisms of TNFR activation. Ligand binding studies are also a basic method required for the development and characterization of agonists and antagonists of TNFRs. TNFL-induced formation of fully active TNFR signaling complexes is a complex process. It involves not only reorganization of monomeric and inactive pre-assembled TNFR complexes into trimeric liganded TNFR complexes but also the secondary interaction of the latter. Moreover, various factors, e.g., TNFR modification, special membrane domains, or accessory proteins, may affect TNFL-TNFR interactions in a TNFR type-specific manner. Widely used cell-free methods for the analysis of protein-protein interactions are thus of limited value for the analysis of TNFL-TNFR interactions and makes therefore in this case cellular binding studies to the method of choice. We and others observed that the genetic fusion of monomeric protein domains to the N-terminus of soluble TNFLs has typically no effect on activity and TNFR binding. We exploited this to generate bioluminescent TNFL fusion proteins which allow simple, sensitive, and highly reproducible cellular binding studies for the investigation of TNFL-TNFR interactions. Here, we report detailed protocols for the production of TNFL fusion proteins with the luciferase of Gaussia princeps and the use of these fusion proteins in various types of cellular binding studies.
    Keywords:  Bioluminescence; Gaussia princeps luciferase; TNF receptor superfamily receptors (TNFRs); TNF superfamily ligands (TNFLs)
    DOI:  https://doi.org/10.1007/978-1-0716-1130-2_13
  4. J Biol Chem. 2020 Nov 09. pii: jbc.RA120.014479. [Epub ahead of print]
    Mashimo M, Onishi M, Uno A, Tanimichi A, Nobeyama A, Mori M, Yamada S, Negi S, Bu X, Kato J, Moss J, Sanada N, Kizu R, Fujii T.
      Poly(ADP-ribose) polymerase (PARP1) is a nuclear protein that is activated by binding to DNA lesions and catalyzes poly(ADP- ribosyl)ation of nuclear acceptor proteins, including PARP1 itself, to recruit DNA repair machinery to DNA lesions. When excessive DNA damage occurs, poly(ADP-ribose) (PAR) produced by PARP1 is translocated to the cytoplasm, changing the activity and localization of cytoplasmic proteins e.g. apoptosis-inducing factor (AIF), hexokinase and resulting in cell death. This cascade, termed parthanatos, is a caspase-independent programmed cell death distinct from necrosis and apoptosis. In contrast, PARP1 is a substrate of activated caspases 3 and 7 in caspase-dependent apoptosis. Once cleaved, PARP1 loses its activity, thereby suppressing DNA repair. Caspase cleavage of PARP1 occurs within a nuclear localization signal near the DNA-binding domain, resulting in the formation of 24-kDa and 89-kDa fragments. In the current study, we found that caspase activation by staurosporine- and actinomycin D-induced PARP1 auto-poly(ADP-ribosyl)ation and fragmentation, generating poly(ADP-ribosyl)ated 89-kDa and 24-kDa PARP1 fragments. The 89-kDa PARP1 fragments with covalently attached PAR polymers were translocated to the cytoplasm, while 24-kDa fragments remained associated with DNA lesions. In the cytoplasm, AIF binding to PAR attached to the 89-kDa PARP1 fragment facilitated its translocation to the nucleus. Thus, the 89-kDa PARP1 fragment is a PAR carrier to the cytoplasm, inducing AIF release from mitochondria. Elucidation of the caspase-mediated interaction between apoptosis and parthanatos pathways extend the current knowledge on mechanisms underlying programmed cell death and may lead to new therapeutic targets.
    Keywords:  ADP-ribosylation; DNA damage; apoptosis; apoptosis-inducing factor; caspase; cell death; parthanatos; poly(ADP-ribose) polymerase 1; poly(ADP-ribosyl)ation; post-translational modification (PTM)
    DOI:  https://doi.org/10.1074/jbc.RA120.014479
  5. Nat Commun. 2020 Nov 13. 11(1): 5769
    Kirsch K, Zeke A, Tőke O, Sok P, Sethi A, Sebő A, Kumar GS, Egri P, Póti ÁL, Gooley P, Peti W, Bento I, Alexa A, Reményi A.
      Transcription factor phosphorylation at specific sites often activates gene expression, but how environmental cues quantitatively control transcription is not well-understood. Activating protein 1 transcription factors are phosphorylated by mitogen-activated protein kinases (MAPK) in their transactivation domains (TAD) at so-called phosphoswitches, which are a hallmark in response to growth factors, cytokines or stress. We show that the ATF2 TAD is controlled by functionally distinct signaling pathways (JNK and p38) through structurally different MAPK binding sites. Moreover, JNK mediated phosphorylation at an evolutionarily more recent site diminishes p38 binding and made the phosphoswitch differently sensitive to JNK and p38 in vertebrates. Structures of MAPK-TAD complexes and mechanistic modeling of ATF2 TAD phosphorylation in cells suggest that kinase binding motifs and phosphorylation sites line up to maximize MAPK based co-regulation. This study shows how the activity of an ancient transcription controlling phosphoswitch became dependent on the relative flux of upstream signals.
