bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020‒07‒26
seventeen papers selected by
John Silke
Walter and Eliza Hall Institute of Medical Research


  1. Int J Mol Sci. 2020 Jul 21. pii: E5142. [Epub ahead of print]21(14):
    Mirando AC, Lima E Silva R, Chu Z, Campochiaro PA, Pandey NB, Popel AS.
      Persistent inflammation is a complication associated with many ocular diseases. Changes in ocular vessels can amplify disease responses and contribute to vision loss by influencing the delivery of leukocytes to the eye, vascular leakage, and perfusion. Here, we report the anti-inflammatory activity for AXT107, a non-RGD, 20-mer αvβ3 and α5β1 integrin-binding peptide that blocks vascular endothelial growth factor (VEGF)-signaling and activates tyrosine kinase with immunoglobulin and EGF-like domains 2 (Tie2) using the normally inhibitory ligand angiopoietin 2 (Ang2). Tumor necrosis factor α (TNFα), a central inflammation mediator, induces Ang2 release from endothelial cells to enhance its stimulation of inflammation and vascular leakage. AXT107 resolves TNFα-induced vascular inflammation in endothelial cells by converting the endogenously released Ang2 into an agonist of Tie2 signaling, thereby disrupting both the synergism between TNFα and Ang2 while also preventing inhibitor of nuclear factor-κB α (IκBα) degradation directly through Tie2 signaling. This recovery of IκBα prevents nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) nuclear localization, thereby blocking NF-κB-induced inflammatory responses, including the production of VCAM-1 and ICAM-1, leukostasis, and vascular leakage in cell and mouse models. AXT107 also decreased the levels of pro-inflammatory TNF receptor 1 (TNFR1) without affecting levels of the more protective TNFR2. These data suggest that AXT107 may provide multiple benefits in the treatment of retinal/choroidal and other vascular diseases by suppressing inflammation and promoting vascular stabilization.
    Keywords:  AXT107; IκBα; NF-κB; TNFα; VCAM-1; endothelial activation; leukostasis; ocular diseases; peptide therapeutic; vascular leakage; vascular permeability
    DOI:  https://doi.org/10.3390/ijms21145142
  2. Int J Mol Sci. 2020 Jul 21. pii: E5164. [Epub ahead of print]21(14):
    Ramadass V, Vaiyapuri T, Tergaonkar V.
      Nuclear factor kappa B (NF-κB) signaling is implicated in all major human chronic diseases, with its role in transcription of hundreds of gene well established in the literature. This has propelled research into targeting the NF-κB pathways for modulating expression of those genes and the diseases mediated by them. In-spite of the critical, but often promiscuous role played by this pathway and the inhibition causing adverse drug reaction, currently many biologics, macromolecules, and small molecules that modulate this pathway are in the market or in clinical trials. Furthermore, many marketed drugs that were later found to also have NF-κB targeting activity were repurposed for new therapeutic interventions. Despite the rising importance of biologics in drug discovery, small molecules got around 76% of US-FDA (Food and Drug Administration-US) approval in the last decade. This encouraged us to review information regarding clinically relevant small molecule inhibitors of the NF-κB pathway from cell surface receptor stimulation to nuclear signaling. We have also highlighted the underexplored targets in this pathway that have potential to succeed in clinic.
    Keywords:  NF-κB pathway; anti-cancer; anti-inflammatory; autoimmune disease; clinical trials; small molecules
    DOI:  https://doi.org/10.3390/ijms21145164
  3. Stem Cell Res Ther. 2020 Jul 22. 11(1): 307
    Shamdani S, Uzan G, Naserian S.
