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Tiwari A, Gautam AS, Pandey SK, Singh S, Singh RK. The role of RIPK1 in chronic obstructive pulmonary disease. Drug Discov Today 2024; 29:104020. [PMID: 38740363 DOI: 10.1016/j.drudis.2024.104020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/21/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Necroptosis has emerged as one of the crucial pathological processes involved in the regulation of cell death and inflammation in chronic obstructive pulmonary disease (COPD). Airway epithelial necroptosis is closely linked to COPD pathogenesis. Necroptotic lung cells can release damage-associated molecular patterns (DAMPs) that can initiate a robust inflammatory response. However, the underlying mechanism of necroptosis in COPD is still not clearly understood. Therefore, we aimed to explore the roles and mechanisms of receptor-interacting serine/threonine-protein kinase 1 (RIPK1)-mediated necroptosis in the regulation of inflammatory responses in COPD to provide insights into RIPK1-inhibitor drug discovery efforts and their therapeutic benefits in COPD.
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Affiliation(s)
- Aman Tiwari
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-Raebareli), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow 226002, Uttar Pradesh, India
| | - Avtar Singh Gautam
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-Raebareli), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow 226002, Uttar Pradesh, India
| | - Shivam Kumar Pandey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-Raebareli), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow 226002, Uttar Pradesh, India
| | - Shreya Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-Raebareli), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow 226002, Uttar Pradesh, India
| | - Rakesh Kumar Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-Raebareli), Transit Campus, Bijnor-Sisendi Road, Sarojini Nagar, Lucknow 226002, Uttar Pradesh, India.
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2
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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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3
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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 PMCID: PMC11157567 DOI: 10.1126/scitranslmed.adf8366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Jones NS, Kshirsagar S, Mohanan V, Ramakrishnan V, Di Nucci F, Ma L, Mao J, Ding H, Klabunde S, Vucic D, Pan L, Lekkerkerker AN, Chen Y, Rothenberg ME. A phase I, randomized, ascending-dose study to assess safety, pharmacokinetics, and activity of GDC-8264, a RIP1 inhibitor, in healthy volunteers. Clin Transl Sci 2023; 16:1997-2009. [PMID: 37596814 PMCID: PMC10582670 DOI: 10.1111/cts.13607] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023] Open
Abstract
Receptor-interacting protein 1 (RIP1) is a key regulator of multiple signaling pathways that mediate inflammatory responses and cell death. RIP1 kinase activity mediates apoptosis and necroptosis induced by tumor necrosis factor (TNF)-α, Toll-like receptors, and ischemic tissue damage. RIP1 has been implicated in several human pathologies and consequently, RIP1 inhibition may represent a therapeutic approach for diseases dependent on RIP1-mediated inflammation and cell death. GDC-8264 is a potent, selective, and reversible small molecule inhibitor of RIP1 kinase activity. This phase I, randomized, placebo-controlled, double-blinded trial examined safety, pharmacokinetics (PKs), and pharmacodynamics (PDs) of single- (5-225 mg) and multiple- (50 and 100 mg once daily, up to 14 days) ascending oral doses of GDC-8264 in healthy volunteers, and also tested the effect of food on the PKs of GDC-8264. All adverse events in GDC-8264-treated subjects in both stages were mild. GDC-8264 exhibited dose-proportional increases in systemic exposure; the mean terminal half-life ranged from 10-13 h, with limited accumulation on multiple dosing (accumulation ratio [AR] ~ 1.4); GDC-8264 had minimal renal excretion at all doses. A high-fat meal had no significant effect on the PKs of GDC-8264. In an ex vivo stimulation assay of whole blood, GDC-8264 rapidly and completely inhibited release of CCL4, a downstream marker of RIP1 pathway activation, indicating a potent pharmacological effect. Based on PK-PD modeling, the GDC-8264 half-maximal inhibitory concentration for the inhibition of CCL4 release was estimated to be 0.58 ng/mL. The favorable safety, PKs, and PDs of GDC-8264 support its further development for treatment of RIP1-driven diseases.
