1
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Solon M, Ge N, Hambro S, Haller S, Jiang J, Baca M, Preston J, Maltzman A, Wickliffe KE, Liang Y, Reja R, Nickles D, Newton K, Webster JD. ZBP1 and TRIF trigger lethal necroptosis in mice lacking caspase-8 and TNFR1. Cell Death Differ 2024; 31:672-682. [PMID: 38548850 DOI: 10.1038/s41418-024-01286-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 05/16/2024] Open
Abstract
Necroptosis is a lytic form of cell death that is mediated by the kinase RIPK3 and the pseudokinase MLKL when caspase-8 is inhibited downstream of death receptors, toll-like receptor 3 (TLR3), TLR4, and the intracellular Z-form nucleic acid sensor ZBP1. Oligomerization and activation of RIPK3 is driven by interactions with the kinase RIPK1, the TLR adaptor TRIF, or ZBP1. In this study, we use immunohistochemistry (IHC) and in situ hybridization (ISH) assays to generate a tissue atlas characterizing RIPK1, RIPK3, Mlkl, and ZBP1 expression in mouse tissues. RIPK1, RIPK3, and Mlkl were co-expressed in most immune cell populations, endothelial cells, and many barrier epithelia. ZBP1 was expressed in many immune populations, but had more variable expression in epithelia compared to RIPK1, RIPK3, and Mlkl. Intriguingly, expression of ZBP1 was elevated in Casp8-/- Tnfr1-/- embryos prior to their succumbing to aberrant necroptosis around embryonic day 15 (E15). ZBP1 contributed to this embryonic lethality because rare Casp8-/- Tnfr1-/- Zbp1-/- mice survived until after birth. Necroptosis mediated by TRIF contributed to the demise of Casp8-/- Tnfr1-/- Zbp1-/- pups in the perinatal period. Of note, Casp8-/- Tnfr1-/- Trif-/- Zbp1-/- mice exhibited autoinflammation and morbidity, typically within 5-7 weeks of being born, which is not seen in Casp8-/- Ripk1-/- Trif-/- Zbp1-/-, Casp8-/- Ripk3-/-, or Casp8-/- Mlkl-/- mice. Therefore, after birth, loss of caspase-8 probably unleashes RIPK1-dependent necroptosis driven by death receptors other than TNFR1.
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Affiliation(s)
- Margaret Solon
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Nianfeng Ge
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Shannon Hambro
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Susan Haller
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jian Jiang
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Miriam Baca
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jessica Preston
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Allie Maltzman
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Katherine E Wickliffe
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics, Lipidomics, and Next Generation Sequencing, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Rohit Reja
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Oncology Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Dorothee Nickles
- Department of Oncology Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Translational Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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2
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Gitlin AD, Maltzman A, Kanno Y, Heger K, Reja R, Schubert AF, Wierciszewski LJ, Pantua H, Kapadia SB, Harris SF, Webster JD, Newton K, Dixit VM. N4BP1 coordinates ubiquitin-dependent crosstalk within the IκB kinase family to limit Toll-like receptor signaling and inflammation. Immunity 2024:S1074-7613(24)00209-7. [PMID: 38697117 DOI: 10.1016/j.immuni.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/15/2023] [Accepted: 04/08/2024] [Indexed: 05/04/2024]
Abstract
The ubiquitin-binding endoribonuclease N4BP1 potently suppresses cytokine production by Toll-like receptors (TLRs) that signal through the adaptor MyD88 but is inactivated via caspase-8-mediated cleavage downstream of death receptors, TLR3, or TLR4. Here, we examined the mechanism whereby N4BP1 limits inflammatory responses. In macrophages, deletion of N4BP1 prolonged activation of inflammatory gene transcription at late time points after TRIF-independent TLR activation. Optimal suppression of inflammatory cytokines by N4BP1 depended on its ability to bind polyubiquitin chains, as macrophages and mice-bearing inactivating mutations in a ubiquitin-binding motif in N4BP1 displayed increased TLR-induced cytokine production. Deletion of the noncanonical IκB kinases (ncIKKs), Tbk1 and Ikke, or their adaptor Tank phenocopied N4bp1 deficiency and enhanced macrophage responses to TLR1/2, TLR7, or TLR9 stimulation. Mechanistically, N4BP1 acted in concert with the ncIKKs to limit the duration of canonical IκB kinase (IKKα/β) signaling. Thus, N4BP1 and the ncIKKs serve as an important checkpoint against over-exuberant innate immune responses.
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Affiliation(s)
- Alexander D Gitlin
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
| | - Allie Maltzman
- Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yuzuka Kanno
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Klaus Heger
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Oncology Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexander F Schubert
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Linsey J Wierciszewski
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Homer Pantua
- Infectious Diseases, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sharookh B Kapadia
- Infectious Diseases, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Seth F Harris
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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3
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Newton K, Wickliffe KE, Maltzman A, Dugger DL, Webster JD, Guo H, Dixit VM. Caspase cleavage of RIPK3 after Asp 333 is dispensable for mouse embryogenesis. Cell Death Differ 2024; 31:254-262. [PMID: 38191748 PMCID: PMC10850060 DOI: 10.1038/s41418-023-01255-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
The proteolytic activity of caspase-8 suppresses lethal RIPK1-, RIPK3- and MLKL-dependent necroptosis during mouse embryogenesis. Caspase-8 is reported to cleave RIPK3 in addition to the RIPK3-interacting kinase RIPK1, but whether cleavage of RIPK3 is crucial for necroptosis suppression is unclear. Here we show that caspase-8-driven cleavage of endogenous mouse RIPK3 after Asp333 is dependent on downstream caspase-3. Consistent with RIPK3 cleavage being a consequence of apoptosis rather than a critical brake on necroptosis, Ripk3D333A/D333A knock-in mice lacking the Asp333 cleavage site are viable and develop normally. Moreover, in contrast to mice lacking caspase-8 in their intestinal epithelial cells, Ripk3D333A/D333A mice do not exhibit increased sensitivity to high dose tumor necrosis factor (TNF). Ripk3D333A/D333A macrophages died at the same rate as wild-type (WT) macrophages in response to TNF plus cycloheximide, TNF plus emricasan, or infection with murine cytomegalovirus (MCMV) lacking M36 and M45 to inhibit caspase-8 and RIPK3 activation, respectively. We conclude that caspase cleavage of RIPK3 is dispensable for mouse development, and that cleavage of caspase-8 substrates, including RIPK1, is sufficient to prevent necroptosis.
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Affiliation(s)
- Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Katherine E Wickliffe
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Allie Maltzman
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Hongyan Guo
- Department of Microbiology and Immunology, LSU Health Shreveport, Shreveport, LA, 71103, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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4
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Abstract
Apoptosis, necroptosis, and pyroptosis are genetically programmed cell death mechanisms that eliminate obsolete, damaged, infected, and self-reactive cells. Apoptosis fragments cells in a manner that limits immune cell activation, whereas the lytic death programs of necroptosis and pyroptosis release proinflammatory intracellular contents. Apoptosis fine-tunes tissue architecture during mammalian development, promotes tissue homeostasis, and is crucial for averting cancer and autoimmunity. All three cell death mechanisms are deployed to thwart the spread of pathogens. Disabling regulators of cell death signaling in mice has revealed how excessive cell death can fuel acute or chronic inflammation. Here we review strategies for modulating cell death in the context of disease. For example, BCL-2 inhibitor venetoclax, an inducer of apoptosis, is approved for the treatment of certain hematologic malignancies. By contrast, inhibition of RIPK1, NLRP3, GSDMD, or NINJ1 to limit proinflammatory cell death and/or the release of large proinflammatory molecules from dying cells may benefit patients with inflammatory diseases.
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Affiliation(s)
- Nobuhiko Kayagaki
- Physiological Chemistry Department, Genentech, South San Francisco, California, USA;
| | - Joshua D Webster
- Pathology Department, Genentech, South San Francisco, California, USA
| | - Kim Newton
- Physiological Chemistry Department, Genentech, South San Francisco, California, USA;
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5
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Prado-Acosta M, Jeong S, Utrero-Rico A, Goncharov T, Webster JD, Holler E, Morales G, Dellepiane S, Levine JE, Rothenberg ME, Vucic D, Ferrara JLM. Inhibition of RIP1 improves immune reconstitution and reduces GVHD mortality while preserving graft-versus-leukemia effects. Sci Transl Med 2023; 15:eadf8366. [PMID: 38117900 DOI: 10.1126/scitranslmed.adf8366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
Graft-versus-host disease (GVHD) remains the major cause of morbidity and nonrelapse mortality (NRM) after hematopoietic cell transplantation (HCT). Inflammatory cytokines mediate damage to key GVHD targets such as intestinal stem cells (ISCs) and also activate receptor interacting protein kinase 1 (RIP1; RIPK1), a critical regulator of apoptosis and necroptosis. We therefore investigated the role of RIP1 in acute GVHD using samples from HCT patients, modeling GVHD damage in vitro with both human and mouse gastrointestinal (GI) organoids, and blocking RIP1 activation in vivo using several well-characterized mouse HCT models. Increased phospho-RIP1 expression in GI biopsies from patients with acute GVHD correlated with tissue damage and predicted NRM. Both the genetic inactivation of RIP1 and the RIP1 inhibitor GNE684 prevented GVHD-induced apoptosis of ISCs in vivo and in vitro. Daily administration of GNE684 for 14 days reduced inflammatory infiltrates in three GVHD target organs (intestine, liver, and spleen) in mice. Unexpectedly, GNE684 administration also reversed the marked loss of regulatory T cells in the intestines and liver during GVHD and reduced splenic T cell exhaustion, thus improving immune reconstitution. Pharmacological and genetic inhibition of RIP1 improved long-term survival without compromising the graft-versus-leukemia (GVL) effect in lymphocytic and myeloid leukemia mouse models. Thus, RIP1inhibition may represent a nonimmunosuppressive treatment for GVHD.
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Affiliation(s)
- Mariano Prado-Acosta
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seihwan Jeong
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alberto Utrero-Rico
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Ernst Holler
- Department of Hematology and Oncology, University of Regensburg, Regensburg 93042, Germany
| | - George Morales
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Dellepiane
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John E Levine
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Domagoj Vucic
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - James L M Ferrara
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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6
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Nabhan AN, Webster JD, Adams JJ, Blazer L, Everrett C, Eidenschenk C, Arlantico A, Fleming I, Brightbill HD, Wolters PJ, Modrusan Z, Seshagiri S, Angers S, Sidhu SS, Newton K, Arron JR, Dixit VM. Targeted alveolar regeneration with Frizzled-specific agonists. Cell 2023; 186:2995-3012.e15. [PMID: 37321220 DOI: 10.1016/j.cell.2023.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Wnt ligands oligomerize Frizzled (Fzd) and Lrp5/6 receptors to control the specification and activity of stem cells in many species. How Wnt signaling is selectively activated in different stem cell populations, often within the same organ, is not understood. In lung alveoli, we show that distinct Wnt receptors are expressed by epithelial (Fzd5/6), endothelial (Fzd4), and stromal (Fzd1) cells. Fzd5 is uniquely required for alveolar epithelial stem cell activity, whereas fibroblasts utilize distinct Fzd receptors. Using an expanded repertoire of Fzd-Lrp agonists, we could activate canonical Wnt signaling in alveolar epithelial stem cells via either Fzd5 or, unexpectedly, non-canonical Fzd6. A Fzd5 agonist (Fzd5ag) or Fzd6ag stimulated alveolar epithelial stem cell activity and promoted survival in mice after lung injury, but only Fzd6ag promoted an alveolar fate in airway-derived progenitors. Therefore, we identify a potential strategy for promoting regeneration without exacerbating fibrosis during lung injury.