      BACKGROUND: Stem cells have a vast range of functions from tissue regeneration to immunoregulation. They have the ability to modulate immune responses and change the progression of different inflammatory and autoimmune disorders. Tumor cells share many characteristics of stem/progenitor cells too. Both can inhibit effector T cells and other immune cells, while inducing regulatory T cells (T regs), thus, reducing the production of pro-inflammatory cytokines and increasing the production of anti-inflammatory ones. In this context, some cytokines like TNFα are able to control the direction of the immune response. 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.MAIN BODY: We think the expression of TNFR2 confers a level of immunomodulatory properties to its expressing cell and this could be crucially important, particularly, for stem/progenitor and tumor cells. This idea has been already proven in many TNFR2+ cells. Different immunosuppressive cells like T regs, regulatory B cells (B regs), myeloid-derived suppressor cells (MDSCs), mesenchymal stem cells (MSCs) and endothelial progenitor cells (EPCs) express TNFR2 and are able to suppress immune cells in presence of TNFα. The other category of rare cells that express TNFR2 is neural cells (NCs). Although little is known about the immunological function of these latter cells, few studies showed their progenitors are able to suppress T cells. Therefore, we hypothesize that the immunosuppressive effect of neural stem cells (NSCs) is potentially TNFα-TNFR2 dependent.
    CONCLUSIONS: NSCs are among the rare cells that express TNFR2 marker and are able to supress T cells. We believe TNFα-TNFR2 immune checkpoint signaling pathway could be responsible for this immunosuppressive effect.
    Keywords:  Immune checkpoint; Immunoregulation; Immunosuppression; Neural progenitor cells; Neural stem cells; TNF-TNFR2 signaling pathway
    DOI:  https://doi.org/10.1186/s13287-020-01816-2
  4. Proc Natl Acad Sci U S A. 2020 Jul 20. pii: 202001887. [Epub ahead of print]
    Fletcher-Etherington A, Nobre L, Nightingale K, Antrobus R, Nichols J, Davison AJ, Stanton RJ, Weekes MP.
      Human cytomegalovirus (HCMV) is an important human pathogen and a paradigm of intrinsic, innate, and adaptive viral immune evasion. Here, we employed multiplexed tandem mass tag-based proteomics to characterize host proteins targeted for degradation late during HCMV infection. This approach revealed that mixed lineage kinase domain-like protein (MLKL), a key terminal mediator of cellular necroptosis, was rapidly and persistently degraded by the minimally passaged HCMV strain Merlin but not the extensively passaged strain AD169. The strain Merlin viral inhibitor of apoptosis pUL36 was necessary and sufficient both to degrade MLKL and to inhibit necroptosis. Furthermore, mutation of pUL36 Cys131 abrogated MLKL degradation and restored necroptosis. As the same residue is also required for pUL36-mediated inhibition of apoptosis by preventing proteolytic activation of procaspase-8, we define pUL36 as a multifunctional inhibitor of both apoptotic and necroptotic cell death.
    Keywords:  MLKL; cell death; human cytomegalovirus; necroptosis; protein degradation
    DOI:  https://doi.org/10.1073/pnas.2001887117
  5. Scand J Immunol. 2020 Jul 22. e12946
    Ten Bergen LL, Petrovic A, Aarebrot AK, Appel S.
      Psoriasis is a T cell-mediated disease with autoimmune characteristics modulated by genetic susceptibility along with environmental triggers. Inflammatory pathways marked with excessive production of cytokines IL-12 and IL-23, drive differentiation of pathogenic T cell responses resulting in TNF and IL-17 production. These cytokines are an integral part of the TNF/IL-23/IL-17 axis, which is responsible for maintaining inflammation in psoriatic skin. Our improved understanding of the immunopathogenesis led to the development of biological drugs in the treatment of moderate-to-severe disease. Biologics have revolutionized the management of psoriasis, highlighting the central role of TNF/IL-23/IL-17 axis in the physiopathology of the disease. Still, psoriasis usually requires long-term treatment, aiming to fully remove psoriatic lesions without experiencing adverse events. In this review, we discuss the recent findings of all 27 available head-to-head trials investigating the efficacy and safety of systemic and biologic therapies in moderate-to-severe psoriasis vulgaris, as it is thought to provide more useful knowledge than placebo intervention alone. According to our evaluation, inhibitors that specifically target IL-23 or IL-17 are clinically more beneficial than inhibitors of IL-12/IL-23 and TNF. More informative results might be obtained by comparing these more efficient biological agents to each other. In addition, newer therapies for psoriasis using small-molecule drugs, may represent important advances compared to well-established biologics as these are less expensive and orally administered.
