bims-tunefa 2020-05-17 papers

bims-tunefa

Biomed News

on Tumor necrosis factor superfamily and post-translational modifications

Issue of 2020–05–17
forty-two papers selected by
John Silke, Walter and Eliza Hall Institute of Medical Research

Proteolysis-targeting chimera (PROTAC) for targeted protein degradation and cancer therapy.
The HOIL-1L ligase modulates immune signalling and cell death via monoubiquitination of LUBAC.
Targeted Degradation of SLC Transporters Reveals Amenability of Multi-Pass Transmembrane Proteins to Ligand-Induced Proteolysis.
Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders.
The death-inducing activity of RIPK1 is regulated by the pH environment.
A Cell-Based Target Engagement Assay for the Identification of Cereblon E3 Ubiquitin Ligase Ligands and Their Application in HDAC6 Degraders.
Molecular Mechanisms of the Teratogenic Effects of Thalidomide.
Quantitative single-molecule imaging of TNFR1 reveals zafirlukast as antagonist of TNFR1 clustering and TNFα-induced NF-ĸB signaling.
Structural optimization of a TNFR1-selective antagonistic TNF-α mutant to create new-modality TNF-regulating biologics.
Discovery of IAP-recruiting BCL-XL PROTACs as potent degraders across multiple cancer cell lines.
Role of Extrinsic Apoptotic Signaling Pathway during Definitive Erythropoiesis in Normal Patients and in Patients with β-Thalassemia.
Ubiquitin chain-elongating enzyme UBE2S activates the RING E3 ligase APC/C for substrate priming.
Biological functions and therapeutic opportunities of soluble cytokine receptors.
Uncovering the PIDDosome and caspase-2 as regulators of organogenesis and cellular differentiation.
Less-well known functions of cyclin/CDK complexes.
Targeting RIPK3 oligomerization blocks necroptosis without inducing apoptosis.
TDP-43 a protein central to amyotrophic lateral sclerosis is destabilized by Tankyrase-1/2.
Dysregulated haematopoietic stem cell behaviour in myeloid leukaemogenesis.
Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma.
Basal Signalling Through Death Receptor 5 and Caspase 3 Activates p38 Kinase to Regulate Serum Response Factor (SRF)-Mediated MyoD Transcription.
A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi.
The Role of TNFR2 and DR3 in the In Vivo Expansion of Tregs in T Cell Depleting Transplantation Regimens.
Platelets Fuel the Inflammasome Activation of Innate Immune Cells.
Taking aim with IAP antagonists at triple-negative breast cancer: a moving target no more?
p53: 800 million years of evolution and 40 years of discovery.
Nutlin-3a suppresses poly (ADP-ribose) polymerase 1 by mechanisms different from conventional PARP1 suppressors in a human breast cancer cell line.
TRAF4 knockdown triggers synergistic lethality with simultaneous PARP1 inhibition in endometrial cancer.
A combinatorial view of old and new RNA polymerase II modifications.
Cell Surface Labeling by Engineered Extracellular Vesicles.
Guselkumab versus secukinumab for the treatment of moderate-to-severe psoriasis: a critical appraisal.
TNF-α Pretreatment Improves the Survival and Function of Transplanted Human Neural Progenitor Cells Following Hypoxic-Ischemic Brain Injury.
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Discovery of novel resorcinol diphenyl ether-based PROTAC-like molecules as dual inhibitors and degraders of PD-L1.
Lipidomics Profiling of Hidradenitis Suppurativa Skin Lesions Reveals Lipoxygenase Pathway Dysregulation and Accumulation of Pro-Inflammatory Leukotriene B4.
Concerns about the safety of anti-TNF agents when treating rheumatic diseases.
Transcription Factors and DNA Play Hide and Seek.
COVID-19 and biologics for psoriasis: a high-epidemic area experience - Bergamo, Lombardy, Italy.
Phosphatidylserine exposure in living cells.
Reevaluation of Lung Injury in TNF-Induced Shock: The Role of the Acid Sphingomyelinase.
The p38-interacting protein p38IP suppresses TCR and LPS signaling by targeting TAK1.
Anti-TNF response falls short in real-world cohort.
TAK1 lessens the activity of the paracaspase MALT1 during T cell receptor signaling.

J Hematol Oncol. 2020 May 13. 13(1): 50

Proteolysis-targeting chimera (PROTAC) for targeted protein degradation and cancer therapy.

Xin Li, Yongcheng Song.

  Proteolysis-targeting chimera (PROTAC) has been developed to be a useful technology for targeted protein degradation. A bifunctional PROTAC molecule consists of a ligand (mostly small-molecule inhibitor) of the protein of interest (POI) and a covalently linked ligand of an E3 ubiquitin ligase (E3). Upon binding to the POI, the PROTAC can recruit E3 for POI ubiquitination, which is subjected to proteasome-mediated degradation. PROTAC complements nucleic acid-based gene knockdown/out technologies for targeted protein reduction and could mimic pharmacological protein inhibition. To date, PROTACs targeting ~ 50 proteins, many of which are clinically validated drug targets, have been successfully developed with several in clinical trials for cancer therapy. This article reviews PROTAC-mediated degradation of critical oncoproteins in cancer, particularly those in hematological malignancies. Chemical structures, cellular and in vivo activities, pharmacokinetics, and pharmacodynamics of these PROTACs are summarized. In addition, potential advantages, challenges, and perspectives of PROTAC technology in cancer therapy are discussed.

Keywords:  Cancer therapy; Hematological malignancies; PROTAC; Targeted protein degradation

DOI:  https://doi.org/10.1186/s13045-020-00885-3
Nat Cell Biol. 2020 May 11.

The HOIL-1L ligase modulates immune signalling and cell death via monoubiquitination of LUBAC.

Yasuhiro Fuseya, Hiroaki Fujita, Minsoo Kim, Fumiaki Ohtake, Akira Nishide, Katsuhiro Sasaki, Yasushi Saeki, Keiji Tanaka, Ryosuke Takahashi, Kazuhiro Iwai.

The linear ubiquitin chain assembly complex (LUBAC), which consists of HOIP, SHARPIN and HOIL-1L, promotes NF-κB activation and protects against cell death by generating linear ubiquitin chains. LUBAC contains two RING-IBR-RING (RBR) ubiquitin ligases (E3), and the HOIP RBR is responsible for catalysing linear ubiquitination. We found that HOIL-1L RBR plays a crucial role in regulating LUBAC. HOIL-1L RBR conjugates monoubiquitin onto all LUBAC subunits, followed by HOIP-mediated conjugation of linear chains onto monoubiquitin, and these linear chains attenuate the functions of LUBAC. The introduction of E3-defective HOIL-1L mutants into cells augmented linear ubiquitination, which protected the cells against Salmonella infection and cured dermatitis caused by reduced LUBAC levels due to SHARPIN loss. Our results reveal a regulatory mode of E3 ligases in which the accessory E3 in LUBAC downregulates the main E3 by providing preferred substrates for autolinear ubiquitination. Thus, inhibition of HOIL-1L E3 represents a promising strategy for treating severe infections or immunodeficiency.

DOI: https://doi.org/10.1038/s41556-020-0517-9
Cell Chem Biol. 2020 Apr 18. pii: S2451-9456(20)30117-3. [Epub ahead of print]

Targeted Degradation of SLC Transporters Reveals Amenability of Multi-Pass Transmembrane Proteins to Ligand-Induced Proteolysis.

Ariel Bensimon, Mattia D Pizzagalli, Felix Kartnig, Vojtech Dvorak, Patrick Essletzbichler, Georg E Winter, Giulio Superti-Furga.

  With more than 450 members, the solute carrier (SLC) group of proteins represents the largest class of transporters encoded in the human genome. Their several-pass transmembrane domain structure and hydrophobicity contribute to the orphan status of many SLCs, devoid of known cargos or chemical inhibitors. We report that SLC proteins belonging to different families and subcellular compartments are amenable to induced degradation by heterobifunctional ligands. Engineering endogenous alleles via the degradation tag (dTAG) technology enabled chemical control of abundance of the transporter protein, SLC38A2. Moreover, we report the design of d9A-2, a chimeric compound engaging several members of the SLC9 family and leading to their degradation. d9A-2 impairs cellular pH homeostasis and promotes cell death in a range of cancer cell lines. These findings open the era of SLC-targeting chimeric degraders and demonstrate potential access of multi-pass transmembrane proteins of different subcellular localizations to the chemically exploitable degradation machinery.