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Affiliation(s)
- Ahmad N Nabhan
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jarret J Adams
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA
| | - Levi Blazer
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA
| | - Christine Everrett
- Department of Molecular Discovery and Cancer Cell Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Celine Eidenschenk
- Department of Molecular Discovery and Cancer Cell Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexander Arlantico
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isabel Fleming
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Paul J Wolters
- Department of Medicine, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | | | - Stephane Angers
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 1A2, Canada; Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sachdev S Sidhu
- AntlerA Therapeutics, 348 Hatch Drive, Foster City, CA 94404, USA; School of Pharmacy, University of Waterloo, Kitchener, ON N2G 1C5, Canada
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Joseph R Arron
- Department of Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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7
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Kayagaki N, Stowe IB, Alegre K, Deshpande I, Wu S, Lin Z, Kornfeld OS, Lee BL, Zhang J, Liu J, Suto E, Lee WP, Schneider K, Lin W, Seshasayee D, Bhangale T, Chalouni C, Johnson MC, Joshi P, Mossemann J, Zhao S, Ali D, Goldenberg NM, Sayed BA, Steinberg BE, Newton K, Webster JD, Kelly RL, Dixit VM. Inhibiting membrane rupture with NINJ1 antibodies limits tissue injury. Nature 2023:10.1038/s41586-023-06191-5. [PMID: 37196676 DOI: 10.1038/s41586-023-06191-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Plasma membrane rupture (PMR) in dying cells undergoing pyroptosis or apoptosis requires the cell-surface protein NINJ11. PMR releases proinflammatory cytoplasmic molecules, collectively called damage-associated molecular patterns (DAMPs), that activate immune cells. Therefore, inhibiting NINJ1 and PMR may limit the inflammation that is associated with excessive cell death. Here we describe an anti-NINJ1 monoclonal antibody, specifically targeting murine NINJ1, that blocks oligomerization of NINJ1 and prevents PMR. By electron microscopy, this antibody prevented NINJ1 from forming oligomeric filaments. In mice, inhibition of NINJ1 or Ninj1 deficiency ameliorated hepatocellular PMR induced with TNF plus D-Galactosamine, concanavalin A, Jo2 anti-Fas agonist antibody, or ischemia-reperfusion injury (IRI). Accordingly, serum levels of lactate dehydrogenase (LDH), liver enzymes alanine aminotransaminase (ALT) and aspartate aminotransferase (AST), and DAMPs interleukin 18 (IL-18) and HMGB1 were reduced. Moreover, in the liver IRI model, there was an attendant reduction in neutrophil infiltration. These data indicate that NINJ1 mediates PMR and inflammation in diseases driven by aberrant hepatocellular death.
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Affiliation(s)
- Nobuhiko Kayagaki
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA.
| | - Irma B Stowe
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Kamela Alegre
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Ishan Deshpande
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Shuang Wu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Opher S Kornfeld
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Bettina L Lee
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - John Liu
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Eric Suto
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - WeiYu Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Cecile Chalouni
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Matthew C Johnson
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Prajakta Joshi
- Department of Biomolecular Resources, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Jan Mossemann
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Sarah Zhao
- Program in Neuroscience and Mental Health, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Danish Ali
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Neil M Goldenberg
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
- Department of Anesthesia and Pain Medicine, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Blayne A Sayed
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
- Division of General Surgery, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Benjamin E Steinberg
- Program in Neuroscience and Mental Health, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
- Department of Anesthesia and Pain Medicine, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Kim Newton
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Joshua D Webster
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Ryan L Kelly
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA.
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8
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Witt A, Goncharov T, Lee YM, Kist M, Dohse M, Eastham J, Dugger D, Newton K, Webster JD, Vucic D. XIAP deletion sensitizes mice to TNF-induced and RIP1-mediated death. Cell Death Dis 2023; 14:262. [PMID: 37041175 PMCID: PMC10090100 DOI: 10.1038/s41419-023-05793-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023]
Abstract
XIAP is a caspase-inhibitory protein that blocks several cell death pathways, and mediates proper activation of inflammatory NOD2-RIP2 signaling. XIAP deficiency in patients with inflammatory diseases such as Crohn's disease, or those needing allogeneic hematopoietic cell transplantation, is associated with a worse prognosis. In this study, we show that XIAP absence sensitizes cells and mice to LPS- and TNF-mediated cell death without affecting LPS- or TNF-induced NF-κB and MAPK signaling. In XIAP deficient mice, RIP1 inhibition effectively blocks TNF-stimulated cell death, hypothermia, lethality, cytokine/chemokine release, intestinal tissue damage and granulocyte migration. By contrast, inhibition of the related kinase RIP2 does not affect TNF-stimulated events, suggesting a lack of involvement for the RIP2-NOD2 signaling pathway. Overall, our data indicate that in XIAP's absence RIP1 is a critical component of TNF-mediated inflammation, suggesting that RIP1 inhibition could be an attractive option for patients with XIAP deficiency.
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Affiliation(s)
- Axel Witt
- Department of Immunology Discovery, Genentech, South San Francisco, CA, 94080, USA
- Neovii Pharmaceutical AG, 8640, Rapperswil, Switzerland
| | - Tatiana Goncharov
- Department of Immunology Discovery, Genentech, South San Francisco, CA, 94080, USA
| | - Yujung Michelle Lee
- Department of Immunology Discovery, Genentech, South San Francisco, CA, 94080, USA
| | - Matthias Kist
- Department of Immunology Discovery, Genentech, South San Francisco, CA, 94080, USA
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Monika Dohse
- Department of Pathology, Genentech, South San Francisco, CA, 94080, USA
| | - Jeff Eastham
- Department of Pathology, Genentech, South San Francisco, CA, 94080, USA
| | - Debra Dugger
- Department of Physiological Chemistry, Genentech, South San Francisco, CA, 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA, 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA, 94080, USA
| | - Domagoj Vucic
- Department of Immunology Discovery, Genentech, South San Francisco, CA, 94080, USA.
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9
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Himmels P, Nguyen TTT, Mitzner MC, Arrazate A, Yeung S, Burton J, Clark R, Totpal K, Jesudason R, Yang A, Solon M, Eastham J, Modrusan Z, Webster JD, Lo AA, Piskol R, Ye W. T cell-dependent bispecific antibodies alter organ-specific endothelial cell-T cell interaction. EMBO Rep 2023; 24:e55532. [PMID: 36621885 PMCID: PMC9986820 DOI: 10.15252/embr.202255532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Preclinical and clinical studies demonstrate that T cell-dependent bispecific antibodies (TDBs) induce systemic changes in addition to tumor killing, leading to adverse events. Here, we report an in-depth characterization of acute responses to TDBs in tumor-bearing mice. Contrary to modest changes in tumors, rapid and substantial lymphocyte accumulation and endothelial cell (EC) activation occur around large blood vessels in normal organs including the liver. We hypothesize that organ-specific ECs may account for the differential responses in normal tissues and tumors, and we identify a list of genes selectively upregulated by TDB in large liver vessels. Using one of the genes as an example, we demonstrate that CD9 facilitates ICAM-1 to support T cell-EC interaction in response to soluble factors released from a TDB-mediated cytotoxic reaction. Our results suggest that multiple factors may cooperatively promote T cell infiltration into normal organs as a secondary response to TDB-mediated tumor killing. These data shed light on how different vascular beds respond to cancer immunotherapy and may help improve their safety and efficacy.
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Affiliation(s)
- Patricia Himmels
- Department of Molecular OncologyGenentechSouth San FranciscoCAUSA
| | | | - Maresa Caunt Mitzner
- Department of Molecular OncologyGenentechSouth San FranciscoCAUSA
- Product DevelopmentGenentechSouth San FranciscoCAUSA
| | - Alfonso Arrazate
- Department of Translational OncologyGenentechSouth San FranciscoCAUSA
| | - Stacey Yeung
- Department of Molecular OncologyGenentechSouth San FranciscoCAUSA
| | - Jeremy Burton
- Department of Molecular OncologyGenentechSouth San FranciscoCAUSA
| | - Robyn Clark
- Department of Translational OncologyGenentechSouth San FranciscoCAUSA
| | - Klara Totpal
- Department of Translational OncologyGenentechSouth San FranciscoCAUSA
| | - Raj Jesudason
- Department of Research PathologyGenentechSouth San FranciscoCAUSA
| | - Angela Yang
- GSK‐Laboratory for Genomic ResearchSan FranciscoCAUSA
- Department of Microchemistry, Proteomics and Lipidomics, and Next Generation Sequencing (MPL‐NGS)GenentechSouth San FranciscoCAUSA
| | - Margaret Solon
- Department of Research PathologyGenentechSouth San FranciscoCAUSA
| | - Jeffrey Eastham
- Department of Research PathologyGenentechSouth San FranciscoCAUSA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, and Next Generation Sequencing (MPL‐NGS)GenentechSouth San FranciscoCAUSA
| | - Joshua D Webster
- Department of Research PathologyGenentechSouth San FranciscoCAUSA
| | - Amy A Lo
- Department of Research PathologyGenentechSouth San FranciscoCAUSA
| | - Robert Piskol
- Department of Oncology BioinformaticsGenentechSouth San FranciscoCAUSA
| | - Weilan Ye
- Department of Molecular OncologyGenentechSouth San FranciscoCAUSA
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10
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Havnar C, Hotzel K, Espiritu C, Lo A, Webster JD. Standardized Processing for Formalin-Fixed, Paraffin-Embedded Cell Pellet Immunohistochemistry Controls. J Vis Exp 2022. [DOI: 10.3791/64276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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11
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Schulman FY, Roccabianca P, Avallone G, Bertram CA, Chalkley M, Chambers JK, Donovan TA, Foster RA, Meuten D, Porcellato I, Priestnall SL, Rasotto R, Uchida K, Webster JD, Wood GA, Caswell JL. Reporting guidelines for manuscripts on tumor prognosis. Vet Pathol 2022; 59:397-398. [DOI: 10.1177/03009858221082207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Luchetti G, Roncaioli JL, Chavez RA, Schubert AF, Kofoed EM, Reja R, Cheung TK, Liang Y, Webster JD, Lehoux I, Skippington E, Reeder J, Haley B, Tan MW, Rose CM, Newton K, Kayagaki N, Vance RE, Dixit VM. Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection. Cell Host Microbe 2021; 29:1521-1530.e10. [PMID: 34492225 DOI: 10.1016/j.chom.2021.08.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/08/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
The pore-forming protein gasdermin D (GSDMD) executes lytic cell death called pyroptosis to eliminate the replicative niche of intracellular pathogens. Evolution favors pathogens that circumvent this host defense mechanism. Here, we show that the Shigella ubiquitin ligase IpaH7.8 functions as an inhibitor of GSDMD. Shigella is an enteroinvasive bacterium that causes hemorrhagic gastroenteritis in primates, but not rodents. IpaH7.8 contributes to species specificity by ubiquitinating human, but not mouse, GSDMD and targeting it for proteasomal degradation. Accordingly, infection of human epithelial cells with IpaH7.8-deficient Shigella flexneri results in increased GSDMD-dependent cell death compared with wild type. Consistent with pyroptosis contributing to murine disease resistance, eliminating GSDMD from NLRC4-deficient mice, which are already sensitized to oral infection with Shigella flexneri, leads to further enhanced bacterial replication and increased disease severity. This work highlights a species-specific pathogen arms race focused on maintenance of host cell viability.