    Keywords:  Biologics; TNF/IL-23/IL-17 axis; cytokines; head-to-head trials; psoriasis
    DOI:  https://doi.org/10.1111/sji.12946
  6. Sci Rep. 2020 Jul 23. 10(1): 12357
    Sowa ST, Vela-Rodríguez C, Galera-Prat A, Cázares-Olivera M, Prunskaite-Hyyryläinen R, Ignatev A, Lehtiö L.
      Tankyrases catalyse poly-ADP-ribosylation of their binding partners and the modification serves as a signal for the subsequent proteasomal degradation of these proteins. Tankyrases thereby regulate the turnover of many proteins involved in multiple and diverse cellular processes, such as mitotic spindle formation, telomere homeostasis and Wnt/β-catenin signalling. In recent years, tankyrases have become attractive targets for the development of inhibitors as potential therapeutics against cancer and fibrosis. Further, it has become clear that tankyrases are not only enzymes, but also act as scaffolding proteins forming large cellular signalling complexes. While many potent and selective tankyrase inhibitors of the poly-ADP-ribosylation function exist, the inhibition of tankyrase scaffolding functions remains scarcely explored. In this work we present a robust, simple and cost-effective high-throughput screening platform based on FRET for the discovery of small molecule probes targeting the protein-protein interactions of tankyrases. Validatory screening with the platform led to the identification of two compounds with modest binding affinity to the tankyrase 2 ARC4 domain, demonstrating the applicability of this approach. The platform will facilitate identification of small molecules binding to tankyrase ARC or SAM domains and help to advance a structure-guided development of improved chemical probes targeting tankyrase oligomerization and substrate protein interactions.
    DOI:  https://doi.org/10.1038/s41598-020-69229-y
  7. Cell Rep. 2020 Jul 21. pii: S2211-1247(20)30903-7. [Epub ahead of print]32(3): 107922
    Koirala S, Klein J, Zheng Y, Glenn NO, Eisemann T, Fon Tacer K, Miller DJ, Kulak O, Lu M, Finkelstein DB, Neale G, Tillman H, Vogel P, Strand DW, Lum L, Brautigam CA, Pascal JM, Clements WK, Potts PR.
      Spatiotemporal control of Wnt/β-catenin signaling is critical for organism development and homeostasis. The poly-(ADP)-ribose polymerase Tankyrase (TNKS1) promotes Wnt/β-catenin signaling through PARylation-mediated degradation of AXIN1, a component of the β-catenin destruction complex. Although Wnt/β-catenin is a niche-restricted signaling program, tissue-specific factors that regulate TNKS1 are not known. Here, we report prostate-associated gene 4 (PAGE4) as a tissue-specific TNKS1 inhibitor that robustly represses canonical Wnt/β-catenin signaling in human cells, zebrafish, and mice. Structural and biochemical studies reveal that PAGE4 acts as an optimal substrate decoy that potently hijacks substrate binding sites on TNKS1 to prevent AXIN1 PARylation and degradation. Consistently, transgenic expression of PAGE4 in mice phenocopies TNKS1 knockout. Physiologically, PAGE4 is selectively expressed in stromal prostate fibroblasts and functions to establish a proper Wnt/β-catenin signaling niche through suppression of autocrine signaling. Our findings reveal a non-canonical mechanism for TNKS1 inhibition that functions to establish tissue-specific control of the Wnt/β-catenin pathway.
