1
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Ruiz-Fernández de Córdoba B, Martínez-Monge R, Lecanda F. ENPP1 Immunobiology as a Therapeutic Target. Clin Cancer Res 2023; 29:2184-2193. [PMID: 36719675 PMCID: PMC10261920 DOI: 10.1158/1078-0432.ccr-22-1681] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/17/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023]
Abstract
ENPP1 (ecto-nucleotide pyrophosphatase/phosphodiesterase) participates in the hydrolysis of different purine nucleotides in an array of physiologic processes. However, ENPP1 is frequently overexpressed in local relapses and tumor metastases, which are associated with poor prognosis and survival in a range of solid tumors. ENPP1 promotes an immunosuppressive tumor microenvironment (TME) by tilting the balance of ATP/adenosine (Ado) in conjunction with other components (CD38, CD39/ENTPD1, and CD73/NT5E). Moreover, ENPP1 intersects with the stimulator of interferon genes (STING), impairing its robust immune response through the hydrolysis of the effector 2´,3´-cyclic GMP-AMP. Thus, ENPP1 blockade emerges as a unique target eliciting immune remodeling and leveraging the STING pathway. Several ENPP1 inhibitors have shown an immunostimulatory effect, and their combination with other therapeutic modalities, such as immune-checkpoint blockade, STING activation, DNA damage response (DDR) inhibitors, and radiotherapy (RT), represents a promising avenue to boost antitumor-immune responses and to improve current clinical outcomes in several tumors. This comprehensive review summarizes the current state of the art and opens new perspectives for novel treatment strategies.
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Affiliation(s)
- Borja Ruiz-Fernández de Córdoba
- Solid Tumors Program. Division of Oncology, Center for Applied Medical Research, University of Navarra (CIMA), Navarra, Spain
| | - Rafael Martínez-Monge
- Oncology, Clínica University of Navarra, Navarra, Spain
- Radiation Oncology, Clínica University of Navarra, Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Fernando Lecanda
- Solid Tumors Program. Division of Oncology, Center for Applied Medical Research, University of Navarra (CIMA), Navarra, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
- School of Medicine, Department of Pathology, Anatomy and Physiology, University of Navarra, Navarra, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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2
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Li S, Yokota T, Wang P, ten Hoeve J, Ma F, Le TM, Abt ER, Zhou Y, Wu R, Nanthavongdouangsy M, Rodriguez A, Wang Y, Lin YJ, Muranaka H, Sharpley M, Braddock DT, MacRae VE, Banerjee U, Chiou PY, Seldin M, Huang D, Teitell M, Gertsman I, Jung M, Bensinger SJ, Damoiseaux R, Faull K, Pellegrini M, Lusis AJ, Graeber TG, Radu CG, Deb A. Cardiomyocytes disrupt pyrimidine biosynthesis in nonmyocytes to regulate heart repair. J Clin Invest 2022; 132:149711. [PMID: 34813507 PMCID: PMC8759793 DOI: 10.1172/jci149711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Various populations of cells are recruited to the heart after cardiac injury, but little is known about whether cardiomyocytes directly regulate heart repair. Using a murine model of ischemic cardiac injury, we demonstrate that cardiomyocytes play a pivotal role in heart repair by regulating nucleotide metabolism and fates of nonmyocytes. Cardiac injury induced the expression of the ectonucleotidase ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which hydrolyzes extracellular ATP to form AMP. In response to AMP, cardiomyocytes released adenine and specific ribonucleosides that disrupted pyrimidine biosynthesis at the orotidine monophosphate (OMP) synthesis step and induced genotoxic stress and p53-mediated cell death of cycling nonmyocytes. As nonmyocytes are critical for heart repair, we showed that rescue of pyrimidine biosynthesis by administration of uridine or by genetic targeting of the ENPP1/AMP pathway enhanced repair after cardiac injury. We identified ENPP1 inhibitors using small molecule screening and showed that systemic administration of an ENPP1 inhibitor after heart injury rescued pyrimidine biosynthesis in nonmyocyte cells and augmented cardiac repair and postinfarct heart function. These observations demonstrate that the cardiac muscle cell regulates pyrimidine metabolism in nonmuscle cells by releasing adenine and specific nucleosides after heart injury and provide insight into how intercellular regulation of pyrimidine biosynthesis can be targeted and monitored for augmenting tissue repair.
