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Luo P, Xie Y, He X, He Y, Wang X, Tan L. Application of Fenton chemistry in electrochemical determination of pyrophosphatase activity and fluoride. Talanta 2024; 274:125943. [PMID: 38564823 DOI: 10.1016/j.talanta.2024.125943] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/28/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
Fenton chemistry has aroused widespread concern due to its application in the green oxidation and mineralization of organic wastes. Inorganic pyrophosphatase (PPase) catalyzes the hydrolysis of pyrophosphate ions (PPi) and provides a thermodynamic driving force for many biosynthetic reactions. Fluoride (F-) is widely applied to fight against tooth decay and reduce cavities. The electrochemical determination of PPase activity and F- was realized based on Fenton chemistry in this work. Glassy carbon electrode modified with poly (azure A) and acetylene black (GCE/PAA-AB) was fabricated. Hydroxyl radicals (∙OH) that were generated from a Cu2+-catalyzed Fenton-type reaction could oxidize PAA in the near-neutral medium, leading to a great increase of the cathodic peak current (Ipc). A coordination reaction between PPi and Cu2+ exerted a negative effect on Fenton reaction and hindered the Ipc enhancement. Cu2+-PPi complex was decomposed due to the hydrolysis of PPi induced by PPase, which caused the reappearance of the notably increased current response. F- could effectively inhibit PPase activity. As a result, the stable Cu2+-PPi complex remained and the high Ipc suffered from the decline again. The Ipc difference was used for the highly sensitive determination of PPase activity in the content range of 0.001-20 mU mL-1 with a detection of limit (LOD) at 0.6 μU mL-1 and that of F- in the concentration range of 0.01-100 μM with a LOD at 7 nM. The proposed PPase and F- sensor displayed a good selectivity, stability and reproducibility, and a high accuracy.
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Affiliation(s)
- Peng Luo
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Yiyan Xie
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Xianhuan He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Yiyu He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Xuan Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Liang Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China.
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Sun F, Yang Y, Jia L, Dong QQ, Hu W, Tao H, Lu C, Yang JJ. TET3 boosts hepatocyte autophagy and impairs non-alcoholic fatty liver disease by increasing ENPP1 promoter hypomethylation. Free Radic Biol Med 2024; 218:166-177. [PMID: 38582229 DOI: 10.1016/j.freeradbiomed.2024.04.207] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Dysregulated ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family occurs in metabolic reprogramming pathological processes. Nonetheless, the epigenetic mechanisms by which ENPP family impacts NAFLD, also known as metabolic dysfunction-associated steatotic liver disease (MASLD), is poorly appreciated. METHODS We investigated the causes and consequences of ENPP1 promoter hypomethylation may boost NAFLD using NAFLD clinical samples, as well as revealed the underlying mechanisms using high-fat diet (HFD) + carbon tetrachloride (CCl4) induced mouse model of NAFLD and FFA treatment of cultured hepatocyte. RESULTS Herein, we report that the expression level of ENPP1 are increased in patients with NAFLD liver tissue and in mouse model of NAFLD. Hypomethylation of ENPP1, is associated with the perpetuation of hepatocyte autophagy and liver fibrosis in the NAFLD. ENPP1 hypomethylation is mediated by the DNA demethylase TET3 in NAFLD liver fibrosis and hepatocyte autophagy. Additionally, knockdown of TET3 methylated ENPP1 promoter, reduced the ENPP1 expression, ameliorated the experimental NAFLD. Mechanistically, TET3 epigenetically promoted ENPP1 expression via hypomethylation of the promoter. Knocking down TET3 can inhibit the hepatocyte autophagy but an overexpression of ENPP1 showing rescue effect. CONCLUSIONS We describe a novel epigenetic mechanism wherein TET3 promoted ENPP1 expression through promoter hypomethylation is a critical mediator of NAFLD. Our findings provide new insight into the development of preventative measures for NAFLD.
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Affiliation(s)
- Feng Sun
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China; School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Yang Yang
- Department of General Surgery, Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, 215153, China
| | - Lin Jia
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China; School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Qi-Qi Dong
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China; School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Wei Hu
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
| | - Chao Lu
- First Affiliated Hospital, Anhui University of Science & Technology, Huainan, 232001, China.