    Keywords:  Axin; PAGE4; PARylation; RNF146; TNKS; Tankyrase; Wnt; cancer-testis antigen; prostate; β-catenin
    DOI:  https://doi.org/10.1016/j.celrep.2020.107922
  8. J Biomol Struct Dyn. 2020 Jul 24. 1-20
    Qaiser H, Saeed M, Nerukh D, Ul-Haq Z.
      Tumor Necrosis Factor-alpha (TNF-α), a multifunctional cytokine responsible for providing resistance against infections, inflammation, and cancers. TNF-α has emerged as a promising drug target against several autoimmune and inflammatory disorders. Several synthetic antibodies (Infliximab, Etanercept, and Adalimumab) are available, but their potential to cause severe side effects has prompted them to develop alternative small molecules-based therapies for inhibition of TNF-α. In the present study, combined in silico approaches based on pharmacophore modeling, virtual screening, molecular docking, and molecular dynamics studies were employed to understand significant direct interactions between TNF-α protein and small molecule inhibitors. Initially, four different small molecule libraries (∼17.5 million molecules) were virtually screened against the selected pharmacophore model. The identified hits were further subjected to molecular docking studies. The three potent lead compounds (ZINC05848961, ZINC09402309, ZINC04502991) were further subjected to 100 ns molecular dynamic studies to examine their stability. Our docking and molecular dynamic analysis revealed that the selected lead compounds target the TNF receptor (TNFR) and efficiently block the production of TNF. Moreover, in silico ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) analysis revealed that all the predicted compounds have good pharmacokinetic properties with high gastrointestinal absorption and a decent bioavailability score. Furthermore, toxicity profiles further evidenced that these compounds have no risk of being mutagenic, tumorigenic, reproductive and irritant except ZINC11915498. In conclusion, the present study could serve as the starting point to develop new therapeutic regimens to treat various TNF- related diseases. Communicated by Ramaswamy H. Sarma.
    Keywords:  Autoimmunity; MD simulation; TNF receptor; docking; pharmacophore
    DOI:  https://doi.org/10.1080/07391102.2020.1796794
  9. J Exp Med. 2020 Sep 07. pii: e20191206. [Epub ahead of print]217(9):
    Potts KS, Farley A, Dawson CA, Rimes J, Biben C, de Graaf C, Potts MA, Stonehouse OJ, Carmagnac A, Gangatirkar P, Josefsson EC, Anttila C, Amann-Zalcenstein D, Naik S, Alexander WS, Hilton DJ, Hawkins ED, Taoudi S.
      How platelets are produced by megakaryocytes in vivo remains controversial despite more than a century of investigation. Megakaryocytes readily produce proplatelet structures in vitro; however, visualization of platelet release from proplatelets in vivo has remained elusive. We show that within the native prenatal and adult environments, the frequency and rate of proplatelet formation is incompatible with the physiological demands of platelet replacement. We resolve this inconsistency by performing in-depth analysis of plasma membrane budding, a cellular process that has previously been dismissed as a source of platelet production. Our studies demonstrate that membrane budding results in the sustained release of platelets directly into the peripheral circulation during both fetal and adult life without induction of cell death or proplatelet formation. In support of this model, we demonstrate that in mice deficient for NF-E2 (the thrombopoietic master regulator), the absence of membrane budding correlates with failure of in vivo platelet production. Accordingly, we propose that membrane budding, rather than proplatelet formation, supplies the majority of the platelet biomass.
    DOI:  https://doi.org/10.1084/jem.20191206
  10. Cell Chem Biol. 2020 Jul 21. pii: S2451-9456(20)30244-0. [Epub ahead of print]
    Wang ZA, Cole PA.