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Affiliation(s)
- Shen Li
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Tomohiro Yokota
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Ping Wang
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Johanna ten Hoeve
- UCLA Metabolomics Center, Crump Institute of Molecular Imaging, California Nanosystems Institute, UCLA, Los Angeles, California, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute
| | - Thuc M. Le
- UCLA Metabolomics Center, Crump Institute of Molecular Imaging, California Nanosystems Institute, UCLA, Los Angeles, California, USA.,Jonsson Comprehensive Cancer Center and,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Evan R. Abt
- UCLA Metabolomics Center, Crump Institute of Molecular Imaging, California Nanosystems Institute, UCLA, Los Angeles, California, USA.,Jonsson Comprehensive Cancer Center and,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Yonggang Zhou
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Rimao Wu
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Maxine Nanthavongdouangsy
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Abraham Rodriguez
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Yijie Wang
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
| | - Yen-Ju Lin
- California Nanosystems Institute, and,Department of Bioengineering, Samueli School of Engineering at UCLA, Los Angeles, California, USA.,Department of Mechanical and Aerospace Engineering and
| | - Hayato Muranaka
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Mark Sharpley
- Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute
| | | | - Vicky E. MacRae
- Division of Functional Genetics and Development, The Roslin Institute and R(D)VS, University of Edinburgh, Edinburgh, United Kingdom
| | - Utpal Banerjee
- Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Pei-Yu Chiou
- California Nanosystems Institute, and,Department of Bioengineering, Samueli School of Engineering at UCLA, Los Angeles, California, USA.,Department of Mechanical and Aerospace Engineering and
| | - Marcus Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, California, USA
| | - Dian Huang
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,California Nanosystems Institute, and,Jonsson Comprehensive Cancer Center and,Department of Pathology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Michael Teitell
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,California Nanosystems Institute, and,Jonsson Comprehensive Cancer Center and,Department of Pathology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | | | - Michael Jung
- Department of Chemistry, College of Physical Sciences, UCLA, Los Angeles, California, USA
| | - Steven J. Bensinger
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Robert Damoiseaux
- California Nanosystems Institute, and,Jonsson Comprehensive Cancer Center and,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Bioengineering, Samueli School of Engineering at UCLA, Los Angeles, California, USA
| | - Kym Faull
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior and Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute
| | - Aldons J. Lusis
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Thomas G. Graeber
- UCLA Metabolomics Center, Crump Institute of Molecular Imaging, California Nanosystems Institute, UCLA, Los Angeles, California, USA.,Jonsson Comprehensive Cancer Center and,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Caius G. Radu
- UCLA Metabolomics Center, Crump Institute of Molecular Imaging, California Nanosystems Institute, UCLA, Los Angeles, California, USA.,Jonsson Comprehensive Cancer Center and,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Arjun Deb
- Division of Cardiology, Department of Medicine and,UCLA Cardiovascular Theme, David Geffen School of Medicine, UCLA, Los Angeles, California, USA.,Department of Molecular, Cell and Developmental Biology, College of Life Sciences,,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research,,Molecular Biology Institute,,California Nanosystems Institute, and
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3
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Carozza JA, Brown JA, Böhnert V, Fernandez D, AlSaif Y, Mardjuki RE, Smith M, Li L. Structure-Aided Development of Small-Molecule Inhibitors of ENPP1, the Extracellular Phosphodiesterase of the Immunotransmitter cGAMP. Cell Chem Biol 2020; 27:1347-1358.e5. [PMID: 32726585 PMCID: PMC7680421 DOI: 10.1016/j.chembiol.2020.07.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/28/2020] [Accepted: 07/08/2020] [Indexed: 11/23/2022]
Abstract
Cancer cells initiate an innate immune response by synthesizing and exporting the small-molecule immunotransmitter cGAMP, which activates the anti-cancer Stimulator of Interferon Genes (STING) pathway in the host. An extracellular enzyme, ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1), hydrolyzes cGAMP and negatively regulates this anti-cancer immune response. Small-molecule ENPP1 inhibitors are much needed as tools to study the basic biology of extracellular cGAMP and as investigational cancer immunotherapy drugs. Here, we surveyed structure-activity relationships around a series of cell-impermeable and thus extracellular-targeting phosphonate inhibitors of ENPP1. In addition, we solved the crystal structure of an exemplary phosphonate inhibitor to elucidate the interactions that drive potency. This study yielded several best-in-class inhibitors with Ki < 2 nM and excellent physicochemical and pharmacokinetic properties. Finally, we demonstrate that an ENPP1 inhibitor delays tumor growth in a breast cancer mouse model. Together, we have developed ENPP1 inhibitors that are excellent tool compounds and potential therapeutics.