Keywords:  E3 ligase; SLC38A2; SLC9A1; degrader; multi-pass transmembrane protein; proteasome; proteolysis targeting chimera (PROTAC); solute carrier; targeted degradation; transporter

DOI:  https://doi.org/10.1016/j.chembiol.2020.04.003
Int J Mol Sci. 2020 May 11. pii: E3381. [Epub ahead of print]21(9):

Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders.

Daisuke Oikawa, Yusuke Sato, Hidefumi Ito, Fuminori Tokunaga.

  The linear ubiquitin chain assembly complex (LUBAC) is a ubiquitin ligase composed of the Heme-oxidized IRP2 ubiquitin ligase-1L (HOIL-1L), HOIL-1L-interacting protein (HOIP), and Shank-associated RH domain interactor (SHARPIN) subunits. LUBAC specifically generates the N-terminal Met1-linked linear ubiquitin chain and regulates acquired and innate immune responses, such as the canonical nuclear factor-κB (NF-κB) and interferon antiviral pathways. Deubiquitinating enzymes, OTULIN and CYLD, physiologically bind to HOIP and control its function by hydrolyzing the linear ubiquitin chain. Moreover, proteins containing linear ubiquitin-specific binding domains, such as NF-κB-essential modulator (NEMO), optineurin, A20-binding inhibitors of NF-κB (ABINs), and A20, modulate the functions of LUBAC, and the dysregulation of the LUBAC-mediated linear ubiquitination pathway induces cancer and inflammatory, autoimmune, and neurodegenerative diseases. Therefore, inhibitors of LUBAC would be valuable to facilitate investigations of the molecular and cellular bases for LUBAC-mediated linear ubiquitination and signal transduction, and for potential therapeutic purposes. We identified and characterized α,β-unsaturated carbonyl-containing chemicals, named HOIPINs (HOIP inhibitors), as LUBAC inhibitors. We summarize recent advances in elucidations of the pathophysiological functions of LUBAC-mediated linear ubiquitination and identifications of its regulators, toward the development of LUBAC inhibitors.

Keywords:  LUBAC; NF-κB; inflammation; inhibitor; innate immune; interferon; ubiquitin

DOI:  https://doi.org/10.3390/ijms21093381
Sci Signal. 2020 May 12. pii: eaay7066. [Epub ahead of print]13(631):

The death-inducing activity of RIPK1 is regulated by the pH environment.

Kenta Moriwaki, Sakthi Balaji, Francis Ka-Ming Chan.

Receptor-interacting protein kinase 1 (RIPK1) is a serine/threonine kinase that dictates whether cells survive or die in response to the cytokine tumor necrosis factor (TNF) and other inflammatory stimuli. The activity of RIPK1 is tightly controlled by multiple posttranslational modification mechanisms, including ubiquitination and phosphorylation. Here, we report that sensitivity to TNF-induced, RIPK1-dependent cell death was tunable by the pH environment. We found that an acidic extracellular pH, which led to a concomitant decrease in intracellular pH, impaired the kinase activation of RIPK1 and autophosphorylation at Ser166 Consequently, formation of the cytosolic death-inducing complex II and subsequent RIPK1-dependent necroptosis and apoptosis were inhibited. By contrast, low pH did not affect the formation of membrane-anchored TNFR1-containing signaling complex (complex I), RIPK1 ubiquitination, and NF-κB activation. TNF-induced cell death in Ripk1 -/- cells was not sensitive to pH changes. Furthermore, mutation of the conserved His151 abolished the pH dependence of RIPK1 activation, suggesting that this histidine residue functions as a proton acceptor to modulate RIPK1 activity in response to pH changes. These results revealed an unexpected environmental factor that controls the death-inducing activity of RIPK1.

DOI: https://doi.org/10.1126/scisignal.aay7066
Cell Chem Biol. 2020 May 10. pii: S2451-9456(20)30145-8. [Epub ahead of print]

A Cell-Based Target Engagement Assay for the Identification of Cereblon E3 Ubiquitin Ligase Ligands and Their Application in HDAC6 Degraders.

Ka Yang, Yu Zhao, Xueqing Nie, Hao Wu, Bo Wang, Chelsi M Almodovar-Rivera, Haibo Xie, Weiping Tang.

  Proteolysis-targeting chimeras (PROTACs) is a paradigm shift for small-molecule drug discovery. However, limited E3 ubiquitin ligase ligands with cellular activity are available. In vitro binding assays involve the expression and purification of a large amount of proteins and they often yield ligands that are inactive in cell-based assays due to poor cell permeability, stability, and other reasons. Herein, we report the development of a practical and efficient cell-based target engagement assay to evaluate the binding affinity of a small library of cereblon ligands to its E3 ligase in cells. Selected cell-permeable E3 ligase ligands derived from this assay are then used to construct HDAC6 degraders with cellular protein degradation activity. Because the assay does not involve any genetic engineering, it is relatively easy to transfer from one cell type to a different one.

Keywords:  CRBN; E3 ligase; HDAC6; IMiD; Lenalidomide; PROTAC; Pomalidomide; Thalidomide; target engagement; targeted protein degradation

DOI:  https://doi.org/10.1016/j.chembiol.2020.04.008
Pharmaceuticals (Basel). 2020 May 13. pii: E95. [Epub ahead of print]13(5):

Molecular Mechanisms of the Teratogenic Effects of Thalidomide.

Tomoko Asatsuma-Okumura, Takumi Ito, Hiroshi Handa.

  Thalidomide was sold worldwide as a sedative over 60 years ago, but it was quickly withdrawn from the market due to its teratogenic effects. Thalidomide was later found to have therapeutic effects in several diseases, although the molecular mechanisms remained unclear. The discovery of cereblon (CRBN), the direct target of thalidomide, a decade ago greatly improved our understanding of its mechanism of action. Accumulating evidence has shown that CRBN functions as a substrate of Cullin RING E3 ligase (CRL4CRBN), whose specificity is controlled by ligands such as thalidomide. For example, lenalidomide and pomalidomide, well-known thalidomide derivatives, degrade the neosubstrates Ikaros and Aiolos, resulting in anti-proliferative effects in multiple myeloma. Recently, novel CRBN-binding drugs have been developed. However, for the safe handling of thalidomide and its derivatives, a greater understanding of the mechanisms of its adverse effects is required. The teratogenic effects of thalidomide occur in multiple tissues in the developing fetus and vary in phenotype, making it difficult to clarify this issue. Recently, several CRBN neosubstrates (e.g., SALL4 (Spalt Like Transcription Factor 4) and p63 (Tumor Protein P63)) have been identified as candidate mediators of thalidomide teratogenicity. In this review, we describe the current understanding of molecular mechanisms of thalidomide, particularly in the context of its teratogenicity.

Keywords:  PROTACs; cereblon; lenalidomide; protein degradation; teratogenicity; thalidomide; ubiquitin

DOI:  https://doi.org/10.3390/ph13050095
J Leukoc Biol. 2020 May 13.

Quantitative single-molecule imaging of TNFR1 reveals zafirlukast as antagonist of TNFR1 clustering and TNFα-induced NF-ĸB signaling.

Nadine Weinelt, Christos Karathanasis, Sonja Smith, Juliane Medler, Sebastian Malkusch, Simone Fulda, Harald Wajant, Mike Heilemann, Sjoerd J L van Wijk.

  TNFR 1 is a crucial regulator of NF-ĸB-mediated proinflammatory cell survival responses and programmed cell death (PCD). Deregulation of TNFα- and TNFR1-controlled NF-ĸB signaling underlies major diseases, like cancer, inflammation, and autoimmune diseases. Therefore, although being routinely used, antagonists of TNFα might also affect TNFR2-mediated processes, so that alternative approaches to directly antagonize TNFR1 are beneficial. Here, we apply quantitative single-molecule localization microscopy (SMLM) of TNFR1 in physiologic cellular settings to validate and characterize TNFR1 inhibitory substances, exemplified by the recently described TNFR1 antagonist zafirlukast. Treatment of TNFR1-mEos2 reconstituted TNFR1/2 knockout mouse embryonic fibroblasts (MEFs) with zafirlukast inhibited both ligand-independent preligand assembly domain (PLAD)-mediated TNFR1 dimerization as well as TNFα-induced TNFR1 oligomerization. In addition, zafirlukast-mediated inhibition of TNFR1 clustering was accompanied by deregulation of acute and prolonged NF-ĸB signaling in reconstituted TNFR1-mEos2 MEFs and human cervical carcinoma cells. These findings reveal the necessity of PLAD-mediated, ligand-independent TNFR1 dimerization for NF-ĸB activation, highlight the PLAD as central regulator of TNFα-induced TNFR1 oligomerization, and demonstrate that TNFR1-mEos2 MEFs can be used to investigate TNFR1-antagonizing compounds employing single-molecule quantification and functional NF-ĸB assays at physiologic conditions.

