bims-tunefa Biomed News
on Tumor necrosis factor superfamily and post-translational modifications
Issue of 2020–06–14
fiveteen papers selected by
John Silke, Walter and Eliza Hall Institute of Medical Research
  1. Multiple roles of caspase-8 in cell death, inflammation, and innate immunity.
  2. Selective Targeting of TNF Receptors as a Novel Therapeutic Approach.
  3. Hepatocyte-specific TAK1 deficiency drives RIPK1 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.
  4. DDI2 Is a Ubiquitin-Directed Endoprotease Responsible for Cleavage of Transcription Factor NRF1.
  5. Cell Death in the Origin and Treatment of Cancer.
  6. Haploinsufficiency of A20 Due to Novel Mutations in TNFAIP3.
  7. Circulating tumor necrosis factor-α DNA are elevated in psoriasis.
  8. p38 Kinase: A Key Target for Driving Potent T Cells for Adoptive Immunotherapy.
  9. Scaffold hopping enables direct access to more potent PROTACs with in vivo activity.
  10. Biologics for psoriasis: what does drug survival tell us?
  11. Editorial: Probing the Ubiquitin Landscape.
  12. Activity-Based Screening Assay for Mono-ADP-Ribosylhydrolases.
  13. Reform retractions to make them more transparent.
  14. Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand.
  15. Very fast CRISPR on demand.
  1. J Leukoc Biol. 2020 Jun 12.
    Multiple roles of caspase-8 in cell death, inflammation, and innate immunity.
    Pontus Orning, Egil Lien.
      Caspase-8 is an apical caspase involved in the programmed form of cell death called apoptosis that is critically important for mammalian development and immunity. Apoptosis was historically described as immunologically silent in contrast to other types of programmed cell death such as necroptosis or pyroptosis. Recent reports suggest considerable crosstalk between these different forms of cell death. It is becoming increasingly clear that caspase-8 has many non-apoptotic roles, participating in multiple processes including regulation of necroptosis (mediated by receptor-interacting serine/threonine kinases, RIPK1-RIPK3), inflammatory cytokine expression, inflammasome activation, and cleavage of IL-1β and gasdermin D, and protection against shock and microbial infection. In this review, we discuss the involvement of caspase-8 in cell death and inflammation and highlight its role in innate immune responses and in the relationship between different forms of cell death. Caspase-8 is one of the central components in this type of crosstalk.
    Keywords:  TNF; apoptosis; caspase; inflammasomes; necroptosis; pyroptosis
    DOI:  https://doi.org/10.1002/JLB.3MR0420-305R
  2. Front Cell Dev Biol. 2020 ;8 401
    Selective Targeting of TNF Receptors as a Novel Therapeutic Approach.
    Roman Fischer, Roland E Kontermann, Klaus Pfizenmaier.
      Tumor necrosis factor (TNF) is a central regulator of immunity. Due to its dominant pro-inflammatory effects, drugs that neutralize TNF were developed and are clinically used to treat inflammatory and autoimmune diseases, such as rheumatoid arthritis, inflammatory bowel disease and psoriasis. However, despite their clinical success the use of anti-TNF drugs is limited, in part due to unwanted, severe side effects and in some diseases its use even is contraindicative. With gaining knowledge about the signaling mechanisms of TNF and the differential role of the two TNF receptors (TNFR), alternative therapeutic concepts based on receptor selective intervention have led to the development of novel protein therapeutics targeting TNFR1 with antagonists and TNFR2 with agonists. These antibodies and bio-engineered ligands are currently in preclinical and early clinical stages of development. Preclinical data obtained in different disease models show that selective targeting of TNFRs has therapeutic potential and may be superior to global TNF blockade in several disease indications.
    Keywords:  TNF; TNFR1; TNFR2; inflammation; therapy; tissue regeneration
    DOI:  https://doi.org/10.3389/fcell.2020.00401
  3. Proc Natl Acad Sci U S A. 2020 Jun 08. pii: 202005353. [Epub ahead of print]
    Hepatocyte-specific TAK1 deficiency drives RIPK1 kinase-dependent inflammation to promote liver fibrosis and hepatocellular carcinoma.