      Lysine (Lys) residues in proteins undergo a wide range of reversible post-translational modifications (PTMs), which can regulate enzyme activities, chromatin structure, protein-protein interactions, protein stability, and cellular localization. Here we discuss the "writers," "erasers," and "readers" of some of the common protein Lys PTMs and summarize examples of their major biological impacts. We also review chemical biology approaches, from small-molecule probes to protein chemistry technologies, that have helped to delineate Lys PTM functions and show promise for a diverse set of biomedical applications.
    Keywords:  acetylation; acetyltransferase; bromodomain; deacetylase; enzyme; methylation; ubiquitination
    DOI:  https://doi.org/10.1016/j.chembiol.2020.07.002
  11. Drug Discov Today. 2020 Jul 18. pii: S1359-6446(20)30293-2. [Epub ahead of print]
    Pike A, Williamson B, Harlfinger S, Martin S, McGinnity DF.
      Proteolysis-targeting chimeras (PROTACs) are an emerging therapeutic modality with the potential to open target space not accessible to conventional small molecules via a degradation-based mechanism; however, their bifunctional nature can result in physicochemical properties that breach commonly accepted limits for small-molecule oral drugs. We offer a drug metabolism and pharmacokinetics (DMPK) perspective on the optimisation of oral PROTACs across a diverse set of projects within Oncology R&D at AstraZeneca, highlighting some of the challenges that they have presented to our established screening cascade. Furthermore, we challenge some of the perceptions and dogma surrounding the feasibility of oral PROTACS and demonstrate that acceptable oral PK properties for this modality can be regularly achievable despite the physicochemical property challenges they present.
    DOI:  https://doi.org/10.1016/j.drudis.2020.07.013
  12. Development. 2020 Jul 24. pii: dev191882. [Epub ahead of print]147(14):
    Ghose P, Shaham S.
      Cell death is an important facet of animal development. In some developing tissues, death is the ultimate fate of over 80% of generated cells. Although recent studies have delineated a bewildering number of cell death mechanisms, most have only been observed in pathological contexts, and only a small number drive normal development. This Primer outlines the important roles, different types and molecular players regulating developmental cell death, and discusses recent findings with which the field currently grapples. We also clarify terminology, to distinguish between developmental cell death mechanisms, for which there is evidence for evolutionary selection, and cell death that follows genetic, chemical or physical injury. Finally, we suggest how advances in understanding developmental cell death may provide insights into the molecular basis of developmental abnormalities and pathological cell death in disease.
    Keywords:  Apoptosis; Caspase; Cell compartment elimination; Cell death; LCD; Linker cell-type death; Non-apoptotic cell death; Pathological cell death
    DOI:  https://doi.org/10.1242/dev.191882
  13. J Cell Biol. 2020 Aug 03. pii: e202006090. [Epub ahead of print]219(8):
    Pierchala BA.
      Necroptosis is a cell death pathway involved in inflammation and disease. In this issue, Ko et al. (2020. J. Cell Biol.https://doi.org/10.1083/jcb.201912047) link SARM1, the executioner of Wallerian degeneration of axons, to necroptosis, revealing a unique form of axonal disassembly likely involved in neurodegenerative disorders.
    DOI:  https://doi.org/10.1083/jcb.202006090
  14. Cell Calcium. 2020 Jul 13. pii: S0143-4160(20)30095-6. [Epub ahead of print]90 102253
    Sanchez Arias JC, Wicki-Stordeur LE, Candlish RC, van der Slagt E, Paci I, Rao PPN, MacVicar BA, Swayne LA.
      A new study by Yang and colleagues has revealed that TNF-alpha regulates PANX1 levels through an NF-kB-dependent mechanism in human endothelial cells. PANX1 modulates Ca2+ influx contributing to IL-1beta production independent of purinergic signaling. These novel findings expand our understanding of TNF-alpha-mediated upregulation of IL-1beta with implications for responses to tissue injury and infection.