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
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3
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Inazu M, Nemoto T, Omata Y, Suzuki S, Ono S, Kanno Y, Seo M, Oikawa A, Masuda S. Complete Loss of RelA and SpoT Homologs in Arabidopsis Reveals the Importance of the Plastidial Stringent Response in the Interplay between Chloroplast Metabolism and Plant Defense Response. Plant Cell Physiol 2024; 65:631-643. [PMID: 37925598 DOI: 10.1093/pcp/pcad136] [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] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
The highly phosphorylated nucleotide, guanosine tetraphosphate (ppGpp), functions as a secondary messenger in bacteria and chloroplasts. The accumulation of ppGpp alters plastidial gene expression and metabolism, which are required for proper photosynthetic regulation and robust plant growth. However, because four plastid-localized ppGpp synthases/hydrolases function redundantly, the impact of the loss of ppGpp-dependent stringent response on plant physiology remains unclear. We used CRISPR/Cas9 technology to generate an Arabidopsis thaliana mutant lacking all four ppGpp synthases/hydrolases and characterized its phenotype. The mutant showed over 20-fold less ppGpp levels than the wild type under normal growth conditions and exhibited leaf chlorosis and increased expression of defense-related genes as well as salicylic acid and jasmonate levels upon transition to nitrogen-starvation conditions. These results demonstrate that proper levels of ppGpp in plastids are required for controlling not only plastid metabolism but also phytohormone signaling, which is essential for plant defense.
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Affiliation(s)
- Masataka Inazu
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Takanari Nemoto
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Yuto Omata
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Sae Suzuki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Sumire Ono
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
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4
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Balıkçı E, Marques ASMC, Bauer LG, Seupel R, Bennett J, Raux B, Buchan K, Simelis K, Singh U, Rogers C, Ward J, Cheng C, Szommer T, Schützenhofer K, Elkins JM, Sloman DL, Ahel I, Fedorov O, Brennan PE, Huber KVM. Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J Med Chem 2024; 67:7245-7259. [PMID: 38635563 PMCID: PMC11089510 DOI: 10.1021/acs.jmedchem.4c00072] [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: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure-activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.
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Affiliation(s)
- Esra Balıkçı
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Anne-Sophie M. C. Marques
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Ludwig G. Bauer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Raina Seupel
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James Bennett
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Brigitt Raux
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Karly Buchan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Klemensas Simelis
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Usha Singh
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Catherine Rogers
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jennifer Ward
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Carol Cheng
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Tamas Szommer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kira Schützenhofer
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Jonathan M. Elkins
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - David L. Sloman
- Departments
of Discovery Chemistry, Merck & Co.
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Oleg Fedorov
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Paul E. Brennan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Nuffield Department of
Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kilian V. M. Huber
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
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5
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Maillard M, Nishii R, Yang W, Hoshitsuki K, Chepyala D, Lee SHR, Nguyen JQ, Relling MV, Crews KR, Leggas M, Singh M, Suang JLY, Yeoh AEJ, Jeha S, Inaba H, Pui CH, Karol SE, Trehan A, Bhatia P, Antillon Klussmann FG, Bhojwani D, Haidar CE, Yang JJ. Additive effects of TPMT and NUDT15 on thiopurine toxicity in children with acute lymphoblastic leukemia across multiethnic populations. J Natl Cancer Inst 2024; 116:702-710. [PMID: 38230823 PMCID: PMC11077315 DOI: 10.1093/jnci/djae004] [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: 11/05/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Thiopurines such as mercaptopurine (MP) are widely used to treat acute lymphoblastic leukemia (ALL). Thiopurine-S-methyltransferase (TPMT) and Nudix hydrolase 15 (NUDT15) inactivate thiopurines, and no-function variants are associated with drug-induced myelosuppression. Dose adjustment of MP is strongly recommended in patients with intermediate or complete loss of activity of TPMT and NUDT15. However, the extent of dosage reduction recommended for patients with intermediate activity in both enzymes is currently not clear. METHODS MP dosages during maintenance were collected from 1768 patients with ALL in Singapore, Guatemala, India, and North America. Patients were genotyped for TPMT and NUDT15, and actionable variants defined by the Clinical Pharmacogenetics Implementation Consortium were used to classify patients as TPMT and NUDT15 normal metabolizers (TPMT/NUDT15 NM), TPMT or NUDT15 intermediate metabolizers (TPMT IM or NUDT15 IM), or TPMT and NUDT15 compound intermediate metabolizers (TPMT/NUDT15 IM/IM). In parallel, we evaluated MP toxicity, metabolism, and dose adjustment using a Tpmt/Nudt15 combined heterozygous mouse model (Tpmt+/-/Nudt15+/-). RESULTS Twenty-two patients (1.2%) were TPMT/NUDT15 IM/IM in the cohort, with the majority self-reported as Hispanics (68.2%, 15/22). TPMT/NUDT15 IM/IM patients tolerated a median daily MP dose of 25.7 mg/m2 (interquartile range = 19.0-31.1 mg/m2), significantly lower than TPMT IM and NUDT15 IM dosage (P < .001). Similarly, Tpmt+/-/Nudt15+/- mice displayed excessive hematopoietic toxicity and accumulated more metabolite (DNA-TG) than wild-type or single heterozygous mice, which was effectively mitigated by a genotype-guided dose titration of MP. CONCLUSION We recommend more substantial dose reductions to individualize MP therapy and mitigate toxicity in TPMT/NUDT15 IM/IM patients.