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MESH Headings
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Survival/drug effects
- Cells, Cultured
- Dose-Response Relationship, Drug
- Drug Screening Assays, Antitumor
- Enzyme Inhibitors/chemical synthesis
- Enzyme Inhibitors/chemistry
- Enzyme Inhibitors/pharmacology
- Female
- Humans
- Mice
- Mice, Inbred C57BL
- Molecular Structure
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Neurotransmitter Agents/chemistry
- Neurotransmitter Agents/isolation & purification
- Neurotransmitter Agents/metabolism
- Nucleotides, Cyclic/chemistry
- Nucleotides, Cyclic/isolation & purification
- Nucleotides, Cyclic/metabolism
- Phosphoric Diester Hydrolases/metabolism
- Pyrophosphatases/antagonists & inhibitors
- Pyrophosphatases/metabolism
- Small Molecule Libraries/chemical synthesis
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/pharmacology
- Structure-Activity Relationship
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Affiliation(s)
- Jacqueline A Carozza
- Department of Chemistry, Stanford University, Stanford, CA 93405, USA; Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA
| | - Jenifer A Brown
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Biophysics Program, Stanford University, Stanford, CA 93405, USA
| | - Volker Böhnert
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Department of Biochemistry, Stanford University, Stanford, CA 93405, USA
| | - Daniel Fernandez
- Stanford ChEM-H Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA 93405, USA
| | - Yasmeen AlSaif
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Department of Biology, Stanford University, Stanford, CA 93405, USA
| | - Rachel E Mardjuki
- Department of Chemistry, Stanford University, Stanford, CA 93405, USA; Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA
| | - Mark Smith
- Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford, CA 93405, USA
| | - Lingyin Li
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Department of Biochemistry, Stanford University, Stanford, CA 93405, USA.
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4
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Mardjuki RE, Carozza JA, Li L. Development of cGAMP-Luc, a sensitive and precise coupled enzyme assay to measure cGAMP in complex biological samples. J Biol Chem 2020; 295:4881-4892. [PMID: 32127400 PMCID: PMC7152770 DOI: 10.1074/jbc.ra119.012170] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/28/2020] [Indexed: 11/06/2022] Open
Abstract
2',5'/3',5'-cGMP-AMP (cGAMP) is a second messenger produced in response to cytosolic dsDNA that activates the stimulator of interferon genes (STING) pathway. We recently discovered that cGAMP is exported by cancer cells and that this extracellular signal is an immunotransmitter key to tumor detection and elimination by the innate immune system. The enhancement of extracellular cGAMP levels therefore holds great promise for managing cancer. However, there is still much more to understand about the basic biology of cGAMP before its full therapeutic potential can be realized. To answer these questions, we must be able to detect and quantitate cGAMP with an assay that is high-throughput, sensitive, and precise. Existing assays fall short of these needs. Here, we describe the development of cGAMP-Luc, a coupled enzyme assay that relies on the degradation of cGAMP to AMP by ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) and an optimized assay for the detection of AMP by luciferase. We also developed STING-CAP, a STING-mediated method to concentrate and purify cGAMP from any type of biological sample. We conclude that cGAMP-Luc is an economical high-throughput assay that matches the accuracy of and surpasses the detection limit of MS, the current gold standard of cGAMP quantitation. We propose that cGAMP-Luc is a powerful tool that may enable discoveries that advance insights into extracellular cGAMP levels in healthy and diseased tissues, such as cancer.