    Shuixia Tan, Jing Zhao, Ziyu Sun, Shuangyi Cao, Kongyan Niu, Yedan Zhong, Han Wang, Linyu Shi, Heling Pan, Junhao Hu, Lihui Qian, Nan Liu, Junying Yuan.
      Transforming growth factor β-activated kinase1 (TAK1) encoded by the gene MAP3K7 regulates multiple important downstream effectors involved in immune response, cell death, and carcinogenesis. Hepatocyte-specific deletion of TAK1 in Tak1 ΔHEP mice promotes liver fibrosis and hepatocellular carcinoma (HCC) formation. Here, we report that genetic inactivation of RIPK1 kinase using a kinase dead knockin D138N mutation in Tak1 ΔHEP mice inhibits the expression of liver tumor biomarkers, liver fibrosis, and HCC formation. Inhibition of RIPK1, however, has no or minimum effect on hepatocyte loss and compensatory proliferation, which are the recognized factors important for liver fibrosis and HCC development. Using single-cell RNA sequencing, we discovered that inhibition of RIPK1 strongly suppresses inflammation induced by hepatocyte-specific loss of TAK1. Activation of RIPK1 promotes the transcription of key proinflammatory cytokines, such as CCL2, and CCR2+ macrophage infiltration. Our study demonstrates the role and mechanism of RIPK1 kinase in promoting inflammation, both cell-autonomously and cell-nonautonomously, in the development of liver fibrosis and HCC, independent of cell death, and compensatory proliferation. We suggest the possibility of inhibiting RIPK1 kinase as a therapeutic strategy for reducing liver fibrosis and HCC development by inhibiting inflammation.
    Keywords:  RIPK1; TAK1; cancer; cell death; inflammation
    DOI:  https://doi.org/10.1073/pnas.2005353117
  4. Mol Cell. 2020 Jun 08. pii: S1097-2765(20)30356-7. [Epub ahead of print]
    DDI2 Is a Ubiquitin-Directed Endoprotease Responsible for Cleavage of Transcription Factor NRF1.
    A Barbara Dirac-Svejstrup, Jane Walker, Peter Faull, Vesela Encheva, Vyacheslav Akimov, Michele Puglia, David Perkins, Sandra Kümper, Suchete S Hunjan, Blagoy Blagoev, Ambrosius P Snijders, David J Powell, Jesper Q Svejstrup.
      The Ddi1/DDI2 proteins are ubiquitin shuttling factors, implicated in a variety of cellular functions. In addition to ubiquitin-binding and ubiquitin-like domains, they contain a conserved region with similarity to retroviral proteases, but whether and how DDI2 functions as a protease has remained unknown. Here, we show that DDI2 knockout cells are sensitive to proteasome inhibition and accumulate high-molecular weight, ubiquitylated proteins that are poorly degraded by the proteasome. These proteins are targets for the protease activity of purified DDI2. No evidence for DDI2 acting as a de-ubiquitylating enzyme was uncovered, which could suggest that it cleaves the ubiquitylated protein itself. In support of this idea, cleavage of transcription factor NRF1 is known to require DDI2 activity in vivo. We show that DDI2 is indeed capable of cleaving NRF1 in vitro but only when NRF1 protein is highly poly-ubiquitylated. Together, these data suggest that DDI2 is a ubiquitin-directed endoprotease.
    Keywords:  Bortezomib; DDI2; Ddi1; NFE2L1; NRF1; proteasome; proteasome inhibition; ubiquitin; ubiquitin protease
    DOI:  https://doi.org/10.1016/j.molcel.2020.05.035
  5. Mol Cell. 2020 May 28. pii: S1097-2765(20)30315-4. [Epub ahead of print]
    Cell Death in the Origin and Treatment of Cancer.
    Andreas Strasser, David L Vaux.