Keywords:  CysLTR1; Cysteine-Rich Domain (CRD); Pre-Ligand Assembly Domain (PLAD); Single-Molecule Localization Microscopy (SMLM)

DOI:  https://doi.org/10.1002/JLB.2AB0420-572RR
J Biol Chem. 2020 May 12. pii: jbc.RA120.012723. [Epub ahead of print]

Structural optimization of a TNFR1-selective antagonistic TNF-α mutant to create new-modality TNF-regulating biologics.

Masaki Inoue, Yuta Tsuji, Chinatsu Yoshimine, Shota Enomoto, Yuki Morita, Natsuki Osaki, Masahiro Kunishige, Midori Miki, Shota Amano, Kanako Yamashita, Haruhiko Kamada, Yasuo Tsutsumi, Shin-Ichi Tsunoda.

  Excessive activation of the proinflammatory cytokine tumor necrosis factor-α (TNF-α) is a major cause of autoimmune diseases, including rheumatoid arthritis. TNF-α induces immune responses via TNF receptor 1 (TNFR1) and TNFR2. Signaling via TNFR1 induces proinflammatory responses, whereas TNFR2 signaling is suggested to suppress the pathophysiology of inflammatory diseases. Therefore, selective inhibition of TNFR1 signaling and preservation of TNFR2 signaling activities may be beneficial for managing autoimmune diseases. To this end, we developed a TNFR1-selective, antagonistic TNF-α mutant (R1antTNF). Here, we developed an R1antTNF derivative, scR1antTNF-Fc, which represents a single-chain form of trimeric R1antTNF with a human IgG-Fc domain. scR1antTNF-Fc had properties similar to those of R1antTNF, including TNFR1-selective binding avidity, TNFR1 antagonistic activity, and thermal stability, and had a significantly extended plasma half-life in vivo In a murine rheumatoid arthritis model, scR1antTNF-Fc and 40-kDa PEG-scR1antTNF (a previously reported PEGylated form) delayed the onset of collagen-induced arthritis, suppressed arthritis progression in mice, and required a reduced frequency of administration. Interestingly, with these biologic treatments, we observed an increased ratio of regulatory T cells to conventional T cells in lymph nodes compared with etanercept, a commonly used TNF-inhibitor. Therefore, scR1antTNF-Fc and 40-kDa PEG-scR1antTNF indirectly induced immunosuppression. These results suggest that selective TNFR1 inhibition benefits the management of autoimmune diseases and that R1antTNF derivatives hold promise as new-modality TNF-regulating biologics.

Keywords:  antagonist; arthritis; autoimmune disease; cytokine; drug delivery; drug design; forkhead box P3 (FOXP3); inflammation; inhibition mechanism; protein engineering; single-chain; tumor necrosis factor (TNF)

DOI:  https://doi.org/10.1074/jbc.RA120.012723
Eur J Med Chem. 2020 May 04. pii: S0223-5234(20)30367-6. [Epub ahead of print]199 112397

Discovery of IAP-recruiting BCL-XL PROTACs as potent degraders across multiple cancer cell lines.

Xuan Zhang, Yonghan He, Peiyi Zhang, Vivekananda Budamagunta, Dongwen Lv, Dinesh Thummuri, Yang Yang, Jing Pei, Yaxia Yuan, Daohong Zhou, Guangrong Zheng.

  Targeting BCL-XL via PROTACs is a promising strategy in reducing BCL-XL inhibition associated platelet toxicity. Recently, we reported potent BCL-XL PROTAC degraders that recruit VHL or CRBN E3 ligase. However, low protein expression or mutation of the responsible E3 ligase has been known to result in decreased protein degradation efficiency of the corresponding PROTACs. To overcome these mechanisms of resistance, PROTACs based on recruiting alternative E3 ligases could be generated. Thus, we designed and synthesized a series of PROTACs that recruit IAP E3 ligases for BCL-XL degradation. Among those PROTACs, compound 8a efficiently degrades BCL-XL in malignant T-cell lymphoma cell line MyLa 1929 while CRBN-based PROTACs that have high potency in other cancer cell lines show compromised potency, likely due to the low CRBN expression. Moreover, compared with the parent compound ABT-263, PROTAC 8a shows comparable cell killing effects in MyLa 1929 cells whereas the on-target platelet toxicity is significantly reduced. Our findings expand the anti-tumor spectra of BCL-XL degraders and further highlight the importance of selecting suitable E3 members to achieve effective cellular activity.

Keywords:  BCL-X(L); Degradation; IAPs; PROTAC; SNIPER

DOI:  https://doi.org/10.1016/j.ejmech.2020.112397
Int J Mol Sci. 2020 May 08. pii: E3325. [Epub ahead of print]21(9):

Role of Extrinsic Apoptotic Signaling Pathway during Definitive Erythropoiesis in Normal Patients and in Patients with β-Thalassemia.

Olga Raducka-Jaszul, Dżamila M Bogusławska, Natalia Jędruchniewicz, Aleksander F Sikorski.

  Apoptosis is a process of programmed cell death which has an important role in tissue homeostasis and in the control of organism development. Here, we focus on information concerning the role of the extrinsic apoptotic pathway in the control of human erythropoiesis. We discuss the role of tumor necrosis factor α (TNFα), tumor necrosis factor ligand superfamily member 6 (FasL), tumor necrosis factor-related apoptosis-inducing (TRAIL) and caspases in normal erythroid maturation. We also attempt to initiate a discussion on the observations that mature erythrocytes contain most components of the receptor-dependent apoptotic pathway. Finally, we point to the role of the extrinsic apoptotic pathway in ineffective erythropoiesis of different types of β-thalassemia.

Keywords:  Fas/FasL; TRAIL/TRAILR; apoptosis: apoptotic extrinsic pathway; death domains; erythropoiesis; β-thalassemia

DOI:  https://doi.org/10.3390/ijms21093325
Nat Struct Mol Biol. 2020 May 11.

Ubiquitin chain-elongating enzyme UBE2S activates the RING E3 ligase APC/C for substrate priming.

Raquel C Martinez-Chacin, Tatyana Bodrug, Derek L Bolhuis, Katarzyna M Kedziora, Thomas Bonacci, Alban Ordureau, Morgan E Gibbs, Florian Weissmann, Renping Qiao, Gavin D Grant, Jeanette G Cook, Jan-Michael Peters, J Wade Harper, Michael J Emanuele, Nicholas G Brown.

The interplay between E2 and E3 enzymes regulates the polyubiquitination of substrates in eukaryotes. Among the several RING-domain E3 ligases in humans, many utilize two distinct E2s for polyubiquitination. For example, the cell cycle regulatory E3, human anaphase-promoting complex/cyclosome (APC/C), relies on UBE2C to prime substrates with ubiquitin (Ub) and on UBE2S to extend polyubiquitin chains. However, the potential coordination between these steps in ubiquitin chain formation remains undefined. While numerous studies have unveiled how RING E3s stimulate individual E2s for Ub transfer, here we change perspective to describe a case where the chain-elongating E2 UBE2S feeds back and directly stimulates the E3 APC/C to promote substrate priming and subsequent multiubiquitination by UBE2C. Our work reveals an unexpected model for the mechanisms of RING E3-dependent ubiquitination and for the diverse and complex interrelationship between components of the ubiquitination cascade.

DOI: https://doi.org/10.1038/s41594-020-0424-6
Cytokine Growth Factor Rev. 2020 Apr 18. pii: S1359-6101(20)30054-X. [Epub ahead of print]

Biological functions and therapeutic opportunities of soluble cytokine receptors.

Juliane Lokau, Christoph Garbers.