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Affiliation(s)
- Maud Maillard
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Rina Nishii
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Keito Hoshitsuki
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Divyabharathi Chepyala
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Shawn H R Lee
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
- Khoo Teck Puat-National University Children’s Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jenny Q Nguyen
- Personalized Care Program, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mark Leggas
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Meenu Singh
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Joshua L Y Suang
- Khoo Teck Puat-National University Children’s Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Allen E J Yeoh
- Khoo Teck Puat-National University Children’s Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sima Jeha
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hiroto Inaba
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Seth E Karol
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Amita Trehan
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prateek Bhatia
- Haematology-Oncology Unit, Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Deepa Bhojwani
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cyrine E Haidar
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
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6
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Karthikeyan D, Kumar S, Jayaprakash NS. A comprehensive review of recent developments in the gram-negative bacterial UDP-2,3-diacylglucosamine hydrolase (LpxH) enzyme. Int J Biol Macromol 2024; 267:131327. [PMID: 38574903 DOI: 10.1016/j.ijbiomac.2024.131327] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/09/2024] [Accepted: 03/31/2024] [Indexed: 04/06/2024]
Abstract
The emergence of multidrug resistance has provided a great challenge to treat nosocomial infections, which have become a major health threat around the globe. Lipid A (an active endotoxin component), the final product of the Raetz lipid A metabolism pathway, is a membrane anchor of lipopolysaccharide (LPS) of the gram-negative bacterial outer membrane. It shields bacterial cells and serves as a protective barrier from antibiotics, thereby eliciting host response and making it difficult to destroy. UDP-2,3-diacylglucosamine pyrophosphate hydrolase (LpxH), a crucial peripheral membrane enzyme of the Raetz pathway, turned out to be the potential target to inhibit the production of Lipid A. This review provides a comprehensive compilation of information regarding the structural and functional aspects of LpxH, as well as its analogous LpxI and LpxG. In addition, apart from by providing a broader understanding of the enzyme-inhibitor mechanism, this review facilitates the development of novel drug candidates that can inhibit the pathogenicity of the lethal bacterium.
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Affiliation(s)
- Divyapriya Karthikeyan
- Centre for Bioseparation Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Sanjit Kumar
- Department of Biotechnology, School of Interdisciplinary Education and Research, Guru Ghasidas Vishwavidyalaya, Bilaspur (A Central University), Chhattisgarh 495009, India
| | - N S Jayaprakash
- Centre for Bioseparation Technology, Vellore Institute of Technology, Vellore 632014, India.
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7
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Yang P, Chen YX, Wang TT, Huang XS, Zhan RT, Yang JF, Ma DM. Nudix hydrolase WvNUDX24 is involved in borneol biosynthesis in Wurfbainia villosa. Plant J 2024; 118:1218-1231. [PMID: 38323895 DOI: 10.1111/tpj.16669] [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] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/13/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
Borneol, camphor, and bornyl acetate are highly promising monoterpenoids widely used in medicine, flavor, food, and chemical applications. Bornyl diphosphate (BPP) serves as a common precursor for the biosynthesis of these monoterpenoids. Although bornyl diphosphate synthase (BPPS) that catalyzes the cyclization of geranyl diphosphate (GPP) to BPP has been identified in multiple plants, the enzyme responsible for the hydrolysis of BPP to produce borneol has not been reported. Here, we conducted in vitro and in vivo functional characterization to identify the Nudix hydrolase WvNUDX24 from W. villosa, which specifically catalyzes the hydrolysis of BPP to generate bornyl phosphate (BP), and then BP forms borneol under the action of phosphatase. Subcellular localization experiments indicated that the hydrolysis of BPP likely occurs in the cytoplasm. Furthermore, site-directed mutagenesis experiments revealed that four critical residues (R84, S96, P98, and G99) for the hydrolysis activity of WvNUDX24. Additionally, the functional identification of phosphatidic acid phosphatase (PAP) demonstrated that WvPAP5 and WvPAP10 were able to hydrolyze geranylgeranyl diphosphate (GGPP) and farnesyl diphosphate (FPP) to generate geranylgeranyl phosphate (GGP) and farnesyl phosphate (FP), respectively, but could not hydrolyze BPP, GPP, and neryl diphosphate (NPP) to produce corresponding monophosphate products. These findings highlight the essential role of WvNUDX24 in the first step of BPP hydrolysis to produce borneol and provide genetic elements for the production of BPP-related terpenoids through plant metabolic engineering and synthetic biology.