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Affiliation(s)
- Rachel E Mardjuki
- Department of Chemistry, Stanford University School of Medicine, Stanford, California 94306
| | - Jacqueline A Carozza
- Department of Chemistry, Stanford University School of Medicine, Stanford, California 94306
- Stanford ChEM-H, Stanford University School of Medicine, Stanford, California 94306
| | - Lingyin Li
- Stanford ChEM-H, Stanford University School of Medicine, Stanford, California 94306
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94306
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5
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Carozza JA, Böhnert V, Nguyen KC, Skariah G, Shaw KE, Brown JA, Rafat M, von Eyben R, Graves EE, Glenn JS, Smith M, Li L. Extracellular cGAMP is a cancer cell-produced immunotransmitter involved in radiation-induced anti-cancer immunity. NATURE CANCER 2020; 1:184-196. [PMID: 33768207 PMCID: PMC7990037 DOI: 10.1038/s43018-020-0028-4] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/15/2020] [Indexed: 12/18/2022]
Abstract
2'3'-cyclic GMP-AMP (cGAMP) is an intracellular second messenger that is synthesized in response to cytosolic double-stranded DNA and activates the innate immune STING pathway. Our previous discovery of its extracellular hydrolase ENPP1 hinted at the existence of extracellular cGAMP. Here, we detected that cGAMP is continuously exported but then efficiently cleared by ENPP1, explaining why it has previously escaped detection. By developing potent, specific, and cell impermeable ENPP1 inhibitors, we found that cancer cells continuously export cGAMP in culture at steady state and at higher levels when treated with ionizing radiation (IR). In mouse tumors, depletion of extracellular cGAMP decreased tumor-associated immune cell infiltration and abolished the curative effect of IR. Boosting extracellular cGAMP with ENPP1 inhibitors synergized with IR to delay tumor growth. In conclusion, extracellular cGAMP is an anti-cancer immunotransmitter that could be harnessed to treat cancers with low immunogenicity.
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Affiliation(s)
- Jacqueline A Carozza
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Volker Böhnert
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA
| | - Khanh C Nguyen
- Departments of Medicine and Microbiology & Immunology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gemini Skariah
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA
| | - Kelsey E Shaw
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jenifer A Brown
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Marjan Rafat
- Department of Radiation Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Rie von Eyben
- Department of Radiation Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Edward E Graves
- Department of Radiation Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jeffrey S Glenn
- Departments of Medicine and Microbiology & Immunology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Mark Smith
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Lingyin Li
- Stanford ChEM-H, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA, USA.
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6
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Kato K, Nishimasu H, Oikawa D, Hirano S, Hirano H, Kasuya G, Ishitani R, Tokunaga F, Nureki O. Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1. Nat Commun 2018; 9:4424. [PMID: 30356045 PMCID: PMC6200793 DOI: 10.1038/s41467-018-06922-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/04/2018] [Indexed: 12/03/2022] Open
Abstract
ENPP1 (Ecto-nucleotide pyrophosphatase phosphodiesterase 1), a type II transmembrane glycoprotein, hydrolyzes ATP to produce AMP and diphosphate, thereby inhibiting bone mineralization. A recent study showed that ENPP1 also preferentially hydrolyzes 2′3′-cGAMP (cyclic GMP-AMP) but not its linkage isomer 3′3′-cGAMP, and negatively regulates the cGAS-STING pathway in the innate immune system. Here, we present the high-resolution crystal structures of ENPP1 in complex with 3′3′-cGAMP and the reaction intermediate pA(3′,5′)pG. The structures revealed that the adenine and guanine bases of the dinucleotides are recognized by nucleotide- and guanine-pockets, respectively. Furthermore, the structures indicate that 2′3′-cGAMP, but not 3′3′-cGAMP, binds to the active site in a conformation suitable for catalysis, thereby explaining the specific degradation of 2′3′-cGAMP by ENPP1. Our findings provide insights into how ENPP1 hydrolyzes both ATP and cGAMP to participate in the two distinct biological processes. Ecto-nucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) is a type II transmembrane glycoprotein that hydrolyzes both ATP and cGAMP. Here the authors present the crystal structures of the extracellular domain of mouse ENPP1 in complex with 3′3′-cGAMP and the reaction intermediate pA(3′,5′)pG and discuss mechanistic implications.