      Cell death, or, more specifically, cell suicide, is a process of fundamental importance to human health. Throughout our lives, over a million cells are produced every second. When organismal growth has stopped, to balance cell division, a similar number of cells must be removed. This is achieved by activation of molecular mechanisms that have evolved so that cells can destroy themselves. The first clues regarding the nature of one of these mechanisms came from studying genes associated with cancer, in particular the gene for BCL-2. Subsequent studies revealed that mutations or other defects that inhibit cell death allow cells to accumulate, prevent removal of cells with damaged DNA, and increase the resistance of malignant cells to chemotherapy. Knowledge of this mechanism has allowed development of drugs that kill cancer cells by directly activating the cell death machinery and by synergizing with conventional chemotherapy as well as targeted agents to achieve improved outcomes for cancer patients.
    DOI:  https://doi.org/10.1016/j.molcel.2020.05.014
  6. J Clin Immunol. 2020 Jun 08.
    Haploinsufficiency of A20 Due to Novel Mutations in TNFAIP3.
    Tingyan He, Yanyan Huang, Ying Luo, Yu Xia, LinLin Wang, Huan Zhang, Jiayun Ling, Jun Yang.
      Haploinsufficiency of A20 (HA20) is a newly described immune dysregulation disease due to the loss-of-function mutation in TNFAIP3. In the present study, we report six patients from four unrelated Chinese families with distinct pathogenic mutations in TNFAIP3, including three novel variants. All of the patients presented with early-onset autoimmune/auto-inflammatory diseases, including Crohn's disease, Behcet's disease, systemic lupus erythematosus, and unclassified auto-inflammatory syndrome. Immunological phenotype tests showed elevated levels of serum pro-inflammatory cytokines, reduced naïve B cells and TFH cells, an inverted CD4:CD8 ratio, and increased susceptibility to restimulation-induced cell death (RICD) and FASL-induced apoptosis in derived T cells. Insufficient expression of A20 was found in these patients. A20 truncated protein was detected in mutant-transfected 293T cells. Upon TNF-α stimulation, the NF-κB pathway was over-activated in both derived T cells of these patients and mutant-transfected Hela cells. In conclusion, clinical manifestations are diverse in patients with HA20, even in those with the same TNFAIP3 mutation. A20 inhibits the NF-κB pathway and plays a crucial role in the regulation of cell death. Haploinsufficiency of A20 leads to defects in both innate and adaptive immunity.
    Keywords:  A20 haploinsufficiency; TNFAIP3; auto-inflammatory disease; autoimmunity; immune dysregulation
    DOI:  https://doi.org/10.1007/s10875-020-00792-9
  7. J Dermatol. 2020 Jun 08.
    Circulating tumor necrosis factor-α DNA are elevated in psoriasis.
    Ryoko Sakamoto, Soichiro Sawamura, Ikko Kajihara, Hitomi Miyauchi, Kazumi Urata, Saki Otsuka-Maeda, Hisashi Kanemaru, Saori Kanazawa-Yamada, Noritoshi Honda, Katsunari Makino, Azusa Miyashita, Jun Aoi, Takamitsu Makino, Satoshi Fukushima, Hironobu Ihn.