  Cytokines control the immune system by regulating the proliferation, differentiation and function of immune cells. They activate their target cells through binding to specific receptors, which either are transmembrane proteins or attached to the cell-surface via a GPI-anchor. Different tissues and individual cell types have unique expression profiles of cytokine receptors, and consequently this expression pattern dictates to which cytokines a given cell can respond. Furthermore, soluble variants of several cytokine receptors exist, which are generated by different molecular mechanisms, namely differential mRNA splicing, proteolytic cleavage of the membrane-tethered precursors, and release on extracellular vesicles. These soluble receptors shape the function of cytokines in different ways: they can serve as antagonistic decoy receptors which compete with their membrane-bound counterparts for the ligand, or they can form functional receptor/cytokine complexes which act as agonists and can even activate cells that would usually not respond to the ligand alone. In this review, we focus on the IL-2 and IL-6 families of cytokines and the so-called Th2 cytokines. We summarize for each cytokine which soluble receptors exist, were they originate from, how they are generated, and what their biological functions are. Furthermore, we give an outlook on how these soluble receptors can be exploited for therapeutic purposes.

Keywords:  cytokine receptors; proteolysis; soluble cytokine receptors; therapy

DOI:  https://doi.org/10.1016/j.cytogfr.2020.04.003
Cell Death Differ. 2020 May 15.

Uncovering the PIDDosome and caspase-2 as regulators of organogenesis and cellular differentiation.

Valentina C Sladky, Andreas Villunger.

The PIDDosome is a multiprotein complex that drives activation of caspase-2, an endopeptidase originally implicated in apoptosis. Yet, unlike other caspases involved in cell death and inflammation, caspase-2 seems to exert additional versatile functions unrelated to cell death. These emerging roles range from control of transcription factor activity to ploidy surveillance. Thus, caspase-2 and the PIDDosome act as a critical regulatory unit controlling cellular differentiation processes during organogenesis and regeneration. These newly established functions of the PIDDosome and its downstream effector render its components attractive targets for drug-development aiming to prevent fatty liver diseases, neurodegenerative disorders or osteoporosis.

DOI: https://doi.org/10.1038/s41418-020-0556-6
Semin Cell Dev Biol. 2020 May 05. pii: S1084-9521(19)30203-4. [Epub ahead of print]

Less-well known functions of cyclin/CDK complexes.

Nathan Palmer, Philipp Kaldis.

  Cyclin-dependent kinases (CDKs) are activated by cyclins, which play important roles in dictating the actions of CDK/cyclin complexes. Cyclin binding influences the substrate specificity of these complexes in addition to their susceptibility to inhibition or degradation. CDK/cyclin complexes are best known to promote cell cycle progression in the mitotic cell cycle but are also crucial for important cellular processes not strictly associated with cellular division. This chapter primarily explores the understudied topic of CDK/cyclin complex functionality during the DNA damage response. We detail how CDK/cyclin complexes perform dual roles both as targets of DNA damage checkpoint signaling as well as effectors of DNA repair. Additionally, we discuss the potential CDK-independent roles of cyclins in these processes and the impact of such roles in human diseases such as cancer. Our goal is to place the spotlight on these important functions of cyclins either acting as independent entities or within CDK/cyclin complexes which have attracted less attention in the past. We consider that this will be important for a more complete understanding of the intricate functions of cell cycle proteins in the DNA damage response.

Keywords:  Checkpoint; Cyclin-Dependent kinase (CDK); Cyclins; DNA damage; DNA repair; Double-Strand breaks

DOI:  https://doi.org/10.1016/j.semcdb.2020.04.003
FEBS Lett. 2020 May 15.

Targeting RIPK3 oligomerization blocks necroptosis without inducing apoptosis.

Wenjuan Li, Hengxiao Ni, Shaofeng Wu, Shang Han, Chang'an Chen, Li Li, Yunzhan Li, Fu Gui, Jiahuai Han, Xianming Deng.

  Receptor-interacting serine/threonine-protein kinase 3 (RIPK3) is a central protein in necroptosis with great potential as a target for treating necroptosis-associated diseases, such as Crohn's disease. However, blockade of RIPK3 kinase activity leads to unexpected RIPK3-initiated apoptosis. Herein, we found that PP2, a known SRC inhibitor, inhibits TNF-α-induced necroptosis without initiating apoptosis. Further investigation showed that PP2 acts as an inhibitor of not only SRC but also RIPK3. PP2 does not disturb the integrity of the RIPK1-RIPK3-mixed lineage kinase domain-like pseudokinase (MLKL) necroptosome or the autophosphorylation of RIPK3 at T231/S232 but disrupts RIPK3 oligomerization, thereby impairing the phosphorylation and oligomerization of MLKL. These results demonstrate the essential role of RIPK3 oligomerization in necroptosis and suggest a potential RIPK3 oligomerization-targeting strategy for therapeutic development.

Keywords:  RIPK3; apoptosis; necroptosis; oligomerization; phosphorylation

DOI:  https://doi.org/10.1002/1873-3468.13812
J Cell Sci. 2020 May 14. pii: jcs.245811. [Epub ahead of print]

TDP-43 a protein central to amyotrophic lateral sclerosis is destabilized by Tankyrase-1/2.

Leeanne McGurk, Olivia Rifai, Nancy M Bonini.

  In >95% of amyotrophic lateral sclerosis (ALS) and ∼45% of frontotemporal degeneration (FTD), the RNA/DNA-binding protein TDP-43 is cleared from the nucleus and abnormally accumulates in the cytoplasm of affected brain cells. Although the cellular triggers of disease pathology remain enigmatic, mounting evidence implicates the poly(ADP-ribose) polymerases (PARPs) in TDP-43 neurotoxicity. Here we show that inhibition of the PARP enzymes Tankyrase 1 and Tankyrase 2 (referred to as Tnks-1/2) protect primary rodent neurons from TDP-43-associated neurotoxicity. We demonstrate that Tnks-1/2 interacts with TDP-43 via a newly defined Tankyrase-binding domain. Upon investigating the functional effect, we find that interaction with Tnks-1/2 inhibits the ubiquitination and proteasomal turnover of TDP-43, leading to its stabilization. We further show that proteasomal turnover of TDP-43 occurs preferentially in the nucleus; our data indicate that Tnks-1/2 stabilizes TDP-43 by promoting cytoplasmic accumulation, which sequesters the protein from nuclear proteasome degradation. Thus, Tnks-1/2 activity modulates TDP-43 and is a potential therapeutic target in diseases associated with TDP-43, such as ALS and FTD.

Keywords:  ALS; FTD; PARP; Poly(ADP-ribose); Proteasome; Ubiquitin

DOI:  https://doi.org/10.1242/jcs.245811
Nat Rev Cancer. 2020 May 15.

Dysregulated haematopoietic stem cell behaviour in myeloid leukaemogenesis.

Masayuki Yamashita, Paul V Dellorusso, Oakley C Olson, Emmanuelle Passegué.

Haematopoiesis is governed by haematopoietic stem cells (HSCs) that produce all lineages of blood and immune cells. The maintenance of blood homeostasis requires a dynamic response of HSCs to stress, and dysregulation of these adaptive-response mechanisms underlies the development of myeloid leukaemia. Leukaemogenesis often occurs in a stepwise manner, with genetic and epigenetic changes accumulating in pre-leukaemic HSCs prior to the emergence of leukaemic stem cells (LSCs) and the development of acute myeloid leukaemia. Clinical data have revealed the existence of age-related clonal haematopoiesis, or the asymptomatic clonal expansion of mutated blood cells in the elderly, and this phenomenon is connected to susceptibility to leukaemic transformation. Here we describe how selection for specific mutations that increase HSC competitive fitness, in conjunction with additional endogenous and environmental changes, drives leukaemic transformation. We review the ways in which LSCs take advantage of normal HSC properties to promote survival and expansion, thus underlying disease recurrence and resistance to conventional therapies, and we detail our current understanding of leukaemic 'stemness' regulation. Overall, we link the cellular and molecular mechanisms regulating HSC behaviour with the functional dysregulation of these mechanisms in myeloid leukaemia and discuss opportunities for targeting LSC-specific mechanisms for the prevention or cure of malignant diseases.

DOI: https://doi.org/10.1038/s41568-020-0260-3
Cell Res. 2020 May 12.

Whole-genome sequencing of 508 patients identifies key molecular features associated with poor prognosis in esophageal squamous cell carcinoma.

Yongping Cui, Hongyan Chen, Ruibin Xi, Heyang Cui, Yahui Zhao, Enwei Xu, Ting Yan, Xiaomei Lu, Furong Huang, Pengzhou Kong, Yang Li, Xiaolin Zhu, Jiawei Wang, Wenjie Zhu, Jie Wang, Yanchun Ma, Yong Zhou, Shiping Guo, Ling Zhang, Yiqian Liu, Bin Wang, Yanfeng Xi, Ruifang Sun, Xiao Yu, Yuanfang Zhai, Fang Wang, Jian Yang, Bin Yang, Caixia Cheng, Jing Liu, Bin Song, Hongyi Li, Yi Wang, Yingchun Zhang, Xiaolong Cheng, Qimin Zhan, Yanhong Li, Zhihua Liu.