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Affiliation(s)
| | | | | | | | | | - Ling Ma
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | - Jialin Mao
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | - Hao Ding
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | | | | | - Lin Pan
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | | | - Yuan Chen
- Genentech, Inc.South San FranciscoCaliforniaUSA
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Wang Y, Wu T, Tsai MC, Rezzonico MG, Abdel-Haleem AM, Xie L, Gandham VD, Ngu H, Stark K, Glock C, Xu D, Foreman O, Friedman BA, Sheng M, Hanson JE. TPL2 kinase activity regulates microglial inflammatory responses and promotes neurodegeneration in tauopathy mice. eLife 2023; 12:e83451. [PMID: 37555828 PMCID: PMC10411973 DOI: 10.7554/elife.83451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Tumor progression locus 2 (TPL2) (MAP3K8) is a central signaling node in the inflammatory response of peripheral immune cells. We find that TPL2 kinase activity modulates microglial cytokine release and is required for microglia-mediated neuron death in vitro. In acute in vivo neuroinflammation settings, TPL2 kinase activity regulates microglia activation states and brain cytokine levels. In a tauopathy model of chronic neurodegeneration, loss of TPL2 kinase activity reduces neuroinflammation and rescues synapse loss, brain volume loss, and behavioral deficits. Single-cell RNA sequencing analysis indicates that protection in the tauopathy model was associated with reductions in activated microglia subpopulations as well as infiltrating peripheral immune cells. Overall, using various models, we find that TPL2 kinase activity can promote multiple harmful consequences of microglial activation in the brain including cytokine release, iNOS (inducible nitric oxide synthase) induction, astrocyte activation, and immune cell infiltration. Consequently, inhibiting TPL2 kinase activity could represent a potential therapeutic strategy in neurodegenerative conditions.
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Affiliation(s)
- Yuanyuan Wang
- Department of Neuroscience, Genentech IncSouth San FranciscoUnited States
| | - Tiffany Wu
- Department of Neuroscience, Genentech IncSouth San FranciscoUnited States
| | - Ming-Chi Tsai
- Department of Neuroscience, Genentech IncSouth San FranciscoUnited States
| | - Mitchell G Rezzonico
- Department of OMNI Bioinformatics, Genentech IncSouth San FranciscoUnited States
| | - Alyaa M Abdel-Haleem
- Computational Science & Exploratory Analytics, Roche IT, Hoffmann-La Roche LimitedMississaugaCanada
| | - Luke Xie
- Department of Translational Imaging, Genentech IncSouth San FranciscoUnited States
| | - Vineela D Gandham
- Department of Translational Imaging, Genentech IncSouth San FranciscoUnited States
| | - Hai Ngu
- Department of Pathology, Genentech IncSouth San FranciscoUnited States
| | - Kimberly Stark
- Department of Neuroscience, Genentech IncSouth San FranciscoUnited States
| | - Caspar Glock
- Department of OMNI Bioinformatics, Genentech IncSouth San FranciscoUnited States
| | - Daqi Xu
- Department of Immunology, Genentech IncSouth San FranciscoUnited States
| | - Oded Foreman
- Department of Pathology, Genentech IncSouth San FranciscoUnited States
| | - Brad A Friedman
- Department of OMNI Bioinformatics, Genentech IncSouth San FranciscoUnited States
| | - Morgan Sheng
- Department of Neuroscience, Genentech IncSouth San FranciscoUnited States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jesse E Hanson
- Department of Neuroscience, Genentech IncSouth San FranciscoUnited States
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Liu X, Tang AL, Chen J, Gao N, Zhang G, Xiao C. RIPK1 in the inflammatory response and sepsis: Recent advances, drug discovery and beyond. Front Immunol 2023; 14:1114103. [PMID: 37090690 PMCID: PMC10113447 DOI: 10.3389/fimmu.2023.1114103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/24/2023] [Indexed: 04/25/2023] Open
Abstract
Cytokine storms are an important mechanism of sepsis. TNF-α is an important cytokine. As a regulator of TNF superfamily receptors, RIPK1 not only serves as the basis of the scaffold structure in complex I to promote the activation of the NF-κB and MAPK pathways but also represents an important protein in complex II to promote programmed cell death. Ubiquitination of RIPK1 is an important regulatory function that determines the activation of cellular inflammatory pathways or the activation of death pathways. In this paper, we introduce the regulation of RIPK1, RIPK1 PANoptosome's role in Inflammatory and sepsis, and perspectives.