      In psoriasis, tumor necrosis factor (TNF)-α is a key pro-inflammatory cytokine that activates keratinocytes to produce other inflammatory mediators. In addition, increased serum or plasma TNF-α levels are considered to be biomarkers of psoriasis. Circulating cell-free DNA (cfDNA) originates from apoptotic or necrotic cells and reflects the severity of cellular damage. Although cfDNA has recently attracted attention as a marker in the diagnosis and prognosis of various disorders, there are few reports of its clinical implications in the field of dermatology including psoriasis. The aim of this study was to investigate whether the TNF-α gene is present in the cfDNA, and whether its levels can be utilized as a biomarker for patients with psoriasis. cfDNA was isolated from serum samples of 79 patients with psoriasis vulgaris and 29 with psoriatic arthritis. The levels of TNF-α in the cfDNA were assessed by droplet digital polymerase chain reaction. In this study, we made two novel findings. First, circulating TNF-α DNA levels in the cfDNA were significantly higher in patients with psoriasis than in healthy controls. In addition, the area under the curve was 0.91, suggesting that serum TNF-α DNA levels are effective as a diagnostic biomarker. Second, the levels of TNF-α DNA copies in the cfDNA were positively correlated with the Psoriasis Area and Severity Index (PASI) score in the group of patients with a PASI score higher than 10. Generally, a PASI score of more than 10 is defined as severe psoriasis; therefore, the levels of TNF-α DNA copies in the cfDNA could be a biomarker for severity in patients with severe psoriasis. Further studies are needed to establish serum TNF-α DNA levels as a novel biomarker of psoriasis.
    Keywords:  biomarker; cell-free DNA; cytokine; inflammation; psoriasis
    DOI:  https://doi.org/10.1111/1346-8138.15422
  8. Cancer Cell. 2020 Jun 08. pii: S1535-6108(20)30262-2. [Epub ahead of print]37(6): 756-758
    p38 Kinase: A Key Target for Driving Potent T Cells for Adoptive Immunotherapy.
    Jack D Chan, Paul A Beavis, Phillip K Darcy.
      In this issue of Cancer Cell, Gurusamy et al. use a CRISPR-Cas9 screening approach to demonstrate that deletion of p38 increases multiple phenotypic qualities of effective anti-tumor T cells. Preconditioning T cells with a p38 inhibitor enhances anti-tumor efficacy of adoptive immunotherapy.
    DOI:  https://doi.org/10.1016/j.ccell.2020.05.012
  9. Chem Commun (Camb). 2020 Jun 10.
    Scaffold hopping enables direct access to more potent PROTACs with in vivo activity.
    George M Burslem, Daniel P Bondeson, Craig M Crews.
      Herein we employ a scaffold hopping approach to enhance the activity of a previously reported BCR-Abl PROTAC. This represents a significant advance in the PROTAC field since it can abrogate the need to optimize the linker to access a more potent degrader. The new PROTAC demonstrates a >10 fold increase in ability to induce degradation and demonstrates in vivo activity.
    DOI:  https://doi.org/10.1039/d0cc02201b
  10. Br J Dermatol. 2020 Jun 10.
    Biologics for psoriasis: what does drug survival tell us?
    E Veysey.
      
    DOI:  https://doi.org/10.1111/bjd.19189
  11. Front Chem. 2020 ;8 449
    Editorial: Probing the Ubiquitin Landscape.
    Monique P C Mulder, Zhihao Zhuang, Lei Liu, Benedikt M Kessler, Huib Ovaa.
      
    Keywords:  activity-based probes; applications; inhibitors; proteomics; toolbox development; ubiquitin(-like)
    DOI:  https://doi.org/10.3389/fchem.2020.00449
  12. SLAS Discov. 2020 Jun 12. 2472555220928911
    Activity-Based Screening Assay for Mono-ADP-Ribosylhydrolases.
    Sarah Wazir, Mirko M Maksimainen, Heli I Alanen, Albert Galera-Prat, Lari Lehtiö.
      ADP-ribosylation is a post-translational modification involved in the regulation of many vital cellular processes. This posttranslational modification is carried out by ADP-ribosyltransferases converting β-NAD+ into nicotinamide and a protein-linked ADP-ribosyl group or a chain of PAR. The reverse reaction, release of ADP-ribose from the acceptor molecule, is catalyzed by ADP-ribosylhydrolases. Several hydrolases contain a macrodomain fold, and activities of human macrodomain protein modules vary from reading or erasing mono- and poly-ADP-ribosylation. Macrodomains have been linked to diseases such as cancer, making them potential drug targets. Discovery of inhibitors requires robust biochemical tools mostly lacking for hydrolases, and here we describe an inhibitor screening assay against mono-ADP-ribosylhydrolyzing enzymes. The activity-based assay uses an α-NAD+, anomer of β-NAD+, which is accepted as a substrate by MacroD1, MacroD2, and ARH3 due to its resemblance to the protein-linked ADP-ribose. The amount of α-NAD+ present after hydrolysis is measured by chemically converting it on a microtiter plate to a fluorescent compound. We optimized the assay for MacroD2 and performed a proof-of-concept compound screening. Three compounds were identified as screening hits with micromolar potency. However, further characterization of the compounds identified them as protein destabilizers, excluding further follow-up studies. Validation and screening demonstrated the usability of the in vitro assay for MacroD2, and we also demonstrate the applicability of the assay as a tool for other human ADP-ribosylhydrolases.