    DOI:  https://doi.org/10.1038/s41467-020-19582-3
  6. Front Cell Dev Biol. 2020 ;8 569684
    Zhao L, Fu Q, Pan L, Piai A, Chou JJ.
      Receptors in the tumor necrosis factor receptor superfamily (TNFRSF) regulate proliferation of immune cells or induce programmed cell death, and many of them are candidates for antibody-based immunotherapy. Previous studies on several death receptors in the TNFRSF including Fas, p75NTR, and DR5 showed that the transmembrane helix (TMH) of these receptors can specifically oligomerize and their oligomeric states have direct consequences on receptor activation, suggesting a much more active role of TMH in receptor signaling than previously appreciated. Here, we report the structure of the TMH of TNFR1, another well studied member of the TNFRSF, in neutral bicelles that mimic a lipid bilayer. We find that TNFR1 TMH forms a defined trimeric complex in bicelles, and no evidences of higher-order clustering of trimers have been detected. Unexpectedly, a conserved proline, which is critical for Fas TMH trimerization, does not appear to play an important role in TNFR1 TMH trimerization, which is instead mediated by a glycine near the middle of the TMH. Further, TNFR1 TMH trimer shows a larger hydrophobic core than that of Fas or DR5, with four layers of hydrophobic interaction along the threefold axis. Comparison of the TNFR1 TMH structure with that of Fas and DR5 reveals reassuring similarities that have functional implications but also significant structural diversity that warrants systematic investigation of TMH oligomerization property for other members of the TNFRSF.
    Keywords:  NMR; TNFR1; oligomerization; receptor activation; transmembrane domain
    DOI:  https://doi.org/10.3389/fcell.2020.569684
  7. Methods Mol Biol. 2021 ;2248 81-90
    Medler J, Wajant H.
      In vivo research of the last decade revealed that the anchoring of antitumor necrosis factor (TNF) receptor superfamily (TNFRSF) receptor antibodies to cell-expressed Fcγ receptors (FcγR) can be of decisive relevance for their receptor-stimulatory activity. Indeed, FcγR anchoring may even result in the conversion of antagonistic to agonistic anti-TNFR antibody activity. The knowledge on this issue is obviously not only relevant to understand the in vivo effects of anti-TNFR antibodies but also of overwhelming importance for the rational clinical development of antibodies and antibody derivatives. Based on the fact that with exception of the decoy TNFRSF receptors (TNFRs) all TNFRs are able to trigger proinflammatory NFκB signaling, resulting in the production of chemokines and cytokines, we established an easy and broadly applicable coculture assay for the evaluation of the FcγR-dependency of the agonism of anti-TNFR antibodies. In this assay, TNFR responder cells, which produce high amounts of IL8 in response to TNFR stimulation, were pairwise incubated with empty vector- and FcγR-transfected HEK293 cells, which produce only very low amounts of IL8. This cocultures were then comparatively analyzed with respect to anti-TNFR antibody-induced IL8 production as a readout for TNFR activation to uncover proagonistic effects of FcγR binding.
    Keywords:  ELISA; FcγR; IL8; NFκB; TNFRSF; agonistic antibodies; coculture
    DOI:  https://doi.org/10.1007/978-1-0716-1130-2_6
  8. Proc Natl Acad Sci U S A. 2020 Nov 09. pii: 202008213. [Epub ahead of print]
    Kressel AM, Tsaava T, Levine YA, Chang EH, Addorisio ME, Chang Q, Burbach BJ, Carnevale D, Lembo G, Zador AM, Andersson U, Pavlov VA, Chavan SS, Tracey KJ.
      In the brain, compact clusters of neuron cell bodies, termed nuclei, are essential for maintaining parameters of host physiology within a narrow range optimal for health. Neurons residing in the brainstem dorsal motor nucleus (DMN) project in the vagus nerve to communicate with the lungs, liver, gastrointestinal tract, and other organs. Vagus nerve-mediated reflexes also control immune system responses to infection and injury by inhibiting the production of tumor necrosis factor (TNF) and other cytokines in the spleen, although the function of DMN neurons in regulating TNF release is not known. Here, optogenetics and functional mapping reveal cholinergic neurons in the DMN, which project to the celiac-superior mesenteric ganglia, significantly increase splenic nerve activity and inhibit TNF production. Efferent vagus nerve fibers terminating in the celiac-superior mesenteric ganglia form varicose-like structures surrounding individual nerve cell bodies innervating the spleen. Selective optogenetic activation of DMN cholinergic neurons or electrical activation of the cervical vagus nerve evokes action potentials in the splenic nerve. Pharmacological blockade and surgical transection of the vagus nerve inhibit vagus nerve-evoked splenic nerve responses. These results indicate that cholinergic neurons residing in the brainstem DMN control TNF production, revealing a role for brainstem coordination of immunity.
    Keywords:  TNF; cytokines; dorsal motor nucleus; inflammatory reflex; vagus nerve
    DOI:  https://doi.org/10.1073/pnas.2008213117