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Affiliation(s)
- Giovanni Luchetti
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Justin L Roncaioli
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA
| | - Roberto A Chavez
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA
| | - Alexander F Schubert
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eric M Kofoed
- Department of Immunology and Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Oncology Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tommy K Cheung
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Isabelle Lehoux
- Department of Biomolecular Resources, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Elizabeth Skippington
- Department of OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janina Reeder
- Department of OMNI Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Man Wah Tan
- Department of Immunology and Infectious Diseases, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nobuhiko Kayagaki
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Russell E Vance
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, Berkeley CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley CA 94720, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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13
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Stark K, Goncharov T, Varfolomeev E, Xie L, Ngu H, Peng I, Anderson KR, Verschueren E, Choi M, Kirkpatrick DS, Easton A, Webster JD, McKenzie BS, Vucic D, Bingol B. Genetic inactivation of RIP1 kinase activity in rats protects against ischemic brain injury. Cell Death Dis 2021; 12:379. [PMID: 33828080 PMCID: PMC8026634 DOI: 10.1038/s41419-021-03651-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 02/01/2023]
Abstract
RIP1 kinase-mediated inflammatory and cell death pathways have been implicated in the pathology of acute and chronic disorders of the nervous system. Here, we describe a novel animal model of RIP1 kinase deficiency, generated by knock-in of the kinase-inactivating RIP1(D138N) mutation in rats. Homozygous RIP1 kinase-dead (KD) rats had normal development, reproduction and did not show any gross phenotypes at baseline. However, cells derived from RIP1 KD rats displayed resistance to necroptotic cell death. In addition, RIP1 KD rats were resistant to TNF-induced systemic shock. We studied the utility of RIP1 KD rats for neurological disorders by testing the efficacy of the genetic inactivation in the transient middle cerebral artery occlusion/reperfusion model of brain injury. RIP1 KD rats were protected in this model in a battery of behavioral, imaging, and histopathological endpoints. In addition, RIP1 KD rats had reduced inflammation and accumulation of neuronal injury biomarkers. Unbiased proteomics in the plasma identified additional changes that were ameliorated by RIP1 genetic inactivation. Together these data highlight the utility of the RIP1 KD rats for target validation and biomarker studies for neurological disorders.
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Affiliation(s)
- Kimberly Stark
- grid.418158.10000 0004 0534 4718Department of Neuroscience, Genentech, South San Francisco, 94080 CA USA
| | - Tatiana Goncharov
- grid.418158.10000 0004 0534 4718Department of Early Discovery Biochemistry, Genentech, South San Francisco, 94080 CA USA
| | - Eugene Varfolomeev
- grid.418158.10000 0004 0534 4718Department of Early Discovery Biochemistry, Genentech, South San Francisco, 94080 CA USA
| | - Luke Xie
- grid.418158.10000 0004 0534 4718Department of Biomedical Imaging, Genentech, South San Francisco, 94080 CA USA
| | - Hai Ngu
- grid.418158.10000 0004 0534 4718Department of Pathology, Genentech, South San Francisco, 94080 CA USA
| | - Ivan Peng
- grid.418158.10000 0004 0534 4718Department of Translational Immunology, Genentech, South San Francisco, 94080 CA USA
| | - Keith R. Anderson
- grid.418158.10000 0004 0534 4718Department of Molecular Biology, Genentech, South San Francisco, 94080 CA USA
| | - Erik Verschueren
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, 94080 CA USA
| | - Meena Choi
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, 94080 CA USA
| | - Donald S. Kirkpatrick
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, 94080 CA USA
| | - Amy Easton
- grid.418158.10000 0004 0534 4718Department of Neuroscience, Genentech, South San Francisco, 94080 CA USA
| | - Joshua D. Webster
- grid.418158.10000 0004 0534 4718Department of Pathology, Genentech, South San Francisco, 94080 CA USA
| | - Brent S. McKenzie
- grid.418158.10000 0004 0534 4718Department of Translational Immunology, Genentech, South San Francisco, 94080 CA USA
| | - Domagoj Vucic
- grid.418158.10000 0004 0534 4718Department of Early Discovery Biochemistry, Genentech, South San Francisco, 94080 CA USA
| | - Baris Bingol
- grid.418158.10000 0004 0534 4718Department of Neuroscience, Genentech, South San Francisco, 94080 CA USA
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14
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Kist M, Kőműves LG, Goncharov T, Dugger DL, Yu C, Roose-Girma M, Newton K, Webster JD, Vucic D. Impaired RIPK1 ubiquitination sensitizes mice to TNF toxicity and inflammatory cell death. Cell Death Differ 2021; 28:985-1000. [PMID: 32999468 PMCID: PMC7937686 DOI: 10.1038/s41418-020-00629-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/13/2020] [Accepted: 09/21/2020] [Indexed: 01/30/2023] Open
Abstract
Receptor-interacting protein 1 (RIP1; RIPK1) is a key regulator of multiple signaling pathways that mediate inflammatory responses and cell death. TNF-TNFR1 triggered signaling complex formation, subsequent NF-κB and MAPK activation and induction of cell death involve RIPK1 ubiquitination at several lysine residues including Lys376 and Lys115. Here we show that mutating the ubiquitination site K376 of RIPK1 (K376R) in mice activates cell death resulting in embryonic lethality. In contrast to Ripk1K376R/K376R mice, Ripk1K115R/K115R mice reached adulthood and showed slightly higher responsiveness to TNF-induced death. Cell death observed in Ripk1K376R/K376R embryos relied on RIPK1 kinase activity as administration of RIPK1 inhibitor GNE684 to pregnant heterozygous mice effectively blocked cell death and prolonged survival. Embryonic lethality of Ripk1K376R/K376R mice was prevented by the loss of TNFR1, or by simultaneous deletion of caspase-8 and RIPK3. Interestingly, elimination of the wild-type allele from adult Ripk1K376R/cko mice was tolerated. However, adult Ripk1K376R/cko mice were exquisitely sensitive to TNF-induced hypothermia and associated lethality. Absence of the K376 ubiquitination site diminished K11-linked, K63-linked, and linear ubiquitination of RIPK1, and promoted the assembly of death-inducing cellular complexes, suggesting that multiple ubiquitin linkages contribute to the stability of the RIPK1 signaling complex that stimulates NF-κB and MAPK activation. In contrast, mutating K115 did not affect RIPK1 ubiquitination or TNF stimulated NF-κB and MAPK signaling. Overall, our data indicate that selective impairment of RIPK1 ubiquitination can lower the threshold for RIPK1 activation by TNF resulting in cell death and embryonic lethality.
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Affiliation(s)
- Matthias Kist
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - László G Kőműves
- Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Tatiana Goncharov
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Debra L Dugger
- Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Charles Yu
- Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Merone Roose-Girma
- Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kim Newton
- Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joshua D Webster
- Pathology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Domagoj Vucic
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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15
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Esen E, Sergin I, Jesudason R, Himmels P, Webster JD, Zhang H, Xu M, Piskol R, McNamara E, Gould S, Capietto AH, Delamarre L, Walsh K, Ye W. MAP4K4 negatively regulates CD8 T cell-mediated antitumor and antiviral immunity. Sci Immunol 2020; 5:5/45/eaay2245. [PMID: 32220977 DOI: 10.1126/sciimmunol.aay2245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/01/2019] [Accepted: 02/27/2020] [Indexed: 12/28/2022]
Abstract
During cytotoxic T cell activation, lymphocyte function-associated antigen-1 (LFA-1) engages its ligands on antigen-presenting cells (APCs) or target cells to enhance T cell priming or lytic activity. Inhibiting LFA-1 dampens T cell-dependent symptoms in inflammation, autoimmune diseases, and graft-versus-host disease. However, the therapeutic potential of augmenting LFA-1 function is less explored. Here, we show that genetic deletion or inhibition of mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) enhances LFA-1 activation on CD8 T cells and improves their adherence to APCs or LFA-1 ligand. In addition, loss of Map4k4 increases CD8 T cell priming, which culminates in enhanced antigen-dependent activation, proliferation, cytokine production, and cytotoxic activity, resulting in impaired tumor growth and improved response to viral infection. LFA-1 inhibition reverses these phenotypes. The ERM (ezrin, radixin, and moesin) proteins reportedly regulate T cell-APC conjugation, but the molecular regulator and effector of ERM proteins in T cells have not been defined. In this study, we demonstrate that the ERM proteins serve as mediators between MAP4K4 and LFA-1. Last, systematic analyses of many organs revealed that inducible whole-body deletion of Map4k4 in adult animals is tolerated under homeostatic conditions. Our results uncover MAP4K4 as a potential target to augment antitumor and antiviral immunity.
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Affiliation(s)
- Emel Esen
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Ismail Sergin
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Rajiv Jesudason
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Patricia Himmels
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Joshua D Webster
- Department of Research Pathology, Genentech, South San Francisco, CA, USA
| | - Hua Zhang
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Min Xu
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Robert Piskol
- Department of Bioinformatics, Genentech, South San Francisco, CA, USA
| | - Erin McNamara
- Department of Translational Oncology, Genentech, South San Francisco, CA, USA
| | - Stephen Gould
- Department of Translational Oncology, Genentech, South San Francisco, CA, USA
| | | | - Lélia Delamarre
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Kevin Walsh
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA.
| | - Weilan Ye
- Department of Molecular Oncology, Genentech, South San Francisco, CA, USA.
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16
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Dominguez S, Varfolomeev E, Brendza R, Stark K, Tea J, Imperio J, Ngu H, Earr T, Foreman O, Webster JD, Easton A, Vucic D, Bingol B. Genetic inactivation of RIP1 kinase does not ameliorate disease in a mouse model of ALS. Cell Death Differ 2020; 28:915-931. [PMID: 32994544 DOI: 10.1038/s41418-020-00625-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/07/2020] [Accepted: 09/11/2020] [Indexed: 12/20/2022] Open
Abstract
RIP1 kinase is proposed to play a critical role in driving necroptosis and inflammation in neurodegenerative disorders, including Amyotrophic Lateral Sclerosis (ALS). Preclinical studies indicated that while pharmacological inhibition of RIP1 kinase can ameliorate axonal pathology and delay disease onset in the mutant SOD1 transgenic (SOD1-Tg) mice, genetic blockade of necroptosis does not provide benefit in this mouse model. To clarify the role of RIP1 kinase activity in driving pathology in SOD1-Tg mice, we crossed SOD1-Tgs to RIP1 kinase-dead knock-in mice, and measured disease progression using functional and histopathological endpoints. Genetic inactivation of the RIP1 kinase activity in the SOD1-Tgs did not benefit the declining muscle strength or nerve function, motor neuron degeneration or neuroinflammation. In addition, we did not find evidence of phosphorylated RIP1 accumulation in the spinal cords of ALS patients. On the other hand, genetic inactivation of RIP1 kinase activity ameliorated the depletion of the neurotransmitter dopamine in a toxin model of dopaminergic neurodegeneration. These findings indicate that RIP1 kinase activity is dispensable for disease pathogenesis in the SOD1-Tg mice while inhibition of kinase activity may provide benefit in acute injury models.
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Affiliation(s)
- Sara Dominguez
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Eugene Varfolomeev
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Robert Brendza
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Kim Stark
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Joy Tea
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Jose Imperio
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Hai Ngu
- Department of Pathology, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Timothy Earr
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Oded Foreman
- Department of Pathology, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Amy Easton
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Baris Bingol
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA.
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17
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Webster JD, Solon M, Gibson-Corley KN. Validating Immunohistochemistry Assay Specificity in Investigative Studies: Considerations for a Weight of Evidence Approach. Vet Pathol 2020; 58:829-840. [PMID: 32975488 DOI: 10.1177/0300985820960132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Immunohistochemistry (IHC) is a fundamental molecular technique that provides information on protein expression in the context of spatial localization and tissue morphology. IHC is used in all facets of pathology from identifying infectious agents or characterizing tumors in diagnostics, to characterizing cellular and molecular processes in investigative and experimental studies. Confidence in an IHC assay is primarily driven by the degree to which it is validated. There are many approaches to validate an IHC assay's specificity including bioinformatics approaches using published protein sequences, careful design of positive and negative tissue controls, use of cell pellets with known target protein expression, corroboration of IHC findings with western blots and other analytical methods, and replacement of the primary antibody with an appropriate negative control reagent. Each approach has inherent strengths and weaknesses, and the thoughtful use of these approaches provides cumulative evidence, or a weight of evidence, to support the IHC assay's specificity and build confidence in a study's conclusions. Although it is difficult to be 100% confident in the specificity of any IHC assay, it is important to consider how validation approaches provide evidence to support or to question the specificity of labeling, and how that evidence affects the overall interpretation of a study's results. In this review, we discuss different approaches for IHC antibody validation, with an emphasis on the characterization of antibody specificity in investigative studies. While this review is not prescriptive, it is hoped that it will be thought provoking when considering the interpretation of IHC results.