Esophageal squamous cell carcinoma (ESCC) is a poor-prognosis cancer type with limited understanding of its molecular etiology. Using 508 ESCC genomes, we identified five novel significantly mutated genes and uncovered mutational signature clusters associated with metastasis and patients' outcomes. Several functional assays implicated that NFE2L2 may act as a tumor suppressor in ESCC and that mutations in NFE2L2 probably impaired its tumor-suppressive function, or even conferred oncogenic activities. Additionally, we found that the NFE2L2 mutations were significantly associated with worse prognosis of ESCC. We also identified potential noncoding driver mutations including hotspot mutations in the promoter region of SLC35E2 that were correlated with worse survival. Approximately 5.9% and 15.2% of patients had high tumor mutation burden or actionable mutations, respectively, and may benefit from immunotherapy or targeted therapies. We found clinically relevant coding and noncoding genomic alterations and revealed three major subtypes that robustly predicted patients' outcomes. Collectively, we report the largest dataset of genomic profiling of ESCC useful for developing ESCC-specific biomarkers for diagnosis and treatment.

DOI: https://doi.org/10.1038/s41422-020-0333-6
J Mol Signal. 2020 May 08. 14 1

Basal Signalling Through Death Receptor 5 and Caspase 3 Activates p38 Kinase to Regulate Serum Response Factor (SRF)-Mediated MyoD Transcription.

Jason A Ross, Brianna Barrett, Victoria Bensimon, Girish Shukla, Crystal M Weyman.

  We have previously reported that stable expression of a dominant negative Death Receptor 5 (dnDR5) in skeletal myoblasts results in decreased basal caspase activity and decreased mRNA and protein expression of the muscle regulatory transcription factor MyoD in growth medium (GM), resulting in inhibited differentation when myoblasts are then cultured in differentiation media (DM). Further, this decreased level of MyoD mRNA was not a consequence of altered message stability, but rather correlated with decreased acetylation of histones in the distal regulatory region (DRR) of the MyoD extended promoter known to control MyoD transcription. As serum response factor (SRF) is the transcription factor known to be responsible for basal MyoD expression in GM, we compared the level of SRF binding to the non-canonical serum response element (SRE) within the DRR in parental and dnDR5 expressing myoblasts. Herein, we report that stable expression of dnDR5 resulted in decreased levels of serum response factor (SRF) binding to the CArG box in the SRE of the DRR. Total SRF expression levels were not affected, but phosphorylation indicative of SRF activation was impaired. This decreased SRF phosphorylation correlated with decreased phosphorylation-induced activation of p38 kinase. Moreover, the aforementioned signaling events affected by expression of dnDR5 could be appropriately recapitulated using either a pharmacological inhibitor of caspase 3 or p38 kinase. Thus, our results have established a signaling pathway from DR5 through caspases to p38 kinase activation, to SRF activation and the basal expression of MyoD.

Keywords:  DR5; MyoD; SRF; caspase 3; p38 kinase

DOI:  https://doi.org/10.5334/1750-2187-14-1
Nat Commun. 2020 May 11. 11(1): 2343

A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi.

Jason M Berk, Christopher Lim, Judith A Ronau, Apala Chaudhuri, Hongli Chen, John F Beckmann, J Patrick Loria, Yong Xiong, Mark Hochstrasser.

Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.

DOI: https://doi.org/10.1038/s41467-020-15985-4
Int J Mol Sci. 2020 May 09. pii: E3347. [Epub ahead of print]21(9):

The Role of TNFR2 and DR3 in the In Vivo Expansion of Tregs in T Cell Depleting Transplantation Regimens.

Jose-Ignacio Rodriguez-Barbosa, Pascal Schneider, Luis Graca, Leo Bühler, Jose-Antonio Perez-Simon, Maria-Luisa Del Rio.

  Regulatory T cells (Tregs) are essential for the maintenance of tolerance to self and non-self through cell-intrinsic and cell-extrinsic mechanisms. Peripheral Tregs survival and clonal expansion largely depend on IL-2 and access to co-stimulatory signals such as CD28. Engagement of tumor necrosis factor receptor (TNFR) superfamily members, in particular TNFR2 and DR3, contribute to promote peripheral Tregs expansion and sustain their survival. This property can be leveraged to enhance tolerance to allogeneic transplants by tipping the balance of Tregs over conventional T cells during the course of immune reconstitution. This is of particular interest in peri-transplant tolerance induction protocols in which T cell depletion is applied to reduce the frequency of alloreactive T cells or in conditioning regimens that allow allogeneic bone marrow transplantation. These conditioning regimens are being implemented to limit long-term side effects of continuous immunosuppression and facilitate the establishment of a state of donor-specific tolerance. Lymphopenia-induced homeostatic proliferation in response to cytoreductive conditioning is a window of opportunity to enhance preferential expansion of Tregs during homeostatic proliferation that can be potentiated by agonist stimulation of TNFR.

Keywords:  TNF/TNF receptors; graft rejection; graft-versus-host disease; homeostatic proliferation; lymphopenia; regulatory T cells; transplantation

DOI:  https://doi.org/10.3390/ijms21093347
Cell Rep. 2020 May 12. pii: S2211-1247(20)30564-7. [Epub ahead of print]31(6): 107615

Platelets Fuel the Inflammasome Activation of Innate Immune Cells.

Verena Rolfes, Lucas Secchim Ribeiro, Ibrahim Hawwari, Lisa Böttcher, Nathalia Rosero, Salie Maasewerd, Marina Lima Silva Santos, Tomasz Próchnicki, Camila Meirelles de Souza Silva, Carlos Wagner de Souza Wanderley, Maximilian Rothe, Susanne V Schmidt, H James Stunden, Damien Bertheloot, Magali Noval Rivas, Cor Jesus Fontes, Luzia Helena Carvalho, Fernando Queiroz Cunha, Eicke Latz, Moshe Arditi, Bernardo Simoes Franklin.

  The inflammasomes control the bioactivity of pro-inflammatory cytokines of the interleukin (IL)-1 family. The inflammasome assembled by NLRP3 has been predominantly studied in homogeneous cell populations in vitro, neglecting the influence of cellular interactions that occur in vivo. Here, we show that platelets boost the inflammasome capacity of human macrophages and neutrophils and are critical for IL-1 production by monocytes. Platelets license NLRP3 transcription, thereby enhancing ASC oligomerization, caspase-1 activity, and IL-1β secretion. Platelets influence IL-1β production in vivo, and blood platelet counts correlate with plasmatic IL-1β levels in malaria. Furthermore, we reveal an enriched platelet gene signature among the highest-expressed transcripts in IL-1β-driven autoinflammatory diseases. The platelet effect is independent of cell-to-cell contact, platelet-derived lipid mediators, purines, nucleic acids, and a host of platelet cytokines, and it involves the triggering of calcium-sensing receptors on macrophages. Hence, platelets provide an additional layer of regulation of inflammasomes and IL-1-driven inflammation.

Keywords:  ASC; Caspase-1; Cell Death; NLRP3; Pyroptosis; auto-inflammatory diseases; inflammasomes; interleukin-1; malaria; platelets

DOI:  https://doi.org/10.1016/j.celrep.2020.107615
Cell Death Dis. 2020 May 11. 11(5): 350

Taking aim with IAP antagonists at triple-negative breast cancer: a moving target no more?

Eric C LaCasse.

DOI: https://doi.org/10.1038/s41419-020-2533-x
Nat Rev Cancer. 2020 May 13.

p53: 800 million years of evolution and 40 years of discovery.

Arnold J Levine.

The evolutionarily conserved p53 protein and its cellular pathways mediate tumour suppression through an informed, regulated and integrated set of responses to environmental perturbations resulting in either cellular death or the maintenance of cellular homeostasis. The p53 and MDM2 proteins form a central hub in this pathway that receives stressful inputs via MDM2 and respond via p53 by informing and altering a great many other pathways and functions in the cell. The MDM2-p53 hub is one of the hubs most highly connected to other signalling pathways in the cell, and this may be why TP53 is the most commonly mutated gene in human cancers. Initial or truncal TP53 gene mutations (the first mutations in a stem cell) are selected for early in cancer development inectodermal and mesodermal-derived tissue-specific stem and progenitor cells and then, following additional mutations, produce tumours from those tissue types. In endodermal-derived tissue-specific stem or progenitor cells, TP53 mutations are functionally selected as late mutations transitioning the mutated cell into a malignant tumour. The order in which oncogenes or tumour suppressor genes are functionally selected for in a stem cell impacts the timing and development of a tumour.