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Affiliation(s)
- Kazuki Kato
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi Nishimasu
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Daisuke Oikawa
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Seiichi Hirano
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hisato Hirano
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Go Kasuya
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryuichiro Ishitani
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, 1-4-3 Asahi-machi, Abeno-ku, Osaka, 545-8585, Japan
| | - Osamu Nureki
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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7
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Shi C, Uda Y, Dedic C, Azab E, Sun N, Hussein AI, Petty CA, Fulzele K, Mitterberger-Vogt MC, Zwerschke W, Pereira R, Wang K, Pajevic PD. Carbonic anhydrase III protects osteocytes from oxidative stress. FASEB J 2017; 32:440-452. [PMID: 28928248 DOI: 10.1096/fj.201700485rr] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/05/2017] [Indexed: 12/26/2022]
Abstract
Osteocytes are master orchestrators of bone remodeling; they control osteoblast and osteoclast activities both directly via cell-to-cell communication and indirectly via secreted factors, and they are the main postnatal source of sclerostin and RANKL (receptor activator of NF-kB ligand), two regulators of osteoblast and osteoclast function. Despite progress in understanding osteocyte biology and function, much remains to be elucidated. Recently developed osteocytic cell lines-together with new genome editing tools-has allowed a closer look at the biology and molecular makeup of these cells. By using single-cell cloning, we identified genes that are associated with high Sost/sclerostin expression and analyzed their regulation and function. Unbiased transcriptome analysis of high- vs. low-Sost/sclerostin-expressing cells identified known and novel genes. Dmp1 (dentin matrix protein 1), Dkk1 (Dickkopf WNT signaling pathway inhibitor 1), and Phex were among the most up-regulated known genes, whereas Srpx2, Cd200, and carbonic anhydrase III (CAIII) were identified as novel markers of differentiated osteocytes. Aspn, Enpp2, Robo2, Nov, and Serpina3g were among the transcripts that were most significantly suppressed in high-Sost cells. Considering that CAII was recently identified as being regulated by Sost/sclerostin and capable of controlling mineral homeostasis, we focused our attention on CAIII. Here, we report that CAIII is highly expressed in osteocytes, is regulated by parathyroid hormone both in vitro and in vivo, and protects osteocytes from oxidative stress.-Shi, C., Uda, Y., Dedic, C., Azab, E., Sun, N., Hussein, A. I., Petty, C. A., Fulzele, K., Mitterberger-Vogt, M. C., Zwerschke, W., Pereira, R., Wang, K., Divieti Pajevic, P. Carbonic anhydrase III protects osteocytes from oxidative stress.
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Affiliation(s)
- Chao Shi
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | - Yuhei Uda
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | - Christopher Dedic
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | - Ehab Azab
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | - Ningyuan Sun
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | - Amira I Hussein
- Department of Orthopedics, School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Christopher A Petty
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | - Keertik Fulzele
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA
| | | | - Werner Zwerschke
- Cell Metabolism and Differentiation Research Group, University of Innsbruck, Innsbruck, Austria
| | - Renata Pereira
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kunzheng Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China;
| | - Paola Divieti Pajevic
- Molecular and Cell Biology, Henry M. Goldman School of Dental Medicine, Boston University, Boston, Massachusetts, USA;
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8
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Palazzo L, Daniels CM, Nettleship JE, Rahman N, McPherson RL, Ong S, Kato K, Nureki O, Leung AKL, Ahel I. ENPP1 processes protein ADP-ribosylation in vitro. FEBS J 2016; 283:3371-88. [PMID: 27406238 PMCID: PMC5030157 DOI: 10.1111/febs.13811] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/27/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022]
Abstract
ADP-ribosylation is a conserved post-translational protein modification that plays a role in all major cellular processes, particularly DNA repair, transcription, translation, stress response and cell death. Hence, dysregulation of ADP-ribosylation is linked to the physiopathology of several human diseases including cancers, diabetes and neurodegenerative disorders. Protein ADP-ribosylation can be reversed by the macrodomain-containing proteins PARG, TARG1, MacroD1 and MacroD2, which hydrolyse the ester bond known to link proteins to ADP-ribose as well as consecutive ADP-ribose subunits; targeting this bond can thus result in the complete removal of the protein modification or the conversion of poly(ADP-ribose) to mono(ADP-ribose). Recently, proteins containing the NUDIX domain - namely human NUDT16 and bacterial RppH - have been shown to process in vitro protein ADP-ribosylation through an alternative mechanism, converting it into protein-conjugated ribose-5'-phosphate (R5P, also known as pR). Though this protein modification was recently identified in mammalian tissues, its physiological relevance and the mechanism of generating protein phosphoribosylation are currently unknown. Here, we identified ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) as the first known mammalian enzyme lacking a NUDIX domain to generate pR from ADP-ribose on modified proteins in vitro. Thus, our data show that at least two enzyme families - Nudix and ENPP/NPP - are able to metabolize protein-conjugated ADP-ribose to pR in vitro, suggesting that pR exists and may be conserved from bacteria to mammals. We also demonstrate the utility of ENPP1 for converting protein-conjugated mono(ADP-ribose) and poly(ADP-ribose) into mass spectrometry-friendly pR tags, thus facilitating the identification of ADP-ribosylation sites.