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18
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Ndoja A, Reja R, Lee SH, Webster JD, Ngu H, Rose CM, Kirkpatrick DS, Modrusan Z, Chen YJJ, Dugger DL, Gandham V, Xie L, Newton K, Dixit VM. Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPβ in Microglia. Cell 2020; 182:1156-1169.e12. [PMID: 32795415 DOI: 10.1016/j.cell.2020.07.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/09/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Dysregulated microglia are intimately involved in neurodegeneration, including Alzheimer's disease (AD) pathogenesis, but the mechanisms controlling pathogenic microglial gene expression remain poorly understood. The transcription factor CCAAT/enhancer binding protein beta (c/EBPβ) regulates pro-inflammatory genes in microglia and is upregulated in AD. We show expression of c/EBPβ in microglia is regulated post-translationally by the ubiquitin ligase COP1 (also called RFWD2). In the absence of COP1, c/EBPβ accumulates rapidly and drives a potent pro-inflammatory and neurodegeneration-related gene program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies reveal that neurotoxicity is almost entirely attributable to complement. Remarkably, loss of a single allele of Cebpb prevented the pro-inflammatory phenotype. COP1-deficient microglia markedly accelerated tau-mediated neurodegeneration in a mouse model where activated microglia play a deleterious role. Thus, COP1 is an important suppressor of pathogenic c/EBPβ-dependent gene expression programs in microglia.
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Affiliation(s)
- Ada Ndoja
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Seung-Hye Lee
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Hai Ngu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Ying-Jiun Jasmine Chen
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Vineela Gandham
- Department of Biomedical Imaging, Genentech, South San Francisco, CA 94080, USA
| | - Luke Xie
- Department of Biomedical Imaging, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
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19
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Zhang J, Webster JD, Dugger DL, Goncharov T, Roose-Girma M, Hung J, Kwon YC, Vucic D, Newton K, Dixit VM. Ubiquitin Ligases cIAP1 and cIAP2 Limit Cell Death to Prevent Inflammation. Cell Rep 2020; 27:2679-2689.e3. [PMID: 31141691 DOI: 10.1016/j.celrep.2019.04.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/29/2019] [Accepted: 04/26/2019] [Indexed: 01/18/2023] Open
Abstract
Cellular inhibitor of apoptosis proteins cIAP1 and cIAP2 ubiquitinate nuclear factor κB (NF-κB)-inducing kinase (NIK) to suppress non-canonical NF-κB signaling and substrates such as receptor interacting protein kinase 1 (RIPK1) to promote cell survival. We investigate how these functions contribute to homeostasis by eliminating cIap2 from adult cIap1-deficient mice. cIAP1 and cIAP2 (cIAP1/2) deficiency causes rapid weight loss and inflammation, with aberrant cell death, indicated by cleaved caspases-3 and -8, prevalent in intestine and liver. Deletion of Casp8 and Ripk3 prevents this aberrant cell death, reduces the inflammation, and prolongs mouse survival, whereas Ripk3 loss alone offers little benefit. Residual inflammation in mice lacking cIap1/2, Casp8, and Ripk3 is reduced by inhibition of NIK. Loss of Casp8 and Mlkl (mixed lineage kinase domain-like), but not Mlkl loss alone, also prevents cIAP1/2-deficient mice from dying around embryonic day 11. Therefore, a major function of cIAP1/2 in vivo is to suppress caspase-8-dependent cell death.
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Affiliation(s)
- Jieqiong Zhang
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Tatiana Goncharov
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Jeffrey Hung
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Youngsu C Kwon
- Department of Translational Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
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20
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Chung JJ, Goldstein L, Chen YJJ, Lee J, Webster JD, Roose-Girma M, Paudyal SC, Modrusan Z, Dey A, Shaw AS. Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury. J Am Soc Nephrol 2020; 31:2341-2354. [PMID: 32651223 DOI: 10.1681/asn.2020020220] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/07/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The glomerulus is a specialized capillary bed that is involved in urine production and BP control. Glomerular injury is a major cause of CKD, which is epidemic and without therapeutic options. Single-cell transcriptomics has radically improved our ability to characterize complex organs, such as the kidney. Cells of the glomerulus, however, have been largely underrepresented in previous single-cell kidney studies due to their paucity and intractability. METHODS Single-cell RNA sequencing comprehensively characterized the types of cells in the glomerulus from healthy mice and from four different disease models (nephrotoxic serum nephritis, diabetes, doxorubicin toxicity, and CD2AP deficiency). RESULTS All cell types in the glomerulus were identified using unsupervised clustering analysis. Novel marker genes and gene signatures of mesangial cells, vascular smooth muscle cells of the afferent and efferent arterioles, parietal epithelial cells, and three types of endothelial cells were identified. Analysis of the disease models revealed cell type-specific and injury type-specific responses in the glomerulus, including acute activation of the Hippo pathway in podocytes after nephrotoxic immune injury. Conditional deletion of YAP or TAZ resulted in more severe and prolonged proteinuria in response to injury, as well as worse glomerulosclerosis. CONCLUSIONS Generation of comprehensive high-resolution, single-cell transcriptomic profiles of the glomerulus from healthy and injured mice provides resources to identify novel disease-related genes and pathways.
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Affiliation(s)
- Jun-Jae Chung
- Department of Research Biology, Genentech, South San Francisco, California
| | - Leonard Goldstein
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Ying-Jiun J Chen
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Jiyeon Lee
- Department of Research Biology, Genentech, South San Francisco, California
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, California
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Sharad C Paudyal
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, California
| | - Anwesha Dey
- Department of Molecular Oncology, Genentech, South San Francisco, California
| | - Andrey S Shaw
- Department of Research Biology, Genentech, South San Francisco, California
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21
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Webster JD, Vucic D. The Balance of TNF Mediated Pathways Regulates Inflammatory Cell Death Signaling in Healthy and Diseased Tissues. Front Cell Dev Biol 2020; 8:365. [PMID: 32671059 PMCID: PMC7326080 DOI: 10.3389/fcell.2020.00365] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/23/2020] [Indexed: 12/17/2022] Open
Abstract
Tumor necrosis factor alpha (TNF; TNFα) is a critical regulator of immune responses in healthy organisms and in disease. TNF is involved in the development and proper functioning of the immune system by mediating cell survival and cell death inducing signaling. TNF stimulated signaling pathways are tightly regulated by a series of phosphorylation and ubiquitination events, which enable timely association of TNF receptors-associated intracellular signaling complexes. Disruption of these signaling events can disturb the balance and the composition of signaling complexes, potentially resulting in severe inflammatory diseases.
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Affiliation(s)
- Joshua D Webster
- Departments of Pathology and Early Discovery Biochemistry, Genentech, South San Francisco, CA, United States
| | - Domagoj Vucic
- Departments of Pathology and Early Discovery Biochemistry, Genentech, South San Francisco, CA, United States
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22
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Webster JD, Kwon YC, Park S, Zhang H, Corr N, Ljumanovic N, Adedeji AO, Varfolomeev E, Goncharov T, Preston J, Santagostino SF, Patel S, Xu M, Maher J, McKenzie BS, Vucic D. RIP1 kinase activity is critical for skin inflammation but not for viral propagation. J Leukoc Biol 2020; 107:941-952. [PMID: 31985117 PMCID: PMC7317411 DOI: 10.1002/jlb.3ma1219-398r] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 12/24/2022] Open
Abstract
Receptor interacting protein kinase 1 (RIP1) is a critical effector of inflammatory responses and cell death activation. Cell death pathways regulated by RIP1 include caspase‐dependent apoptosis and caspase‐independent necroptosis. The kinase activity of RIP1 has been associated with a number of inflammatory, neurodegenerative, and oncogenic diseases. In this study, we use the RIP1 kinase inhibitor GNE684 to demonstrate that RIP1 inhibition can effectively block skin inflammation and immune cell infiltrates in livers of Sharpin mutant (Cpdm; chronic proliferative dermatitis) mice in an interventional setting, after disease onset. On the other hand, genetic inactivation of RIP1 (RIP1 KD) or ablation of RIP3 (RIP3 KO) or MLKL (MLKL KO) did not affect testicular pathology of aging male mice. Likewise, infection with vaccinia virus or with mouse gammaherpesvirus MHV68 resulted in similar viral clearance in wild‐type, RIP1 KD, and RIP3 KO mice. In summary, this study highlights the benefits of inhibiting RIP1 in skin inflammation, as opposed to its lack of relevance for testicular longevity and the response to certain viral infections.
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Affiliation(s)
- Joshua D Webster
- Departments of Pathology, Genentech, South San Francisco, California, USA
| | - Youngsu C Kwon
- Translational Immunology, Genentech, South San Francisco, California, USA
| | - Summer Park
- Translational Immunology, Genentech, South San Francisco, California, USA
| | - Hua Zhang
- Translational Immunology, Genentech, South San Francisco, California, USA
| | - Nick Corr
- Safety Assessment, Genentech, South San Francisco, California, USA
| | - Nina Ljumanovic
- Safety Assessment, Genentech, South San Francisco, California, USA
| | | | - Eugene Varfolomeev
- Early Discovery Biochemistry, Genentech, South San Francisco, California, USA
| | - Tatiana Goncharov
- Early Discovery Biochemistry, Genentech, South San Francisco, California, USA
| | - Jessica Preston
- Departments of Pathology, Genentech, South San Francisco, California, USA
| | | | - Snahel Patel
- Discovery Chemistry, Genentech, South San Francisco, California, USA
| | - Min Xu
- Translational Immunology, Genentech, South San Francisco, California, USA
| | - Jonathan Maher
- Safety Assessment, Genentech, South San Francisco, California, USA
| | - Brent S McKenzie
- Translational Immunology, Genentech, South San Francisco, California, USA
| | - Domagoj Vucic
- Early Discovery Biochemistry, Genentech, South San Francisco, California, USA
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23
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Lee HJ, Pham T, Chang MT, Barnes D, Cai AG, Noubade R, Totpal K, Chen X, Tran C, Hagenbeek T, Wu X, Eastham-Anderson J, Tao J, Lee W, Bastian BC, Carbone M, Webster JD, Dey A. The Tumor Suppressor BAP1 Regulates the Hippo Pathway in Pancreatic Ductal Adenocarcinoma. Cancer Res 2020; 80:1656-1668. [PMID: 31988076 DOI: 10.1158/0008-5472.can-19-1704] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/04/2019] [Accepted: 01/17/2020] [Indexed: 11/16/2022]
Abstract
The deubiquitinating enzyme BAP1 is mutated in a hereditary cancer syndrome with a high risk for mesothelioma and melanocytic tumors. Here, we show that pancreatic intraepithelial neoplasia driven by oncogenic mutant KrasG12D progressed to pancreatic adenocarcinoma in the absence of BAP1. The Hippo pathway was deregulated in BAP1-deficient pancreatic tumors, with the tumor suppressor LATS exhibiting enhanced ubiquitin-dependent proteasomal degradation. Therefore, BAP1 may limit tumor progression by stabilizing LATS and thereby promoting activity of the Hippo tumor suppressor pathway. SIGNIFICANCE: BAP1 is mutated in a broad spectrum of tumors. Pancreatic Bap1 deficiency causes acinar atrophy but combines with oncogenic Ras to produce pancreatic tumors. BAP1-deficient tumors exhibit deregulation of the Hippo pathway.See related commentary by Brekken, p. 1624.