DOI: https://doi.org/10.1038/s41568-020-0262-1
Oncotarget. 2020 May 05. 11(18): 1653-1665

Nutlin-3a suppresses poly (ADP-ribose) polymerase 1 by mechanisms different from conventional PARP1 suppressors in a human breast cancer cell line.

Masaki Kobayashi, Yuka Ishizaki, Mika Owaki, Yoko Matsumoto, Yuri Kakiyama, Shunsuke Hoshino, Ryoma Tagawa, Yuka Sudo, Naoyuki Okita, Kazunori Akimoto, Yoshikazu Higami.

  Poly (ADP-ribose) polymerase 1 (PARP1) plays important roles in single strand DNA repair. PARP1 inhibitors enhance the effects of DNA damaging drugs in homologous recombination-deficient tumors including tumors with breast cancer susceptibility gene (BRCA1) mutation. Nutlin-3a, an analog of cis-imidazoline, inhibits degradation of murine double minute 2 (MDM2) and stabilizes p53. We previously reported that nutlin-3a induces PARP1 degradation in p53-dependent manner in mouse fibroblasts, suggesting nutlin-3a may be a PARP1 suppressor. Here, we investigated the effects of nutlin-3a on PARP1 in MCF-7, a human breast cancer cell line. Consistent with our previous results, nutlin-3a reduced PARP1 levels in dose- and time-dependent manners in MCF-7 cells, but this reduction was suppressed in p53 knockdown cells. RITA, a p53 stabilizer that binds to p53 itself, failed to reduce PARP1 protein levels. Moreover, transient MDM2 knockdown repressed nutlin-3a-mediated PARP1 reduction. The MG132 proteasome inhibitor, and knockdown of checkpoint with forkhead and ring finger domains (CHFR) and ring finger protein 146 (RNF146), E3 ubiquitin ligases targeting PARP1, suppressed nutlin-3a-induced PARP1 reduction. Short-term nutlin-3a treatment elevated the levels of PARylated PARP1, suggesting nutlin-3a promoted PARylation of PARP1, thereby inducing its proteasomal degradation. Furthermore, nutlin-3a-induced PARP1 degradation enhanced DNA-damaging effects of cisplatin in BRCA1 knockdown cells. Our study revealed that nutlin-3a is a PARP1 suppressor that induces PARP1 proteasomal degradation by binding to MDM2 and promoting autoPARylation of PARP1. Further analysis of the mechanisms in nutlin-3a-induced PARP1 degradation may lead to the development of novel PARP1 suppressors applicable for cancers with BRCA1 mutation.

Keywords:  PARP1; autoPARylation; breast cancer; nutlin-3a; proteasomal degradation

DOI:  https://doi.org/10.18632/oncotarget.27581
Hum Cell. 2020 May 09.

TRAF4 knockdown triggers synergistic lethality with simultaneous PARP1 inhibition in endometrial cancer.

Liulin Tang, Min Wang, Li Jiang, Chengying Zeng.

  Endometrial cancer (EC) is one of the most common cancers among females worldwide. Advanced stage patients of EC have poor prognosis. Inevitable side effects and treatment tolerance of chemotherapy for EC remain to be addressed. Our results in this study showed that EC cells with higher tumor necrosis factor receptor-associated factor 4 (TRAF4) expression have lower sensitivity to poly ADP-ribose polymerase 1 (PARP1) inhibitors. Upon TRAF4 knockdown, the colony numbers of EC cells were markedly down-regulated, and the markers of DNA double-strand breakage were significantly up-regulated after the treatment of olaparib, a PARP1 inhibitor. TRAF4 knockdown reduced the phosphorylation of protein kinase B (Akt), promoted DNA double-strand breakage, and decreased levels of DNA repair related proteins, including phosphorylated-DNA-dependent protein kinase (p-DNA-PK) and RAD51 recombinase (RAD51). In addition, TRAF4's effect on the sensitivity of EC cells to olaparib was further found to be mainly mediated by Akt phosphorylation. Moreover, in vivo results showed that TRAF4 knockdown enhanced the sensitivity of EC to PARP1 inhibitors using a mouse xenograft model. Collectively, our data suggest that combined application of TRAF4 knockdown and PARP1 inhibition can be used as a promising strategy for synthetic lethality in EC treatment.

Keywords:  Akt phosphorylation; Endometrial cancer; PARP1 inhibitors; Synthetic lethality; TRAF4

DOI:  https://doi.org/10.1007/s13577-020-00363-5
Transcription. 2020 May 13. 1-17

A combinatorial view of old and new RNA polymerase II modifications.

Danielle E Lyons, Sarah McMahon, Melanie Ott.

  The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.

Keywords:  Crosstalk; Gene regulation; Post-translational modification; RNA polymerase II; Transcription regulation

DOI:  https://doi.org/10.1080/21541264.2020.1762468
Adv Biosyst. 2020 May 10. e2000007

Cell Surface Labeling by Engineered Extracellular Vesicles.

Nicklas Hamilton, Natalie M Claudio, Randall J Armstrong, Ferdinando Pucci.

  Extracellular vesicles (EVs) can mediate local and long-range intercellular communication via cell surface signaling. In order to perform in vivo studies of unmanipulated, endogenously released EVs, sensitive but stringent approaches able to detect EV-cell surface interactions are needed. However, isolation and reinfusion of EVs can introduce biases. A rigorous way to study EVs in vivo is by genetically engineering membrane-bound reporters into parental cells. Still, the amount of reporter molecules that EVs can carry is relatively small, and thus, the sensitivity of the approach is suboptimal. This work addresses this issue by engineering EVs to display a membrane-bound form of Sortase A (SrtA), a bacterial transpeptidase that can catalyze the transfer of reporter molecules on the much bigger surface of EV-binding cells. SrtA design and reaction requirements are optimized and validated. Efficient in vitro labeling of EV-binding cells is achieved, even in the presence of only one N-terminal glycine on cell surface proteins. As compared to indirect labeling of EV-binding cells (e.g., using CD63-GFP fusion), the SrtA-based approach shows 1-2 log increase in sensitivity, depending on the EV source. This novel approach will be useful to identify and study the full set of host cells interacting with native EVs in vivo.

Keywords:  cell surface labeling; exosomes; extracellular vesicles; intercellular communication; squamous cell carcinoma

DOI:  https://doi.org/10.1002/adbi.202000007
Br J Dermatol. 2020 May 14.

Guselkumab versus secukinumab for the treatment of moderate-to-severe psoriasis: a critical appraisal.

M T Wan, J Takeshita.

The last two decades have seen a rapid growth of targeted biologic therapies for moderate-to-severe plaque psoriasis. While undoubtedly a boon for patients and their treating clinicians alike, the growing number of highly efficacious drug options can make treatment choice challenging. As such, head-to-head randomized controlled trials (RCTs) are necessary to compare the efficacy and safety of therapies to one another. While, to date, most head-to-head RCTs of biologic therapies for psoriasis have compared newer drugs (e.g., IL-17 or IL-23 inhibitors) to older ones (e.g., tumor necrosis factor or IL-12/23 inhibitors), active comparator RCTs that simultaneously assess newer drugs are also essential.

DOI: https://doi.org/10.1111/bjd.19216
Cells. 2020 May 11. pii: E1195. [Epub ahead of print]9(5):

TNF-α Pretreatment Improves the Survival and Function of Transplanted Human Neural Progenitor Cells Following Hypoxic-Ischemic Brain Injury.

Miri Kim, Kwangsoo Jung, Younhee Ko, Il-Sun Kim, Kyujin Hwang, Jae-Hyung Jang, Jeong Eun Shin, Kook In Park.