    Keywords:  ADP-ribosylhydrolases; activity assay; macrodomain; screening assay
    DOI:  https://doi.org/10.1177/2472555220928911
  13. Nature. 2020 Jun;582(7811): 149
    Reform retractions to make them more transparent.
    Quan-Hoang Vuong.
      
    Keywords:  Communication; Publishing
    DOI:  https://doi.org/10.1038/d41586-020-01694-x
  14. Proc Natl Acad Sci U S A. 2020 Jun 10. pii: 201922729. [Epub ahead of print]
    Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand.
    Jun W Kim, Cesar P Marquez, R Andres Parra Sperberg, Jiaxiang Wu, Won G Bae, Po-Ssu Huang, E Alejandro Sweet-Cordero, Jennifer R Cochran.
      Interleukin-6 (IL-6) family cytokines signal through multimeric receptor complexes, providing unique opportunities to create novel ligand-based therapeutics. The cardiotrophin-like cytokine factor 1 (CLCF1) ligand has been shown to play a role in cancer, osteoporosis, and atherosclerosis. Once bound to ciliary neurotrophic factor receptor (CNTFR), CLCF1 mediates interactions to coreceptors glycoprotein 130 (gp130) and leukemia inhibitory factor receptor (LIFR). By increasing CNTFR-mediated binding to these coreceptors we generated a receptor superagonist which surpassed the potency of natural CNTFR ligands in neuronal signaling. Through additional mutations, we generated a receptor antagonist with increased binding to CNTFR but lack of binding to the coreceptors that inhibited tumor progression in murine xenograft models of nonsmall cell lung cancer. These studies further validate the CLCF1-CNTFR signaling axis as a therapeutic target and highlight an approach of engineering cytokine activity through a small number of mutations.
    Keywords:  ligand–receptor interaction; protein engineering; yeast surface display
    DOI:  https://doi.org/10.1073/pnas.1922729117
  15. Science. 2020 Jun 12. 368(6496): 1265-1269
    Very fast CRISPR on demand.
    Yang Liu, Roger S Zou, Shuaixin He, Yuta Nihongaki, Xiaoguang Li, Shiva Razavi, Bin Wu, Taekjip Ha.
      CRISPR-Cas systems provide versatile tools for programmable genome editing. Here, we developed a caged RNA strategy that allows Cas9 to bind DNA but not cleave until light-induced activation. This approach, referred to as very fast CRISPR (vfCRISPR), creates double-strand breaks (DSBs) at the submicrometer and second scales. Synchronized cleavage improved kinetic analysis of DNA repair, revealing that cells respond to Cas9-induced DSBs within minutes and can retain MRE11 after DNA ligation. Phosphorylation of H2AX after DNA damage propagated more than 100 kilobases per minute, reaching up to 30 megabases. Using single-cell fluorescence imaging, we characterized multiple cycles of 53BP1 repair foci formation and dissolution, with the first cycle taking longer than subsequent cycles and its duration modulated by inhibition of repair. Imaging-guided subcellular Cas9 activation further facilitated genomic manipulation with single-allele resolution. vfCRISPR enables DNA-repair studies at high resolution in space, time, and genomic coordinates.
    DOI:  https://doi.org/10.1126/science.aay8204
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