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Affiliation(s)
- Luca Palazzo
- Sir William Dunn School of PathologyUniversity of OxfordUK
| | - Casey M. Daniels
- Department of Biochemistry and Molecular BiologyBloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMDUSA,Present address: Laboratory of Systems BiologyNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD20892USA
| | - Joanne E. Nettleship
- OPPF‐UKThe Research Complex at HarwellRutherford Appleton LaboratoryHarwell OxfordUK,Division of Structural BiologyHenry Wellcome Building for Genomic MedicineUniversity of OxfordUK
| | - Nahid Rahman
- OPPF‐UKThe Research Complex at HarwellRutherford Appleton LaboratoryHarwell OxfordUK,Division of Structural BiologyHenry Wellcome Building for Genomic MedicineUniversity of OxfordUK
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular BiologyBloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMDUSA
| | - Shao‐En Ong
- Department of PharmacologyUniversity of WashingtonSeattleWAUSA
| | - Kazuki Kato
- Department of Biophysics and BiochemistryGraduate School of ScienceThe University of TokyoJapan
| | - Osamu Nureki
- Department of Biophysics and BiochemistryGraduate School of ScienceThe University of TokyoJapan
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular BiologyBloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMDUSA,Department of OncologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ivan Ahel
- Sir William Dunn School of PathologyUniversity of OxfordUK
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9
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Structural basis for specific inhibition of Autotaxin by a DNA aptamer. Nat Struct Mol Biol 2016; 23:395-401. [PMID: 27043297 DOI: 10.1038/nsmb.3200] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/10/2016] [Indexed: 12/14/2022]
Abstract
ATX is a plasma lysophospholipase D that hydrolyzes lysophosphatidylcholine (LPC) and produces lysophosphatidic acid. To date, no ATX-inhibition-mediated treatment strategies for human diseases have been established. Here, we report anti-ATX DNA aptamers that inhibit ATX with high specificity and efficacy. We solved the crystal structure of ATX in complex with the anti-ATX aptamer RB011, at 2.0-Å resolution. RB011 binds in the vicinity of the active site through base-specific interactions, thus preventing the access of the choline moiety of LPC substrates. Using the structural information, we developed the modified anti-ATX DNA aptamer RB014, which exhibited in vivo efficacy in a bleomycin-induced pulmonary fibrosis mouse model. Our findings reveal the structural basis for the specific inhibition of ATX by the anti-ATX aptamer and highlight the therapeutic potential of anti-ATX aptamers for the treatment of human diseases, such as pulmonary fibrosis.
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10
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Morita J, Kato K, Mihara E, Ishitani R, Takagi J, Nishimasu H, Aoki J, Nureki O. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:794-9. [PMID: 24915096 DOI: 10.1107/s2053230x14008929] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/19/2014] [Indexed: 01/09/2023]
Abstract
Enpp (ectonucleotide phosphodiesterase/pyrophosphatase) 6 is a membrane-bound glycoprotein that hydrolyzes choline-containing compounds such as lysophosphatidylcholine and glycerophosphorylcholine, and presumably participates in choline metabolism. The catalytic domain of mouse Enpp6 was expressed in HEK293T cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 1.8 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a=63.7, b=68.8, c=69.7 Å, α=60.6, β=87.0, γ=68.1°. Assuming the presence of two protein molecules per asymmetric unit, the solvent content was estimated to be 49.5%.