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Affiliation(s)
- Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China
| | - Yuan-Xia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Tian-Tian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xue-Shuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China
| | - Ruo-Ting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jin-Fen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dong-Ming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
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8
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Wang Y, Chen X, Chen Q, Liu T, Wu Y, Huang L, Chen Y. Expression of human dCTP pyrophosphatase 1 (DCTPP1) and its association with cisplatin resistance characteristics in ovarian cancer. J Cell Mol Med 2024; 28:e18371. [PMID: 38686496 PMCID: PMC11058668 DOI: 10.1111/jcmm.18371] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Cisplatin (DDP) resistance is a major challenge in treating ovarian cancer patients. A recently discovered enzyme called dCTP pyrophosphatase 1 (DCTPP1) has been implicated in regulating cancer characteristics, including drug responses. In this study, we aimed to understand the role of DCTPP1 in cancer progression and cisplatin response. Using publicly available databases, we analysed the expression and clinical significance of DCTPP1 in ovarian cancer. Our bioinformatics analysis confirmed that DCTPP1 is significantly overexpressed in ovarian cancer and is closely associated with tumour progression and poor prognosis after cisplatin treatment. We also found that DCTPP1 located in oxidoreductase complex and may be involved in various biological processes related to cisplatin resistance, including pyrimidine nucleotide metabolism, the P53 signalling pathway and cell cycle signalling pathways. We observed higher expression of DCTPP1 in cisplatin-resistant cells (SKOV3/DDP) and samples compared to their sensitive counterparts. Additionally, we found that DCTPP1 expression was only enhanced in SKOV3/S cells when treated with cisplatin, indicating different expression patterns of DCTPP1 in cisplatin-sensitive and cisplatin-resistant cancer cells. Our study further supports the notion that cisplatin induces intracellular reactive oxygen species (ROS) and triggers cancer cell death through excessive oxidative stress. Knocking out DCTPP1 reversed the drug resistance of ovarian cancer cells by enhancing the intracellular antioxidant stress response and accumulating ROS. Based on our research findings, we conclude that DCTPP1 has prognostic value for ovarian cancer patients, and targeting DCTPP1 may be clinically significant in overcoming cisplatin resistance in ovarian cancer.
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Affiliation(s)
- Yu Wang
- Obstetrics and Gynecology center, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Xiangyun Chen
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Qiduan Chen
- Obstetrics and Gynecology center, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Tiancai Liu
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Yingsong Wu
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Liping Huang
- Obstetrics and Gynecology center, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Yao Chen
- School of medical laboratory and BiotechnologySouthern Medical UniversityGuangzhouChina
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9
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Rao S, Cao H, O'Hanna FJ, Zhou X, Lui A, Wrightstone E, Fish T, Yang Y, Thannhauser T, Cheng L, Dudareva N, Li L. Nudix hydrolase 23 post-translationally regulates carotenoid biosynthesis in plants. Plant Cell 2024; 36:1868-1891. [PMID: 38299382 DOI: 10.1093/plcell/koae030] [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] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/12/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Carotenoids are essential for photosynthesis and photoprotection. Plants must evolve multifaceted regulatory mechanisms to control carotenoid biosynthesis. However, the regulatory mechanisms and the regulators conserved among plant species remain elusive. Phytoene synthase (PSY) catalyzes the highly regulated step of carotenogenesis and geranylgeranyl diphosphate synthase (GGPPS) acts as a hub to interact with GGPP-utilizing enzymes for the synthesis of specific downstream isoprenoids. Here, we report a function of Nudix hydrolase 23 (NUDX23), a Nudix domain-containing protein, in post-translational regulation of PSY and GGPPS for carotenoid biosynthesis. NUDX23 expresses highly in Arabidopsis (Arabidopsis thaliana) leaves. Overexpression of NUDX23 significantly increases PSY and GGPPS protein levels and carotenoid production, whereas knockout of NUDX23 dramatically reduces their abundances and carotenoid accumulation in Arabidopsis. NUDX23 regulates carotenoid biosynthesis via direct interactions with PSY and GGPPS in chloroplasts, which enhances PSY and GGPPS protein stability in a large PSY-GGPPS enzyme complex. NUDX23 was found to co-migrate with PSY and GGPPS proteins and to be required for the enzyme complex assembly. Our findings uncover a regulatory mechanism underlying carotenoid biosynthesis in plants and offer promising genetic tools for developing carotenoid-enriched food crops.