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Affiliation(s)
- Ho-June Lee
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Trang Pham
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Matthew T Chang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California
| | - Dwight Barnes
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Allen G Cai
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Rajkumar Noubade
- Department of Immunology, Genentech, Inc., South San Francisco, California
| | - Klara Totpal
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California
| | - Xu Chen
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Christopher Tran
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Thijs Hagenbeek
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Xiumin Wu
- Translational Immunology, Genentech, Inc., South San Francisco, California
| | | | - Janet Tao
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Wyne Lee
- Translational Immunology, Genentech, Inc., South San Francisco, California
| | - Boris C Bastian
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Michele Carbone
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Joshua D Webster
- Department of Pathology, Genentech, Inc., South San Francisco, California.
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California.
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24
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Webster JD, Santagostino SF, Foreman O. Applications and considerations for the use of genetically engineered mouse models in drug development. Cell Tissue Res 2019; 380:325-340. [DOI: 10.1007/s00441-019-03101-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023]
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25
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Reichelt M, Sagolla M, Katakam AK, Webster JD. Unobstructed Multiscale Imaging of Tissue Sections for Ultrastructural Pathology Analysis by Backscattered Electron Scanning Microscopy. J Histochem Cytochem 2019; 68:9-23. [PMID: 31385742 DOI: 10.1369/0022155419868992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ultrastructural analysis of healthy, diseased, or experimental tissues is essential in diagnostic and investigative pathology. Evaluation of large tissue areas with suborganelle resolution is challenging because biological structures ranging from several millimeters to nanometers in size need to be identified and imaged while maintaining context over multiple scales. Imaging with field emission scanning electron microscopes (FE-SEMs) is uniquely suited for this task. We describe an efficient workflow for the preparation and unobstructed multiscale imaging of tissue sections with backscattered electron scanning electron microscopy (BSE-SEM) for applications in ultrastructural pathology. We demonstrate that a diverse range of tissues, processed by conventional electron microscopy protocols and avoiding the use of mordanting agents, can be imaged on standard glass slides over multiple scales, from the histological to the ultrastructural level, without any visual obstructions. Our workflow takes advantage of the very large scan fields possible with modern FE-SEMs that allow for the acquisition of wide-field overview images which can be explored at the ultrastructural level by digitally zooming into the images. Examples from applications in pulmonary research and neuropathology demonstrate the versatility and efficiency of this method. This BSE-SEM-based multiscale imaging procedure promises to substantially simplify and accelerate ultrastructural tissue analysis in pathology.
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Affiliation(s)
- Mike Reichelt
- Department of Pathology, Genentech Inc., South San Francisco, California
| | - Meredith Sagolla
- Department of Pathology, Genentech Inc., South San Francisco, California
| | - Anand K Katakam
- Department of Pathology, Genentech Inc., South San Francisco, California
| | - Joshua D Webster
- Department of Pathology, Genentech Inc., South San Francisco, California
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26
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Thamm DH, Avery AC, Berlato D, Bulman-Fleming J, Clifford CA, Hershey AE, Intile JL, Jones PD, Kamstock DA, Liptak JM, Pavuk A, Peauroi J, Powell R, Rissetto K, Valli VEO, Webster JD. Prognostic and predictive significance of KIT protein expression and c-kit gene mutation in canine cutaneous mast cell tumours: A consensus of the Oncology-Pathology Working Group. Vet Comp Oncol 2019; 17:451-455. [PMID: 31264352 DOI: 10.1111/vco.12518] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023]
Abstract
One of the primary objectives of the Oncology-Pathology Working Group (OPWG), a joint initiative of the Veterinary Cancer Society and the American College of Veterinary Pathologists, is for oncologists and pathologists to collaboratively generate consensus documents to standardize aspects of and provide guidelines for oncologic pathology. Consensus is established through critical review of peer-reviewed literature relevant to a subgroup's particular focus. Subsequent acceptance and approval of the document by the OPWG membership at large establishes consensus. The intent of this publication is to help educate practitioners and pathologists on the value of diagnostics related to the KIT receptor tyrosine kinase for canine cutaneous mast cell tumours and to provide a guide for the use of these tests in veterinary medicine. This document represents the opinions of the OPWG and the authors and does not constitute a formal endorsement by the American College of Veterinary Pathologists or the Veterinary Cancer Society.
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Affiliation(s)
- Douglas H Thamm
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado
| | - Anne C Avery
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado
| | | | | | | | | | - Joanne L Intile
- Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina
| | | | | | | | - Alana Pavuk
- Antech Diagnostics, Hillsborough, North Carolina
| | | | - Roger Powell
- Powell Torrance Diagnostic Services, Hertfordshire, UK
| | - Kerry Rissetto
- Charleston Veterinary Referral Center, Charleston, South Carolina
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27
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He M, Chaurushiya MS, Webster JD, Kummerfeld S, Reja R, Chaudhuri S, Chen YJ, Modrusan Z, Haley B, Dugger DL, Eastham-Anderson J, Lau S, Dey A, Caothien R, Roose-Girma M, Newton K, Dixit VM. Intrinsic apoptosis shapes the tumor spectrum linked to inactivation of the deubiquitinase BAP1. Science 2019; 364:283-285. [PMID: 31000662 DOI: 10.1126/science.aav4902] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/15/2019] [Indexed: 11/02/2022]
Abstract
Malignancies arising from mutation of tumor suppressors have unexplained tissue proclivity. For example, BAP1 encodes a widely expressed deubiquitinase for histone H2A, but germline mutations are predominantly associated with uveal melanomas and mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells, fibroblasts, liver, and pancreatic tissue but not in melanocytes and mesothelial cells. Ubiquitin ligase RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient cells by suppressing expression of the prosurvival genes Bcl2 and Mcl1. In contrast, BAP1 loss in melanocytes had little impact on expression of prosurvival genes, instead inducing Mitf Thus, BAP1 appears to modulate gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in cells that do not engage an RNF2-dependent apoptotic program.
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Affiliation(s)
- Meng He
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mira S Chaurushiya
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah Kummerfeld
- Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Shari Lau
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Roger Caothien
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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28
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Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM. The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification. PLoS One 2019; 14:e0214110. [PMID: 30951545 PMCID: PMC6450627 DOI: 10.1371/journal.pone.0214110] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023] Open
Abstract
Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotransposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiating TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.
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Affiliation(s)
- Mona Abed
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Erik Verschueren
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Hanna Budayeva
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Peter Liu
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Donald S. Kirkpatrick
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Rohit Reja
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah K. Kummerfeld
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Joshua D. Webster
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah Gierke
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Mike Reichelt
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Keith R. Anderson
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Robert J. Newman
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Merone Roose-Girma
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Zora Modrusan
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Hazal Pektas
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Emin Maltepe
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Kim Newton
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Vishva M. Dixit
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
- * E-mail:
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29
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Webster JD, Pham TH, Wu X, Hughes NW, Li Z, Totpal K, Lee HJ, Calses PC, Chaurushiya MS, Stawiski EW, Modrusan Z, Chang MT, Tran C, Lee WP, Chalasani S, Hung J, Sharma N, Chan S, Hotzel K, Talevich E, Shain A, Xu M, Lill J, Dixit VM, Bastian BC, Dey A. The tumor suppressor BAP1 cooperates with BRAFV600E to promote tumor formation in cutaneous melanoma. Pigment Cell Melanoma Res 2019; 32:269-279. [PMID: 30156010 DOI: 10.1111/pcmr.12735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/19/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022]
Abstract
The deubiquitinating enzyme BAP1 is mutated in a hereditary cancer syndrome with a high risk of mesothelioma and melanocytic tumors. Here, we show that Bap1 deletion in melanocytes cooperates with the constitutively active, oncogenic form of BRAF (BRAFV600E ) and UV to cause melanoma in mice, albeit at very low frequency. In addition, Bap1-null melanoma cells derived from mouse tumors are more aggressive and colonize and grow at distant sites more than their wild-type counterparts. Molecularly, Bap1-null melanoma cell lines have increased DNA damage measured by γH2aX and hyperubiquitination of histone H2a. Therapeutically, these Bap1-null tumors are completely responsive to BRAF- and MEK-targeted therapies. Therefore, BAP1 functions as a tumor suppressor and limits tumor progression in melanoma.
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Affiliation(s)
- Joshua D Webster
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Trang H Pham
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, California
| | - Nicolas W Hughes
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Zhongwu Li
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Klara Totpal
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California
| | - Ho-June Lee
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Philamer C Calses
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Mira S Chaurushiya
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, California
| | - Eric W Stawiski
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California
| | - Matthew T Chang
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California
| | - Christopher Tran
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, California
| | - Sreedevi Chalasani
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Jeffrey Hung
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Neeraj Sharma
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Sara Chan
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Kathy Hotzel
- Department of Pathology, Genentech, Inc., South San Francisco, California
| | - Eric Talevich
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Alan Shain
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Mengshu Xu
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Jennie Lill
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, California
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., South San Francisco, California
| | - Boris C Bastian
- Departments of Dermatology and Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California
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Caswell JL, Bassel LL, Rothenburger JL, Gröne A, Sargeant JM, Beck AP, Ekman S, Gibson-Corley KN, Kuiken T, LaDouceur EEB, Meyerholz DK, Origgi FC, Posthaus H, Priestnall SL, Ressel L, Sharkey L, Teixeira LBC, Uchida K, Ward JM, Webster JD, Yamate J. Observational Study Design in Veterinary Pathology, Part 2: Methodology. Vet Pathol 2018; 55:774-785. [DOI: 10.1177/0300985818798121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Observational studies are a basis for much of our knowledge of veterinary pathology, yet considerations for conducting pathology-based observational studies are not readily available. In part 1 of this series, we offered advice on planning and carrying out an observational study. Part 2 of the series focuses on methodology. Our general recommendations are to consider using already-validated methods, published guidelines, data from primary sources, and quantitative analyses. We discuss 3 common methods in pathology research—histopathologic scoring, immunohistochemistry, and polymerase chain reaction—to illustrate principles of method validation. Some aspects of quality control include use of clear objective grading criteria, validation of key reagents, assessing sample quality, determining specificity and sensitivity, use of technical and biologic negative and positive controls, blinding of investigators, approaches to minimizing operator-dependent variation, measuring technical variation, and consistency in analysis of the different study groups. We close by discussing approaches to increasing the rigor of observational studies by corroborating results with complementary methods, using sufficiently large numbers of study subjects, consideration of the data in light of similar published studies, replicating the results in a second study population, and critical analysis of the study findings.