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Affiliation(s)
- Xiaoyu Liu
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - A-Ling Tang
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Jie Chen
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Gao
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guoqiang Zhang
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
| | - Cheng Xiao
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
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Kohler D, Kaza M, Pasi C, Huang T, Staniak M, Mohandas D, Sabido E, Choi M, Vitek O. MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments. J Proteome Res 2023; 22:551-556. [PMID: 36622173 DOI: 10.1021/acs.jproteome.2c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is a versatile technology for identifying and quantifying proteins in complex biological mixtures. Postidentification, analysis of changes in protein abundances between conditions requires increasingly complex and specialized statistical methods. Many of these methods, in particular the family of open-source Bioconductor packages MSstats, are implemented in a coding language such as R. To make the methods in MSstats accessible to users with limited programming and statistical background, we have created MSstatsShiny, an R-Shiny graphical user interface (GUI) integrated with MSstats, MSstatsTMT, and MSstatsPTM. The GUI provides a point and click analysis pipeline applicable to a wide variety of proteomics experimental types, including label-free data-dependent acquisitions (DDAs) or data-independent acquisitions (DIAs), or tandem mass tag (TMT)-based TMT-DDAs, answering questions such as relative changes in the abundance of peptides, proteins, or post-translational modifications (PTMs). To support reproducible research, the application saves user's selections and builds an R script that programmatically recreates the analysis. MSstatsShiny can be installed locally via Github and Bioconductor, or utilized on the cloud at www.msstatsshiny.com. We illustrate the utility of the platform using two experimental data sets (MassIVE IDs MSV000086623 and MSV000085565).
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Affiliation(s)
- Devon Kohler
- Khoury College of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Maanasa Kaza
- Khoury College of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Cristina Pasi
- Universitat Oberta de Catalunya, Barcelona 08018, Spain
| | - Ting Huang
- Khoury College of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | | | | | - Eduard Sabido
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Meena Choi
- MPL, Genentech, South San Francisco, California 94080, United States
| | - Olga Vitek
- Khoury College of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
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Chen L, Zhang X, Ou Y, Liu M, Yu D, Song Z, Niu L, Zhang L, Shi J. Advances in RIPK1 kinase inhibitors. Front Pharmacol 2022; 13:976435. [PMID: 36249746 PMCID: PMC9554302 DOI: 10.3389/fphar.2022.976435] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/27/2023] Open
Abstract
Programmed necrosis is a new modulated cell death mode with necrotizing morphological characteristics. Receptor interacting protein 1 (RIPK1) is a critical mediator of the programmed necrosis pathway that is involved in stroke, myocardial infarction, fatal systemic inflammatory response syndrome, Alzheimer's disease, and malignancy. At present, the reported inhibitors are divided into four categories. The first category is the type I ATP-competitive kinase inhibitors that targets the area occupied by the ATP adenylate ring; The second category is type Ⅱ ATP competitive kinase inhibitors targeting the DLG-out conformation of RIPK1; The third category is type Ⅲ kinase inhibitors that compete for binding to allosteric sites near ATP pockets; The last category is others. This paper reviews the structure, biological function, and recent research progress of receptor interaction protein-1 kinase inhibitors.
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Affiliation(s)
- Lu Chen
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Zhang
- Department of Critical Care Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Affiliated Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yaqing Ou
- Department of Pharmacy, The Affiliated Chengdu 363 Hospital of Southwest Medical University, Chengdu, Sichuan, China
| | - Maoyu Liu
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongke Yu
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhiheng Song
- Suzhou University of Science and Technology, Suzhou, Jiangsu, China
| | - Lihong Niu
- Institute of Laboratory Animal Sciences, Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China,*Correspondence: Lihong Niu, ; Lijuan Zhang, ; Jianyou Shi,
| | - Lijuan Zhang
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Lihong Niu, ; Lijuan Zhang, ; Jianyou Shi,
| | - Jianyou Shi
- Department of Pharmacy, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China,*Correspondence: Lihong Niu, ; Lijuan Zhang, ; Jianyou Shi,
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