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Affiliation(s)
- Junko Morita
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kazuki Kato
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Emiko Mihara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryuichiro Ishitani
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Nishimasu
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Osamu Nureki
- Department of Biological Science, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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11
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al-Rashida M, Iqbal J. Therapeutic potentials of ecto-nucleoside triphosphate diphosphohydrolase, ecto-nucleotide pyrophosphatase/phosphodiesterase, ecto-5'-nucleotidase, and alkaline phosphatase inhibitors. Med Res Rev 2013; 34:703-43. [PMID: 24115166 DOI: 10.1002/med.21302] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The modulatory role of extracellular nucleotides and adenosine in relevance to purinergic cell signaling mechanisms has long been known and is an object of much research worldwide. These extracellular nucleotides are released by a variety of cell types either innately or as a response to patho-physiological stress or injury. A variety of surface-located ecto-nucleotidases (of four major types; nucleoside triphosphate diphosphohydrolases or NTPDases, nucleotide pyrophosphatase/phosphodiesterases or NPPs, alkaline phosphatases APs or ALPs, and ecto-5'-nucleotidase or e5NT) are responsible for meticulously controlling the availability of these important signaling molecules (at their respective receptors) in extracellular environment and are therefore crucial for maintaining the integrity of normal cell functioning. Overexpression of many of these ubiquitous ecto-enzymes has been implicated in a variety of disorders including cell adhesion, activation, proliferation, apoptosis, and degenerative neurological and immunological responses. Selective inhibition of these ecto-enzymes is an area that is currently being explored with great interest and hopes remain high that development of selective ecto-nucleotidase inhibitors will prove to have many beneficial therapeutic implications. The aim of this review is to emphasize and focus on recent developments made in the field of inhibitors of ecto-nucleotidases and to highlight their structure activity relationships wherever possible. Most recent and significant advances in field of NTPDase, NPP, AP, and e5NT inhibitors is being discussed in detail in anticipation of providing prolific leads and relevant background for research groups interested in synthesis of selective ecto-nucleotidase inhibitors.
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Affiliation(s)
- Mariya al-Rashida
- Department of Pharmaceutical Sciences, COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan
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12
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Jansen S, Perrakis A, Ulens C, Winkler C, Andries M, Joosten RP, Van Acker M, Luyten FP, Moolenaar WH, Bollen M. Structure of NPP1, an ectonucleotide pyrophosphatase/phosphodiesterase involved in tissue calcification. Structure 2012; 20:1948-59. [PMID: 23041369 DOI: 10.1016/j.str.2012.09.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 08/25/2012] [Accepted: 09/02/2012] [Indexed: 10/27/2022]
Abstract
Ectonucleotide pyrophosphatase/phosphodiesterase-1 (NPP1) converts extracellular nucleotides into inorganic pyrophosphate, whereas its close relative NPP2/autotaxin hydrolyzes lysophospholipids. NPP1 regulates calcification in mineralization-competent tissues, and a lack of NPP1 function underlies calcification disorders. Here, we show that NPP1 forms homodimers via intramembrane disulfide bonding, but is also processed intracellularly to a secreted monomer. The structure of secreted NPP1 reveals a characteristic bimetallic active site and a nucleotide-binding groove, but it lacks the lipid-binding pocket and open tunnel present in NPP2. A loop adjacent to the nucleotide-binding site, which is disordered in NPP2, is well ordered in NPP1 and might promote nucleotide binding. Remarkably, the N-terminal somatomedin B-like domains of NPP1, unlike those in NPP2, are flexible and do not contact the catalytic domain. Our results provide a structural basis for the nucleotide pyrophosphatase activity of NPP1 and help to understand how disease-causing mutations may affect NPP1 structure and function.
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Affiliation(s)
- Silvia Jansen
- Laboratory of Biosignaling and Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
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13
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Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling. Proc Natl Acad Sci U S A 2012; 109:16876-81. [PMID: 23027977 DOI: 10.1073/pnas.1208017109] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Enpp1 is a membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing extracellular nucleotide triphosphates to produce pyrophosphate. Enpp1 dysfunction causes human diseases characterized by ectopic calcification. Enpp1 also inhibits insulin signaling, and an Enpp1 polymorphism is associated with insulin resistance. However, the precise mechanism by which Enpp1 functions in these cellular processes remains elusive. Here, we report the crystal structures of the extracellular region of mouse Enpp1 in complex with four different nucleotide monophosphates, at resolutions of 2.7-3.2 Å. The nucleotides are accommodated in a pocket formed by an insertion loop in the catalytic domain, explaining the preference of Enpp1 for an ATP substrate. Structural mapping of disease-associated mutations indicated the functional importance of the interdomain interactions. A structural comparison of Enpp1 with Enpp2, a lysophospholipase D, revealed marked differences in the domain arrangements and active-site architectures. Notably, the Enpp1 mutant lacking the insertion loop lost the nucleotide-hydrolyzing activity but instead gained the lysophospholipid-hydrolyzing activity of Enpp2. Our findings provide structural insights into how the Enpp family proteins evolved to exert their diverse cellular functions.
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