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Affiliation(s)
- Jeff L. Caswell
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Laura L. Bassel
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Jamie L. Rothenburger
- Department of Ecosystem and Public Health; Canadian Wildlife Health Cooperative (Alberta), Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Andrea Gröne
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jan M. Sargeant
- Department of Population Medicine and Centre for Public Health and Zoonoses, University of Guelph, Guelph, ON, Canada
| | | | - Stina Ekman
- Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Katherine N. Gibson-Corley
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Thijs Kuiken
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - David K. Meyerholz
- University of Iowa Carver College of Medicine, 1165 Medical Laboratories, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Francesco C. Origgi
- Centre for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Horst Posthaus
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Simon L. Priestnall
- Department of Pathobiology & Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Lorenzo Ressel
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - Leslie Sharkey
- Department of Clinical Sciences, Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Leandro B. C. Teixeira
- Department of Pathobiological Sciences, University of Wisconsin–Madison, Madison, WI, USA
| | - Kazuyuki Uchida
- Department of Veterinary Pathology, University of Tokyo, Tokyo, Japan
| | | | | | - Jyoji Yamate
- Laboratory of Veterinary Pathology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano City, Osaka, Japan
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Hagenbeek TJ, Webster JD, Kljavin NM, Chang MT, Pham T, Lee HJ, Klijn C, Cai AG, Totpal K, Ravishankar B, Yang N, Lee DH, Walsh KB, Hatzivassiliou G, de la Cruz CC, Gould SE, Wu X, Lee WP, Yang S, Zhang Z, Gu Q, Ji Q, Jackson EL, Lim DS, Dey A. The Hippo pathway effector TAZ induces TEAD-dependent liver inflammation and tumors. Sci Signal 2018; 11:11/547/eaaj1757. [PMID: 30206136 DOI: 10.1126/scisignal.aaj1757] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Hippo signaling pathway regulates organ size and plays critical roles in maintaining tissue growth, homeostasis, and regeneration. Dysregulated in a wide spectrum of cancers, in mammals, this pathway is regulated by two key effectors, YAP and TAZ, that may functionally overlap. We found that TAZ promoted liver inflammation and tumor development. The expression of TAZ, but not YAP, in human liver tumors positively correlated with the expression of proinflammatory cytokines. Hyperactivated TAZ induced substantial myeloid cell infiltration into the liver and the secretion of proinflammatory cytokines through a TEAD-dependent mechanism. Furthermore, tumors with hyperactivated YAP and TAZ had distinct transcriptional signatures, which included the increased expression of inflammatory cytokines in TAZ-driven tumors. Our study elucidated a previously uncharacterized link between TAZ activity and inflammatory responses that influence tumor development in the liver.
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Affiliation(s)
- Thijs J Hagenbeek
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Noelyn M Kljavin
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Matthew T Chang
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Trang Pham
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ho-June Lee
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christiaan Klijn
- Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Allen G Cai
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Klara Totpal
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Buvana Ravishankar
- Department of Cancer Immunotherapy, Genentech Inc., South San Francisco, CA 94080, USA
| | - Naiying Yang
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Da-Hye Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kevin B Walsh
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Cecile C de la Cruz
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Stephen E Gould
- Department of Translational Oncology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Shuqun Yang
- Oncology Business Unit, Research Service Division, WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhixiang Zhang
- Oncology Business Unit, Research Service Division, WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qingyang Gu
- Oncology Business Unit, Research Service Division, WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qunsheng Ji
- Oncology Business Unit, Research Service Division, WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Erica L Jackson
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Dae-Sik Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Raju S, Whalen DM, Mengistu M, Swanson C, Quinn JG, Taylor SS, Webster JD, Newton K, Shaw AS. Kinase domain dimerization drives RIPK3-dependent necroptosis. Sci Signal 2018; 11:11/544/eaar2188. [PMID: 30131368 DOI: 10.1126/scisignal.aar2188] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Necroptosis, an inflammatory form of cell death, is initiated by the activation of receptor-interacting protein kinase 3 (RIPK3), which depends on its interaction with RIPK1. Although catalytically inactive, the RIPK3 mutant D161N still stimulates RIPK1-dependent apoptosis and embryonic lethality in RIPK3 D161N homozygous mice. Whereas the absence of RIPK1 rescues RIPK3 D161N homozygous mice, we report that the absence of RIPK1 leads to embryonic lethality in RIPK3 D161N heterozygous mice. This suggested that the kinase domain of RIPK3 had a noncatalytic function that was enhanced by a conformation induced by the D161N mutation. We found that the RIPK3 kinase domain homodimerized through a surface that is structurally similar to that of the RAF family members. Mutation of residues at the dimer interface impaired dimerization and necroptosis. Kinase domain dimerization stimulated the activation of RIPK3 through cis-autophosphorylation. This noncatalytic, allosteric activity was enhanced by certain kinase-deficient mutants of RIPK3, including D161N. Furthermore, apoptosis induced by certain RIPK3 inhibitors was also dependent on the kinase dimerization interface. Our studies reveal that the RIPK3 kinase domain exhibits catalytically independent function that is important for both RIPK3-dependent necroptosis and apoptosis.
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Affiliation(s)
- Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel M Whalen
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Meron Mengistu
- Department of Research Biology, Genentech, South San Francisco, CA 94080, USA
| | - Carter Swanson
- Department of Research Biology, Genentech, South San Francisco, CA 94080, USA
| | - John G Quinn
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA 94080, USA
| | - Susan S Taylor
- Departments of Chemistry/Biochemistry and Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Andrey S Shaw
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Department of Research Biology, Genentech, South San Francisco, CA 94080, USA
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Caswell JL, Bassel LL, Rothenburger JL, Gröne A, Sargeant JM, Beck AP, Ekman S, Gibson-Corley KN, Kuiken T, LaDouceur EEB, Meyerholz DK, Origgi FC, Posthaus H, Priestnall SL, Ressel L, Sharkey L, Teixeira LBC, Uchida K, Ward JM, Webster JD, Yamate J. Observational Study Design in Veterinary Pathology, Part 1: Study Design. Vet Pathol 2018; 55:607-621. [PMID: 30071806 DOI: 10.1177/0300985818785705] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Observational studies are the basis for much of our knowledge of veterinary pathology and are highly relevant to the daily practice of pathology. However, recommendations for conducting pathology-based observational studies are not readily available. In part 1 of this series, we offer advice on planning and conducting an observational study with examples from the veterinary pathology literature. Investigators should recognize the importance of creativity, insight, and innovation in devising studies that solve problems and fill important gaps in knowledge. Studies should focus on specific and testable hypotheses, questions, or objectives. The methodology is developed to support these goals. We consider the merits and limitations of different types of analytic and descriptive studies, as well as of prospective vs retrospective enrollment. Investigators should define clear inclusion and exclusion criteria and select adequate numbers of study subjects, including careful selection of the most appropriate controls. Studies of causality must consider the temporal relationships between variables and the advantages of measuring incident cases rather than prevalent cases. Investigators must consider unique aspects of studies based on archived laboratory case material and take particular care to consider and mitigate the potential for selection bias and information bias. We close by discussing approaches to adding value and impact to observational studies. Part 2 of the series focuses on methodology and validation of methods.
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Affiliation(s)
- Jeff L Caswell
- 1 Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Laura L Bassel
- 1 Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Jamie L Rothenburger
- 2 Department of Ecosystem and Public Health, Canadian Wildlife Health Cooperative, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrea Gröne
- 3 Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jan M Sargeant
- 4 Department of Population Medicine and Centre for Public Health and Zoonoses, University of Guelph, Guelph, Ontario, Canada
| | - Amanda P Beck
- 5 Albert Einstein College of Medicine, Bronx, NY, USA
| | - Stina Ekman
- 6 Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Katherine N Gibson-Corley
- 7 Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Thijs Kuiken
- 8 Department of Viroscience, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - David K Meyerholz
- 10 University of Iowa Carver College of Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Francesco C Origgi
- 11 Centre for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Horst Posthaus
- 12 Institute of Animal Pathology, Vetsuisse-Faculty, University of Bern, Bern, Switzerland
| | - Simon L Priestnall
- 13 Deparment Pathobiology & Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Lorenzo Ressel
- 14 Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Leslie Sharkey
- 15 Department of Clinical Sciences, Cummings School of Veterinary Medicine, Tufts University, N. Grafton, MA, USA
| | - Leandro B C Teixeira
- 16 Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kazuyuki Uchida
- 17 Department of Veterinary Pathology, University of Tokyo, Tokyo, Japan
| | | | | | - Jyoji Yamate
- 20 Laboratory of Veterinary Pathology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano City, Osaka, Japan
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Abstract
Activation of the kinase RIPK3 (receptor interacting protein kinase 3) is a hallmark of cells dying by necroptosis. RIPK3 phosphorylates both itself and the pseudokinase MLKL (mixed lineage kinase-like) resulting in MLKL translocation to membranes and cell lysis. Antibodies recognizing RIPK3 autophosphorylation or the RIPK3-dependent phosphorylation sites on MLKL have therefore been used to monitor necroptosis induction. Here we describe immunohistochemical labeling for autophosphorylated mouse RIPK3 as a means of detecting cells undergoing necroptosis in mouse tissues.
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Affiliation(s)
- Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Margaret Solon
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Susan Haller
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA, USA.
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36
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Newton K, Wickliffe KE, Maltzman A, Dugger DL, Strasser A, Pham VC, Lill JR, Roose-Girma M, Warming S, Solon M, Ngu H, Webster JD, Dixit VM. RIPK1 inhibits ZBP1-driven necroptosis during development. Nature 2016; 540:129-133. [DOI: 10.1038/nature20559] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/25/2016] [Indexed: 12/31/2022]
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de Almagro MC, Goncharov T, Izrael-Tomasevic A, Duttler S, Kist M, Varfolomeev E, Wu X, Lee WP, Murray J, Webster JD, Yu K, Kirkpatrick DS, Newton K, Vucic D. Coordinated ubiquitination and phosphorylation of RIP1 regulates necroptotic cell death. Cell Death Differ 2016; 24:26-37. [PMID: 27518435 PMCID: PMC5260504 DOI: 10.1038/cdd.2016.78] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/15/2016] [Accepted: 07/07/2016] [Indexed: 12/23/2022] Open
Abstract
Proper regulation of cell death signaling is crucial for the maintenance of homeostasis and prevention of disease. A caspase-independent regulated form of cell death called necroptosis is rapidly emerging as an important mediator of a number of human pathologies including inflammatory bowel disease and ischemia–reperfusion organ injury. Activation of necroptotic signaling through TNF signaling or organ injury leads to the activation of kinases receptor-interacting protein kinases 1 and 3 (RIP1 and RIP3) and culminates in inflammatory cell death. We found that, in addition to phosphorylation, necroptotic cell death is regulated by ubiquitination of RIP1 in the necrosome. Necroptotic RIP1 ubiquitination requires RIP1 kinase activity, but not necroptotic mediators RIP3 and MLKL (mixed lineage kinase-like). Using immunoaffinity enrichment and mass spectrometry, we profiled numerous ubiquitination events on RIP1 that are triggered during necroptotic signaling. Mutation of a necroptosis-related ubiquitination site on RIP1 reduced necroptotic cell death and RIP1 ubiquitination and phosphorylation, and disrupted the assembly of RIP1 and RIP3 in the necrosome, suggesting that necroptotic RIP1 ubiquitination is important for maintaining RIP1 kinase activity in the necrosome complex. We also observed RIP1 ubiquitination in injured kidneys consistent with a physiological role of RIP1 ubiquitination in ischemia–reperfusion disease. Taken together, these data reveal that coordinated and interdependent RIP1 phosphorylation and ubiquitination within the necroptotic complex regulate necroptotic signaling and cell death.
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Affiliation(s)
- M Cristina de Almagro
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tatiana Goncharov
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anita Izrael-Tomasevic
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Stefanie Duttler
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Matthias Kist
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Varfolomeev
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jeremy Murray
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kebing Yu
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Departments of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
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38
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Baughman JM, Rose CM, Kolumam G, Webster JD, Wilkerson EM, Merrill AE, Rhoads TW, Noubade R, Katavolos P, Lesch J, Stapleton DS, Rabaglia ME, Schueler KL, Asuncion R, Domeyer M, Zavala-Solorio J, Reich M, DeVoss J, Keller MP, Attie AD, Hebert AS, Westphall MS, Coon JJ, Kirkpatrick DS, Dey A. NeuCode Proteomics Reveals Bap1 Regulation of Metabolism. Cell Rep 2016; 16:583-595. [PMID: 27373151 PMCID: PMC5546211 DOI: 10.1016/j.celrep.2016.05.096] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/14/2016] [Accepted: 05/28/2016] [Indexed: 12/13/2022] Open
Abstract
We introduce neutron-encoded (NeuCode) amino acid labeling of mice as a strategy for multiplexed proteomic analysis in vivo. Using NeuCode, we characterize an inducible knockout mouse model of Bap1, a tumor suppressor and deubiquitinase whose in vivo roles outside of cancer are not well established. NeuCode proteomics revealed altered metabolic pathways following Bap1 deletion, including profound elevation of cholesterol biosynthetic machinery coincident with reduced expression of gluconeogenic and lipid homeostasis proteins in liver. Bap1 loss increased pancreatitis biomarkers and reduced expression of mitochondrial proteins. These alterations accompany a metabolic remodeling with hypoglycemia, hypercholesterolemia, hepatic lipid loss, and acinar cell degeneration. Liver-specific Bap1 null mice present with fully penetrant perinatal lethality, severe hypoglycemia, and hepatic lipid deficiency. This work reveals Bap1 as a metabolic regulator in liver and pancreas, and it establishes NeuCode as a reliable proteomic method for deciphering in vivo biology.