    Keywords:  IL-1beta; NF-kB; TNF-alpha; cytokines; endothelial cells; inflammation; intracellular calcium; pannexin 1; transcription
    DOI:  https://doi.org/10.1016/j.ceca.2020.102253
  15. Biochem Biophys Res Commun. 2020 Aug 20. pii: S0006-291X(20)31202-X. [Epub ahead of print]529(2): 418-424
    Tanaka Y, Morimoto D, Walinda E, Sugase K, Shirakawa M.
      Ubiquitination is one of the major post-translational modifications and entails conjugation of ubiquitin molecules to target proteins. To make free ubiquitin molecules available for conjugation, in cells ubiquitin is not only synthesized de novo, but is also provided by cleaving off existing conjugated ubiquitin molecules, so-called deubiquitination reaction. Therefore, intracellular ubiquitin molecules are thought to be recycled, but the recycling frequency remains elusive. The main reason for the lack of such mechanistic details is that the original and recycled ubiquitin molecules are indistinguishable in their chemical and physical properties. To tackle this issue, here we applied 18O-labeling to trace how ubiquitin is recycled in a simultaneous ubiquitination/deubiquitination reaction (ubiquitin cycle reaction). Because deubiquitination is a hydrolysis reaction, the two 16O atoms of the C-terminal carboxy group of a ubiquitin molecule can be exchanged with 18O atoms by deubiquitination in 18O-labeled aqueous solution. By using quantitative mass spectrometry, we detected 18O atom incorporation into the C-terminal carboxy group of ubiquitin in the course of a deubiquitination reaction, in addition, we were able to quantify the 18O-incorporation in a ubiquitin cycle reaction. Unexpectedly, kinetic analysis suggested that ubiquitination reactivity was accelerated in the presence of a deubiquitinating enzyme. Collectively, we have established a quantitative method to trace ubiquitin cycle reactions by analyzing deubiquitination-associated 18O-incorporation into ubiquitin.
    Keywords:  (18)O-incorporation; Deubiquitination; Quantitative mass spectrometry; Ubiquitin cycle; Ubiquitination
    DOI:  https://doi.org/10.1016/j.bbrc.2020.06.008
  16. Genomics. 2020 Jul 16. pii: S0888-7543(20)30738-2. [Epub ahead of print]
    Hong W, Gu Y, Guan R, Xie D, Zhou H, Yu M.
      The cysteinyl aspartate protease (caspase, or CASP) gene family plays a significant role in programmed cell death, inflammation and immunity. However, the correlation between CASP family members and prognosis and tumor-infiltrating lymphocytes in different tumors has not been determined. We investigated the role of CASP genes in cancer prognosis and their relationship with clinicopathological parameters. We also evaluated the correlation between the expression of CASP family members and cancer immune infiltration and evaluated whether these molecules can be used as targets for immunotherapy. The CASP1/2/4/5/7/9 genes may represent prognostic factors and therapeutic targets for breast cancer, hepatocellular carcinoma and pancreatic cancer. Another finding is that the CASP1/4/5 genes help to regulate innate immunity and T cell immunity and may also have an important effect on tumor checkpoint inhibition. These findings may elucidate the roles played by CASP family members in cancer progression and identify strategies to promote collaborative activities in the context of immunotherapy.
    Keywords:  Cysteinyl aspartate protease (caspase, CASP) gene family; Lymphocytes; Pan-cancer; Tumor-infiltrating
    DOI:  https://doi.org/10.1016/j.ygeno.2020.07.026
  17. Chem Commun (Camb). 2020 Jul 23.
    Mills B, Norberg D, Dhaliwal K, Akram AR, Bradley M, Megia-Fernandez A.
      A probe that allows specific 'painting' of human tumours is described. Probe activation was mediated by specific matrix metalloproteinases, resulting not only in disruption of a FRET pair, but in the generation of a fragment that "fluorescently paints" human tumours. This probe demonstrated rapid and effective human tumour labelling with the potential to allow margin detection during surgical resection.
    DOI:  https://doi.org/10.1039/d0cc03886e