  Neural progenitor cells (NPCs) therapy offers great promise in hypoxic-ischemic (HI) brain injury. However, the poor survival of implanted NPCs in the HI host environment limits their therapeutic effects. Tumor necrosis factor-alpha (TNF-α) is a pleiotropic cytokine that is induced in response to a variety of pathological processes including inflammation and immunity. On the other hand, TNF-α has protective effects on cell apoptosis and death and affects the differentiation, proliferation, and survival of neural stem/progenitor cells in the brain. The present study investigated whether TNF-α pretreatment on human NPCs (hNPCs) enhances the effectiveness of cell transplantation therapy under ischemic brain. Fetal brain tissue-derived hNPCs were pretreated with TNF-α before being used in vitro experiments or transplantation. TNF-α significantly increased expression of cIAP2, and the use of short hairpin RNA-mediated knockdown of cIAP2 demonstrated that cIAP2 protected hNPCs against HI-induced cytotoxicity. In addition, pretreatment of hNPCs with TNF-α mediated neuroprotection by altering microglia polarization via increased expression of CX3CL1 and by enhancing expression of neurotrophic factors. Furthermore, transplantation of TNF-α-treated hNPCs reduced infarct volume and improved neurological functions in comparison with non-pretreated hNPCs or vehicle. These findings show that TNF-α pretreatment, which protects hNPCs from HI-injured brain-induced apoptosis and increases neuroprotection, is a simple and safe approach to improve the survival of transplanted hNPCs and the therapeutic efficacy of hNPCs in HI brain injury.

Keywords:  CX3CL1; cell survival; cellular inhibitor of apoptosis 2; human neural progenitor cells; hypoxic-ischemic brain injury; tumor necrosis factor-alpha

DOI:  https://doi.org/10.3390/cells9051195
Genomics Proteomics Bioinformatics. 2020 May 12. pii: S1672-0229(20)30053-X. [Epub ahead of print]

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.

Fuyi Li, Andre Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I Webb, A Ian Smith, Tatiana Marquez-Lago, Jian Li, Jiangning Song.

  Proteases are enzymes that cleave and hydrolyse the peptide bonds between two specific amino acid residues of target substrate proteins. Protease-controlled proteolysis plays a key role in the degradation and recycling of proteins, which is essential for various physiological processes. Thus, solving the substrate identification problem will have important implications for the precise understanding of functions and physiological roles of proteases, as well as for therapeutic target identification and pharmaceutical applicability. Consequently, there is a great demand for bioinformatics methods that can predict novel substrate cleavage events with high accuracy by utilizing both sequence and structural information. In this study, we present Procleave, a novel bioinformatics approach for predicting protease-specific substrates and specific cleavage sites by taking into account both their sequence and 3D structural information. Structural features of known cleavage sites were represented by discrete values using a LOWESS data-smoothing optimization method, which turned out to be critical for the performance of Procleave. The optimal approximations of all structural parameter values were encoded in a conditional random field (CRF) computational framework, alongside sequence and chemical group-based features. Here, we demonstrate the outstanding performance of Procleave through extensive benchmarking and independent tests. Procleave is capable of correctly identifying most cleavage sites in the case study. Importantly, when applied to the human structural proteome encompassing 17,628 protein structures, Procleave suggests a number of potential novel target substrates and their corresponding cleavage sites of different proteases. Procleave is implemented as a webserver and is freely accessible at http://procleave.erc.monash.edu/.

Keywords:  Cleavage site prediction; Conditional random field; Machine learning; Protease; Structural determinants

DOI:  https://doi.org/10.1016/j.gpb.2019.08.002
Eur J Med Chem. 2020 May 05. pii: S0223-5234(20)30347-0. [Epub ahead of print]199 112377

Discovery of novel resorcinol diphenyl ether-based PROTAC-like molecules as dual inhibitors and degraders of PD-L1.

Binbin Cheng, Yichang Ren, Hao Cao, Jianjun Chen.

  Novel resorcinol diphenyl ether-based PROTACs (PROteolysis TArgeting Chimeras) were designed and evaluated for their inhibitory activity against the programmed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) pathway and their ability to degrade PD-L1 protein. Most of the compounds displayed excellent inhibitory activities against PD-1/PD-L1, as assessed by the homogenous time-resolved fluorescence (HTRF) binding assay, with IC50 values ranging from 25 nM to 200 nM. Among them, compound P22 is one of the best with an IC50 value of 39.2 nM. In addition to inhibiting PD-1/PD-L1 interaction, P22 also significantly restored the immunity repressed in a co-culture model of Hep3B/OS-8/hPD-L1 and CD3 T cells. Furthermore, flow cytometry (FCM) and western-blot data demonstrated that P22 could moderately reduce the protein levels of PD-L1 in a lysosome-dependent manner, which may contribute to its immune effects. Preliminary FCM and western-blot data suggest that it is possible to build PD-L1-targeting PROTAC-like molecules based on PD-1/PD-L1 small molecule inhibitors, though these compounds showed only modest degradation efficiencies. Collectively, this work suggests that P22 may serve as a starting point for exploring the degradation of PD-L1 by PROTAC-like strategy.

Keywords:  Immunotherapy; PROTACs; Pomalidomide; Small molecule PD-1/PD-L1 inhibitors

DOI:  https://doi.org/10.1016/j.ejmech.2020.112377
J Invest Dermatol. 2020 May 05. pii: S0022-202X(20)31455-X. [Epub ahead of print]

Lipidomics Profiling of Hidradenitis Suppurativa Skin Lesions Reveals Lipoxygenase Pathway Dysregulation and Accumulation of Pro-Inflammatory Leukotriene B4.

Carlos A Penno, Petra Jäger, Claire Laguerre, Franziska Hasler, Andreas Hofmann, Stephanie Gass, Barbara Wettstein-Ling, Dirk Schaefer, Alexandre Avrameas, Friedrich Raulf, Grazyna Wieczorek, Joachim C U Lehmann, Christian Loesche, Lukas Roth, Till A Röhn.

Hidradenitis suppurativa (HS) is a chronic, recurring inflammatory dermatosis characterized by abscesses, deep-seated nodules, sinus tracts and fibrosis in skin lesions around hair follicles of the axillary, inguinal and anogenital regions. While the exact pathogenesis remains poorly defined, clear evidence suggests that HS is a multifactorial inflammatory disease characterized by innate and adaptive immune components. Bioactive lipids are important regulators of cutaneous homeostasis, inflammation as well as resolution of inflammation. Alterations in the lipid mediator profile can lead to malfunction and cutaneous inflammation. We used targeted lipidomics to analyze selected omega 3 and omega 6 poly-unsaturated fatty acids (PUFAs) in skin of HS and healthy patients. Lesional HS skin displayed an enrichment of 5-lipoxygenase (5-LO) derived metabolites, in particular leukotriene B4 (LTB4). Additionally, 15-lipoxygenase (15-LO) derived metabolites were underrepresented in HS lesions. Changes in the lipid mediator profile were accompanied by transcriptomic dysregulation of the 5-LO and 15-LO pathways. Hyper-activation of the 5-LO pathway in lesional macrophages identified these cells as potential source of LTB4, which may cause neutrophil influx and activation. Furthermore, LTB4-induced mediators and pathways were elevated in HS lesions suggesting a contribution of this pro-inflammatory lipid meditator to the pathophysiology of HS.

DOI: https://doi.org/10.1016/j.jid.2020.04.011
Expert Opin Drug Saf. 2020 May 13. 1-11

Concerns about the safety of anti-TNF agents when treating rheumatic diseases.

Fabiola Atzeni, Valeria Nucera, Elisabetta Gerratana, Mariateresa Cirillo, Francesca Marino, Gianfranco Miceli, Donatella Sangari, Laura Boccassini, Ignazio Francesco Masala.

  Introduction: More than 15 years after its introduction, there is still no agreement as to whether anti-TNF treatment increases the risk of developing infections, cardiovascular or neurological diseases, or auto-antibodies. Anti-TNF drugs reduce inflammation and sub-clinical atherosclerosis in rheumatoid arthritis (RA) patients, but they also alter their lipid profiles and can lead to the development of severe infections. Furthermore, as they increase the risk of developing demyelinating diseases, are not recommended in patients with multiple sclerosis or related disorders. The authors searched the Medline database for English language articles concerning the adverse events of anti-TNF drugs published between 1998 and December 2019, and have summarized their contents relating to infections, malignancies, cardiovascular diseases, autoimmunity and neurological diseases. Patients should be fully informed of the increased risks associated with anti-TNF drugs, and physicians should know how to treat them.Areas covered: This review considers these safety concerns, their possible underlying causes, and other aspects that are important in clinical practice.Expert opinion: Growing concern about the safety of anti-TNF drugs underlines the need to ensure that all clinicians are capable of taking appropriate preventive and therapeutic action.