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Affiliation(s)
- Joshua M Baughman
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ganesh Kolumam
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Emily M Wilkerson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna E Merrill
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy W Rhoads
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rajkumar Noubade
- Department of Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Paula Katavolos
- Department of Safety Assessment, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Justin Lesch
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mary E Rabaglia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathy L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Raymond Asuncion
- Department of Transgenic Technology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Melanie Domeyer
- Department of Transgenic Technology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jose Zavala-Solorio
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Michael Reich
- Department of Laboratory Animal Resources, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason DeVoss
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Donald S Kirkpatrick
- Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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Webster JD. Transcriptional profiling of canine mast cell tumors: Searching for candidate targets and prognostic markers. Vet J 2016; 214:84-5. [PMID: 27387731 DOI: 10.1016/j.tvjl.2016.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 11/17/2022]
Affiliation(s)
- Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 90480, USA.
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Kiupel M, Webster JD, Kaneene JB, Miller R, Yuzbasiyan-Gurkan V. The Use of KIT and Tryptase Expression Patterns as Prognostic Tools for Canine Cutaneous Mast Cell Tumors. Vet Pathol 2016; 41:371-7. [PMID: 15232137 DOI: 10.1354/vp.41-4-371] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cutaneous mast cell tumors (MCTs) are one of the most common tumors in dogs. Currently, prognostic and therapeutic determinations for MCTs are primarily based on the histologic grade of the tumor, but a vast majority of MCTs are of an intermediate grade, and the prognostic relevance is highly questioned. A more detailed prognostic evaluation, especially of grade 2 canine MCTs, is greatly needed. To evaluate the prognostic significance of KIT and tryptase expression patterns in canine cutaneous MCTs, we studied 100 cutaneous MCTs from 100 dogs that had been treated with surgery only. The total survival and disease-free survival time and the time to local or distant recurrence of MCTs were recorded for all dogs. Using immuno-histochemistry, 98 of these MCTs were stained with anti-KIT and antitryptase antibodies. Three KIT- and three tryptase-staining patterns were identified. The KIT-staining patterns were identified as 1) membrane-associated staining, 2) focal to stippled cytoplasmic staining with decreased membrane-associated staining, and 3) diffuse cytoplasmic staining. The tryptase-staining patterns were identified as 1) diffuse cytoplasmic staining, 2) stippled cytoplasmic staining, and 3) little to no cytoplasmic staining. Based on univariate and multivariate survival analysis, increased cytoplasmic KIT staining was significantly associated with an increased rate of local recurrence and a decreased survival rate. The tryptase-staining patterns were not significantly associated with any survival parameter. On the basis of these results, we propose a new prognostic classification of canine cutaneous MCTs, according to their KIT-staining pattern, that can be used for the routine prognostic evaluation of canine cutaneous MCTs.
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Affiliation(s)
- M Kiupel
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing 48824, USA.
| | - J D Webster
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing 48824, USA.
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41
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Webster JD, Yuzbasiyan-Gurkan V, Miller RA, Kaneene JB, Kiupel M. Cellular Proliferation in Canine Cutaneous Mast Cell Tumors: Associations with c-KIT and Its Role in Prognostication. Vet Pathol 2016; 44:298-308. [PMID: 17491070 DOI: 10.1354/vp.44-3-298] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Canine cutaneous mast cell tumor (MCT) is a common neoplastic disease in dogs. Due to the prevalence of canine MCTs and the variable biologic behavior of this disease, accurate prognostication and a thorough understanding of MCT biology are critical for the treatment of this disease. The goals of this study were to evaluate and compare the utility of the proliferation markers Ki67, proliferating cell nuclear antigen (PCNA), and argyrophilic nucleolar organizing region (AgNOR) as independent prognostic markers for canine MCTs and to evaluate the use of these markers in combination, as each marker assesses different aspects of cellular proliferation. An additional goal of this study was to evaluate the associations between cellular proliferation and c-KIT mutations and between cellular proliferation and aberrant KIT protein localization in canine MCTs. Fifty-six MCTs treated with surgical excision alone were included in this study. Each MCT was evaluated for Ki67 expression, PCNA expression, and KIT protein localization using immunohistochemistry; for AgNOR counts using histochemical staining; and for the presence of internal tandem duplication c-KIT mutations using polymerase chain reaction amplification. In this study, increased Ki67 and AgNOR counts were both associated with significantly decreased survival. On the basis of these results, we recommend that the evaluation of cellular proliferation, including evaluations of both Ki67 expression and AgNORs, should be routinely used in the prognostication of canine MCTs. Additionally, the results of this study show that MCTs with aberrant KIT protein localization or internal tandem duplication c-KIT mutations are associated with increased cellular proliferation, further suggesting a role for c-KIT in the progression of canine MCTs.
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Affiliation(s)
- J D Webster
- Comparative Medicine and Integrative Biology Program, Michigan State University, Lansing, MI 48910, USA
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Balcone-Boissard H, Boudon G, Cioni R, Webster JD, Zdanowicz G, Orsi G, Civetta L. Chlorine as a geobarometer for alkaline magmas: Evidence from a systematic study of the eruptions of Mount Somma-Vesuvius. Sci Rep 2016; 6:21726. [PMID: 26888358 PMCID: PMC4757863 DOI: 10.1038/srep21726] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/29/2016] [Indexed: 11/24/2022] Open
Abstract
Defining the magma storage conditions of a volcanic system is a major goal in modern volcanology due to its direct implications for the style of a possible eruption, and thus on the associated risk of any crisis and the necessary management and mitigation strategies. Below 200 MPa and at equivalent depths, the strongly non-ideal behaviour of the H-C-O-S-Cl-F system in the silicate melt causes unmixing of the fluid phase to form an H2O-rich vapour and a hydrosaline phase in equilibrium with the silicate melt, both responsible for buffering the chlorine (Cl) concentration. Following this equilibrium, the Cl concentration in melts may be used as a geobarometer for alkaline magmas. Systematic application of this method to the main explosive eruptions of Mount Somma-Vesuvius highlights two main magma ponding zones, at ~180–200 and ~100 MPa. At these pressures, the maximum pre-eruptive H2O contents for the different magma compositions can be estimated; the results obtained, largely in agreement with the current literature, therefore confirm the validity of the method. The Cl geobarometer may help scientists to define the variation of the magmatic reservoir location through time and thus provide strong constraints on pre-eruptive conditions, which are of utmost importance for volcanic crisis management.
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Affiliation(s)
- H Balcone-Boissard
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Institut des Sciences de la Terre de Paris (iSTeP), 4 place Jussieu 75005 Paris, France
| | - G Boudon
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, CNRS, F-75005 Paris, France
| | - R Cioni
- Dip.to Scienze della Terra, Universita' degli Studi di Firenze, Via La Pira 4, 50121 Firenze, Italy
| | - J D Webster
- Department of Earth and Planetary Sciences, American Museum of Natural History, Central Park West at 79th St., NY, NY 10024-5192 USA
| | - G Zdanowicz
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, CNRS, F-75005 Paris, France.,Dipartimento di Scienze della Terra, dell'Ambiente e delle Risorse, Università degli Studi di Napoli Federico II, Largo S. Marcellino 10, 80138 Napoli, Italy
| | - G Orsi
- Dipartimento di Scienze della Terra, dell'Ambiente e delle Risorse, Università degli Studi di Napoli Federico II, Largo S. Marcellino 10, 80138 Napoli, Italy.,Dipartimento di Fisica "E. R. Caianiello" Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - L Civetta
- Dipartimento di Scienze della Terra, dell'Ambiente e delle Risorse, Università degli Studi di Napoli Federico II, Largo S. Marcellino 10, 80138 Napoli, Italy.,Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palermo, Via Ugo La Malfa 153, 90146 Palermo, Italy
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Sun Y, Peng I, Webster JD, Suto E, Lesch J, Wu X, Senger K, Francis G, Barrett K, Collier JL, Burch JD, Zhou M, Chen Y, Chan C, Eastham-Anderson J, Ngu H, Li O, Staton T, Havnar C, Jaochico A, Jackman J, Jeet S, Riol-Blanco L, Wu LC, Choy DF, Arron JR, McKenzie BS, Ghilardi N, Ismaili MHA, Pei Z, DeVoss J, Austin CD, Lee WP, Zarrin AA. Inhibition of the kinase ITK in a mouse model of asthma reduces cell death and fails to inhibit the inflammatory response. Sci Signal 2015; 8:ra122. [PMID: 26628680 DOI: 10.1126/scisignal.aab0949] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Interleukin-2 (IL-2)-inducible T cell kinase (ITK) mediates T cell receptor (TCR) signaling primarily to stimulate the production of cytokines, such as IL-4, IL-5, and IL-13, from T helper 2 (TH2) cells. Compared to wild-type mice, ITK knockout mice are resistant to asthma and exhibit reduced lung inflammation and decreased amounts of TH2-type cytokines in the bronchoalveolar lavage fluid. We found that a small-molecule selective inhibitor of ITK blocked TCR-mediated signaling in cultured TH2 cells, including the tyrosine phosphorylation of phospholipase C-γ1 (PLC-γ1) and the secretion of IL-2 and TH2-type cytokines. Unexpectedly, inhibition of the kinase activity of ITK during or after antigen rechallenge in an ovalbumin-induced mouse model of asthma failed to reduce airway hyperresponsiveness and inflammation. Rather, in mice, pharmacological inhibition of ITK resulted in T cell hyperplasia and the increased production of TH2-type cytokines. Thus, our studies predict that inhibition of the kinase activity of ITK may not be therapeutic in patients with asthma.
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Affiliation(s)
- Yonglian Sun
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Ivan Peng
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Eric Suto
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Justin Lesch
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Kate Senger
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - George Francis
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Kathy Barrett
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Jenna L Collier
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Jason D Burch
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA 94080, USA
| | - Meijuan Zhou
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Yuan Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Connie Chan
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Hai Ngu
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Olga Li
- Department of Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Tracy Staton
- Department of Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Charles Havnar
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Allan Jaochico
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., South San Francisco, CA 94080, USA
| | - Janet Jackman
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Surinder Jeet
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Lorena Riol-Blanco
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Lawren C Wu
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - David F Choy
- Department of Immunology, Tissue Growth, and Repair Diagnostics Discovery, Genentech Inc., South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Brent S McKenzie
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Nico Ghilardi
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Zhonghua Pei
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA 94080, USA
| | - Jason DeVoss
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Ali A Zarrin
- Department of Immunology, Genentech Inc., South San Francisco, CA 94080, USA.
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Maity TK, Venugopalan A, Linnoila I, Cultraro CM, Giannakou A, Nemati R, Zhang X, Webster JD, Ritt D, Ghosal S, Hoschuetzky H, Simpson RM, Biswas R, Politi K, Morrison DK, Varmus HE, Guha U. Loss of MIG6 Accelerates Initiation and Progression of Mutant Epidermal Growth Factor Receptor-Driven Lung Adenocarcinoma. Cancer Discov 2015; 5:534-49. [PMID: 25735773 DOI: 10.1158/2159-8290.cd-14-0750] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/20/2015] [Indexed: 12/19/2022]
Abstract
UNLABELLED Somatic mutations in the EGFR kinase domain drive lung adenocarcinoma. We have previously identified MIG6, an inhibitor of ERBB signaling and a potential tumor suppressor, as a target for phosphorylation by mutant EGFRs. Here, we demonstrate that MIG6 is a tumor suppressor for the initiation and progression of mutant EGFR-driven lung adenocarcinoma in mouse models. Mutant EGFR-induced lung tumor formation was accelerated in Mig6-deficient mice, even with Mig6 haploinsufficiency. We demonstrate that constitutive phosphorylation of MIG6 at Y394/Y395 in EGFR-mutant human lung adenocarcinoma cell lines is associated with an increased interaction of MIG6 with mutant EGFR, which may stabilize EGFR protein. MIG6 also fails to promote mutant EGFR degradation. We propose a model whereby increased tyrosine phosphorylation of MIG6 decreases its capacity to inhibit mutant EGFR. Nonetheless, the residual inhibition is sufficient for MIG6 to delay mutant EGFR-driven tumor initiation and progression in mouse models. SIGNIFICANCE This study demonstrates that MIG6 is a potent tumor suppressor for mutant EGFR-driven lung tumor initiation and progression in mice and provides a possible mechanism by which mutant EGFR can partially circumvent this tumor suppressor in human lung adenocarcinoma.
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Affiliation(s)
- Tapan K Maity
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Abhilash Venugopalan
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Ilona Linnoila
- Cell and Cancer Biology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Constance M Cultraro
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Andreas Giannakou
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roxanne Nemati
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Xu Zhang
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Joshua D Webster
- Laboratory of Cancer Biology and Genetics, NCI, Bethesda, Maryland
| | - Daniel Ritt
- Laboratory of Cell and Developmental Signaling, NCI, Frederick, Maryland
| | - Sarani Ghosal
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | | | - R Mark Simpson
- Laboratory of Cancer Biology and Genetics, NCI, Bethesda, Maryland
| | - Romi Biswas
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Katerina Politi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI, Frederick, Maryland
| | - Harold E Varmus
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Udayan Guha
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Bethesda, Maryland. Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.
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45
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Ferrando RE, Newton K, Chu F, Webster JD, French DM. Immunohistochemical detection of FLAG-tagged endogenous proteins in knock-in mice. J Histochem Cytochem 2015; 63:244-55. [PMID: 25575566 DOI: 10.1369/0022155414568101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
With recent advances in immunohistochemical (IHC) techniques, immunohistochemistry now plays a more important role in research, especially in mouse models where characterization of cellular patterns of protein expression has become critical. Even with these recent advances, a paucity of IHC quality antibodies for some proteins still exists. To address this, we have developed a novel IHC assay that utilizes a commercially available goat anti-DDDDK peptide polyclonal antibody on paraffin-embedded tissues from knock-in mice expressing proteins of interest tagged with a 3 × FLAG epitope at physiologically relevant levels. Focusing on two 3 × FLAG-tagged proteins for which specific antibodies were available, USP48 and RIPK3, we were able to validate our anti-DDDDK assay by comparing the IHC directed against the actual proteins to the anti-DDDDK IHC assay, which recognizes the FLAG epitope. We were also able to detect a third 3 × FLAG-tagged protein, BAP1, for which quality reagents were not available. This universal IHC method will enable researchers to characterize the expression patterns of proteins of interest when specific antibodies are lacking.
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Affiliation(s)
- Ronald E Ferrando
- Departments of Pathology, Genentech, Inc., South San Francisco, California (RF, FC, JW, DF)
| | - Kim Newton
- Physiological Chemistry, Genentech, Inc., South San Francisco, California (KN)
| | - Felix Chu
- Departments of Pathology, Genentech, Inc., South San Francisco, California (RF, FC, JW, DF)
| | - Joshua D Webster
- Departments of Pathology, Genentech, Inc., South San Francisco, California (RF, FC, JW, DF)
| | - Dorothy M French
- Departments of Pathology, Genentech, Inc., South San Francisco, California (RF, FC, JW, DF)
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Nevo I, Woolard K, Cam M, Li A, Webster JD, Kotliarov Y, Kim HS, Ahn S, Walling J, Kotliarova S, Belova G, Song H, Bailey R, Zhang W, Fine HA. Identification of molecular pathways facilitating glioma cell invasion in situ. PLoS One 2014; 9:e111783. [PMID: 25365423 PMCID: PMC4218815 DOI: 10.1371/journal.pone.0111783] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/30/2014] [Indexed: 12/22/2022] Open
Abstract
Gliomas are mostly incurable secondary to their diffuse infiltrative nature. Thus, specific therapeutic targeting of invasive glioma cells is an attractive concept. As cells exit the tumor mass and infiltrate brain parenchyma, they closely interact with a changing micro-environmental landscape that sustains tumor cell invasion. In this study, we used a unique microarray profiling approach on a human glioma stem cell (GSC) xenograft model to explore gene expression changes in situ in Invading Glioma Cells (IGCs) compared to tumor core, as well as changes in host cells residing within the infiltrated microenvironment relative to the unaffected cortex. IGCs were found to have reduced expression of genes within the extracellular matrix compartment, and genes involved in cell adhesion, cell polarity and epithelial to mesenchymal transition (EMT) processes. The infiltrated microenvironment showed activation of wound repair and tissue remodeling networks. We confirmed by protein analysis the downregulation of EMT and polarity related genes such as CD44 and PARD3 in IGCs, and EFNB3, a tissue-remodeling agent enriched at the infiltrated microenvironment. OLIG2, a proliferation regulator and glioma progenitor cell marker upregulated in IGCs was found to function in enhancing migration and stemness of GSCs. Overall, our results unveiled a more comprehensive picture of the complex and dynamic cell autonomous and tumor-host interactive pathways of glioma invasion than has been previously demonstrated. This suggests targeting of multiple pathways at the junction of invading tumor and microenvironment as a viable option for glioma therapy.
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Affiliation(s)
- Ido Nevo
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Woolard
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maggie Cam
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Aiguo Li
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joshua D. Webster
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yuri Kotliarov
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hong Sug Kim
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susie Ahn
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jennifer Walling
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Svetlana Kotliarova
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Galina Belova
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hua Song
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rolanda Bailey
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wei Zhang
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard A. Fine
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Naik E, Webster JD, DeVoss J, Liu J, Suriben R, Dixit VM. Regulation of proximal T cell receptor signaling and tolerance induction by deubiquitinase Usp9X. ACTA ACUST UNITED AC 2014; 211:1947-55. [PMID: 25200027 PMCID: PMC4172213 DOI: 10.1084/jem.20140860] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The T cell hyperproliferation and autoimmune phenotypes that manifest in mice lacking E3 ubiquitin ligases such as Cbl, ITCH, or GRAIL highlight the importance of ubiquitination for the maintenance of peripheral T cell tolerance. Less is known, however, about the deubiquitinating enzymes that regulate T cell proliferation and effector function. Here, we define a cell intrinsic role for the deubiquitinase Usp9X during proximal TCR signaling. Usp9X-deficient T cells were hypoproliferative, yet mice with T cell-specific Usp9x deletion had elevated numbers of antigen-experienced T cells and expanded PD-1 and OX40-expressing populations consistent with immune hyperactivity. Aged Usp9x KO mice developed lupus-like autoimmunity and lymphoproliferative disease, indicating that ubiquitin ligases and deubiquitinases maintain the delicate balance between effective immunity and self-tolerance.
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Affiliation(s)
- Edwina Naik
- Department of Physiological Chemistry, Department of Pathology, Department of Immunology, Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Joshua D Webster
- Department of Physiological Chemistry, Department of Pathology, Department of Immunology, Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Jason DeVoss
- Department of Physiological Chemistry, Department of Pathology, Department of Immunology, Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Jinfeng Liu
- Department of Physiological Chemistry, Department of Pathology, Department of Immunology, Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Rowena Suriben
- Department of Physiological Chemistry, Department of Pathology, Department of Immunology, Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Vishva M Dixit
- Department of Physiological Chemistry, Department of Pathology, Department of Immunology, Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
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48
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Ramos-Vara JA, Webster JD. Special focus on investigative techniques. Vet Pathol 2014; 51:5-6. [PMID: 24395974 DOI: 10.1177/0300985813514949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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49
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Simpson RM, Bastian BC, Michael HT, Webster JD, Prasad ML, Conway CM, Prieto VM, Gary JM, Goldschmidt MH, Esplin DG, Smedley RC, Piris A, Meuten DJ, Kiupel M, Lee CCR, Ward JM, Dwyer JE, Davis BJ, Anver MR, Molinolo AA, Hoover SB, Rodriguez-Canales J, Hewitt SM. Sporadic naturally occurring melanoma in dogs as a preclinical model for human melanoma. Pigment Cell Melanoma Res 2013; 27:37-47. [PMID: 24128326 PMCID: PMC4066658 DOI: 10.1111/pcmr.12185] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/11/2013] [Indexed: 12/20/2022]
Abstract
Melanoma represents a significant malignancy in humans and dogs. Different from genetically engineered models, sporadic canine melanocytic neoplasms share several characteristics with human disease that could make dogs a more relevant preclinical model. Canine melanomas rarely arise in sun-exposed sites. Most occur in the oral cavity, with a subset having intra-epithelial malignant melanocytes mimicking the in situ component of human mucosal melanoma. The spectrum of canine melanocytic neoplasia includes benign lesions with some analogy to nevi, as well as invasive primary melanoma, and widespread metastasis. Growing evidence of distinct subtypes in humans, differing in somatic and predisposing germ-line genetic alterations, cell of origin, epidemiology, relationship to ultraviolet radiation and progression from benign to malignant tumors, may also exist in dogs. Canine and human mucosal melanomas appear to harbor BRAF, NRAS, and c-kit mutations uncommonly, compared with human cutaneous melanomas, although both species share AKT and MAPK signaling activation. We conclude that there is significant overlap in the clinical and histopathological features of canine and human mucosal melanomas. This represents opportunity to explore canine oral cavity melanoma as a preclinical model.
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Affiliation(s)
- R Mark Simpson
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Abstract
Digital pathology, the practice of pathology using digitized images of pathologic specimens, has been transformed in recent years by the development of whole-slide imaging systems, which allow for the evaluation and interpretation of digital images of entire histologic sections. Applications of whole-slide imaging include rapid transmission of pathologic data for consultations and collaborations, standardization and distribution of pathologic materials for education, tissue specimen archiving, and image analysis of histologic specimens. Histologic image analysis allows for the acquisition of objective measurements of histomorphologic, histochemical, and immunohistochemical properties of tissue sections, increasing both the quantity and quality of data obtained from histologic assessments. Currently, numerous histologic image analysis software solutions are commercially available. Choosing the appropriate solution is dependent on considerations of the investigative question, computer programming and image analysis expertise, and cost. However, all studies using histologic image analysis require careful consideration of preanalytical variables, such as tissue collection, fixation, and processing, and experimental design, including sample selection, controls, reference standards, and the variables being measured. The fields of digital pathology and histologic image analysis are continuing to evolve, and their potential impact on pathology is still growing. These methodologies will increasingly transform the practice of pathology, allowing it to mature toward a quantitative science. However, this maturation requires pathologists to be at the forefront of the process, ensuring their appropriate application and the validity of their results. Therefore, histologic image analysis and the field of pathology should co-evolve, creating a symbiotic relationship that results in high-quality reproducible, objective data.
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Affiliation(s)
- J D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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