Keywords:  Rheumatoid arthritis; anti-TNF drugs; autoantibodies; cardiovascular disease; infections

DOI:  https://doi.org/10.1080/14740338.2020.1763299
Trends Cell Biol. 2020 Jun;pii: S0962-8924(20)30059-3. [Epub ahead of print]30(6): 491-500

Transcription Factors and DNA Play Hide and Seek.

David M Suter.

  Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depend on multiple parameters, such as the chromatin environment, TF partitioning into distinct subcellular regions, and cooperativity with other DNA-binding proteins. In this review, how current understanding of the search process has initially been shaped by prokaryotic studies is discussed, as well as what is known about the parameters regulating TF search efficiency in the context of the complex eukaryotic chromatin landscape.

Keywords:  k(off); k(on); nonspecific binding; search efficiency; specific binding; transcription factors

DOI:  https://doi.org/10.1016/j.tcb.2020.03.003
J Am Acad Dermatol. 2020 May 06. pii: S0190-9622(20)30819-7. [Epub ahead of print]

COVID-19 and biologics for psoriasis: a high-epidemic area experience - Bergamo, Lombardy, Italy.

Andrea Carugno, Daniele Mario Gambini, Francesca Raponi, Pamela Vezzoli, Andrea Gustavo C Locatelli, Marco Di Mercurio, Elisa Robustelli Test, Paolo Sena.



Keywords:  2 (SARS-CoV-2); Biologic therapy; COVID-19; Coronavirus; Dermatology; Psoriasis; Severe Acute Respiratory Syndrome; Skin

DOI:  https://doi.org/10.1016/j.jaad.2020.04.165
Crit Rev Biochem Mol Biol. 2020 May 14. 1-13

Phosphatidylserine exposure in living cells.

Hye-Won Shin, Hiroyuki Takatsu.

  P4-ATPases, a subfamily of P-type ATPases, translocate cell membrane phospholipids from the exoplasmic/luminal leaflet to the cytoplasmic leaflet to generate and maintain membrane lipid asymmetry. Exposure of phosphatidylserine (PS) in the exoplasmic leaflet is well known to transduce critical signals for apoptotic cell clearance and platelet coagulation. PS exposure is also involved in many other biological processes, including myoblast and osteoclast fusion, and the immune response. Moreover, mounting evidence suggest that PS exposure is critical for neuronal regeneration and degeneration. In apoptotic cells, PS exposure is induced by irreversible activation of scramblases and inactivation of P4-ATPases. However, how PS is reversibly exposed and restored in viable cells during other biological processes remains poorly understood. In the present review, we discuss the physiological significance of reversible PS exposure in living cells, and the putative roles of flippases, floppases, and scramblases.

Keywords:  Lipid bilayer; P4-ATPase; flippase; phosphatidylserine; scramblase

DOI:  https://doi.org/10.1080/10409238.2020.1758624
Mediators Inflamm. 2020 ;2020 3650508

Reevaluation of Lung Injury in TNF-Induced Shock: The Role of the Acid Sphingomyelinase.

Lucy K Reiss, Ute Raffetseder, Lydia Gibbert, Hannah K Drescher, Konrad L Streetz, Agatha Schwarz, Christian Martin, Stefan Uhlig, Dieter Adam.

Tumor necrosis factor (TNF) is a well-known mediator of sepsis. In many cases, sepsis results in multiple organ injury including the lung with acute respiratory distress syndrome (ARDS). More than 20-year-old studies have suggested that TNF may be directly responsible for organ injury during sepsis. However, these old studies are inconclusive, because they relied on human rather than conspecific TNF, which was contaminated with endotoxin in most studies. In this study, we characterized the direct effects of intravenous murine endotoxin-free TNF on cardiovascular functions and organ injury in mice with a particular focus on the lungs. Because of the relevance of the acid sphingomyelinase in sepsis, ARDS, and caspase-independent cell death, we also included acid sphingomyelinase-deficient (ASM-/-) mice. ASM-/- and wild-type (WT) mice received 50 μg endotoxin-free murine TNF intravenously alone or in combination with the pan-caspase inhibitor carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]-fluoromethylketone (zVAD) and were ventilated at low tidal volume while lung mechanics were followed. Blood pressure was stabilized by intra-arterial fluid support, and body temperature was kept at 37°C to delay lethal shock and to allow investigation of blood gases, lung histopathology, proinflammatory mediators, and microvascular permeability 6 hours after TNF application. Besides the lungs, also the kidneys and liver were examined. TNF elicited the release of inflammatory mediators and a high mortality rate, but failed to injure the lungs, kidneys, or liver of healthy mice significantly within 6 hours. Mortality in WT mice was most likely due to sepsis-like shock, as indicated by metabolic acidosis, high procalcitonin levels, and cardiovascular failure. ASM-/- mice were protected from TNF-induced hypotension and reflex tachycardia and also from mortality. In WT mice, intravenous exogenous TNF does not cause organ injury but induces a systemic inflammatory response with cardiovascular failure, in which the ASM plays a role.

DOI: https://doi.org/10.1155/2020/3650508
EMBO Rep. 2020 May 15. e48035

The p38-interacting protein p38IP suppresses TCR and LPS signaling by targeting TAK1.

Xu-Dong Wang, Chen-Si Zhao, Qi-Long Wang, Qi Zeng, Xing-Zhi Feng, Lianbo Li, Zhi-Long Chen, Yu Gong, Jiahuai Han, Yingqiu Li.

  Negative regulation of immunoreceptor signaling is required for preventing hyperimmune activation and maintaining immune homeostasis. The roles of p38IP in immunoreceptor signaling remain unclear. Here, we show that p38IP suppresses T-cell receptor (TCR)/LPS-activated NF-κB and p38 by targeting TAK1 kinase and that p38IP protein levels are downregulated in human PBMCs from rheumatoid arthritis (RA) patients, inversely correlating with the enhanced activity of NF-κB and p38. Mechanistically, p38IP interacts with TAK1 to disassemble the TAK1-TAB (TAK1-binding protein) complex. p38IP overexpression decreases TCR-induced binding of K63-linked polyubiquitin (polyUb) chains to TAK1 but increases that to TAB2, and p38IP knockdown shows the opposite effects, indicating unanchored K63-linked polyUb chain transfer from TAB2 to TAK1. p38IP dynamically interacts with TAK1 upon stimulation, because of the polyUb chain transfer and the higher binding affinity of TAK1 and p38IP for polyUb-bound TAB2 and TAK1, respectively. Moreover, p38IP scaffolds the deubiquitinase USP4 to deubiquitinate TAK1 once TAK1 is activated. These findings reveal a novel role and the mechanisms of p38IP in controlling TCR/LPS signaling and suggest that p38IP might participate in RA pathogenesis.

Keywords:  TAK1 activity sensor; USP4 scaffold; immunoreceptor signaling; negative regulator; p38IP

DOI:  https://doi.org/10.15252/embr.201948035
Nat Rev Rheumatol. 2020 May 12.

Anti-TNF response falls short in real-world cohort.

Sarah Onuora.

DOI: https://doi.org/10.1038/s41584-020-0439-8
Cell Immunol. 2020 Apr 28. pii: S0008-8749(19)30494-0. [Epub ahead of print]353 104115

TAK1 lessens the activity of the paracaspase MALT1 during T cell receptor signaling.

Carolina Alves Nicolau, Julie Gavard, Nicolas Bidère.

  The CARMA1-BCL10-MALT1 (CBM) complex couples antigen receptors to the activation of Nuclear Factor κB (NF-κB) transcription factors in T/B lymphocytes. Within this signalosome, the MALT1 paracaspase serves dual roles: it is a crucial adaptor for signal transduction to NF-κB signaling, and a protease that shapes NF-κB activity and lymphocyte activation. Although a subtle choreography of ubiquitination and phosphorylation orchestrate the CBM, how precisely this complex and MALT1 enzyme are regulated continue to be elucidated. Here, we report that the chemical inhibition or the siRNA-based silencing of transforming growth factor beta-activated kinase 1 (TAK1), a known partner of the CBM complex required for NF-κB activation, enhanced the processing of MALT1 substrates. We further show that the assembly of the CBM as well as the ubiquitination of MALT1 was augmented when TAK1 was inhibited. Thus, TAK1 may initiate a negative feedback loop to finely tune the CBM complex activity.

Keywords:  CBM complex; Lymphocyte; MALT1; NF-κB; Signaling; TAK1

DOI:  https://doi.org/10.1016/j.cellimm.2020.104115