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Affiliation(s)
- Sombir Rao
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Hongbo Cao
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Franz Joseph O'Hanna
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Xuesong Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andy Lui
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Emalee Wrightstone
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Theodore Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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10
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Tasleem M, Pelletier J, Sévigny J, Hussain Z, Khan A, Al-Harrasi A, El-Kott AF, Taslimi P, Negm S, Shafiq Z, Iqbal J. Synthesis, in vitro, and in silico studies of morpholine-based thiosemicarbazones as ectonucleotide pyrophosphatase/phosphodiesterase-1 and -3 inhibitors. Int J Biol Macromol 2024; 266:131068. [PMID: 38531526 DOI: 10.1016/j.ijbiomac.2024.131068] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/06/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024]
Abstract
An extensive range of new biologically active morpholine based thiosemicarbazones derivatives 3a-r were synthesized, characterized by spectral techniques and evaluated as inhibitors of ENPP isozymes. Most of the novel thiosemicarbazones exhibit potent inhibition towards NPP1 and NPP3 isozymes. Compound 3 h was potent inhibitor of NPP1 with IC50 value of 0.55 ± 0.02. However, the most powerful inhibitor of NPP3 was 3e with an IC50 value of 0.24 ± 0.02. Furthermore, Lineweaver-Burk plot for compound 3 h against NPP1 and for compound 3e against NPP3 was devised through enzymes kinetics studies. Molecular docking and in silico studies was also done for analysis of interaction pattern of all newly synthesized compounds. The results were further validated by molecular dynamic (MD) simulation where the stability of conformational transformation of the best protein-ligand complex (3e) were justified on the basis of RMSD and RMSF analysis.
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Affiliation(s)
- Mussarat Tasleem
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Julie Pelletier
- Centre de Recherche du CHU de Québec-Université Laval, Québec G1V 4G2, Canada
| | - Jean Sévigny
- Centre de Recherche du CHU de Québec-Université Laval, Québec G1V 4G2, Canada; Département de Microbiologie-infectiologie et d'immunologie, Faculté de Médecine, Université Laval, Québec G1V 0A6, Canada
| | - Zahid Hussain
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, P.O. Box 33, PC 616, Birkat Al Mauz, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, P.O. Box 33, PC 616, Birkat Al Mauz, Nizwa, Sultanate of Oman.
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia; Department of Zoology, College of Science, Damanhour University, Egypt
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, 74100 Bartin, Türkiye
| | - Sally Negm
- Department of Life Sciences, College of Science and Art Mahyel Aseer, King Khalid University, Abha 62529, Saudi Arabia
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan; Department of Pharmaceutical & Medicinal Chemistry, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan.
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11
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Elgizawy EI, Amer GS, Ali EA, Alqalashy FS, Ibrahim MM, Latif AAA, Shaban AM. Comparing the efficacy of concomitant treatment of resistance exercise and creatine monohydrate versus multiple individual therapies in age related sarcopenia. Sci Rep 2024; 14:9798. [PMID: 38684784 PMCID: PMC11058861 DOI: 10.1038/s41598-024-59884-w] [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: 10/17/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Aging-related sarcopenia is a degenerative loss of strength and skeletal muscle mass that impairs quality of life. Evaluating NUDT3 gene and myogenin expression as new diagnostic tools in sarcopenia. Also, comparing the concomitant treatment of resistance exercise (EX) and creatine monohydrate (CrM) versus single therapy by EX, coenzyme Q10 (CoQ10), and CrM using aged rats. Sixty male rats were equally divided into groups. The control group, aging group, EX-treated group, the CoQ10 group were administered (500 mg/kg) of CoQ10, the CrM group supplied (0.3 mg/kg of CrM), and a group of CrM concomitant with resistance exercise. Serum lipid profiles, certain antioxidant markers, electromyography (EMG), nudix hydrolase 3 (NUDT3) expression, creatine kinase (CK), and sarcopenic index markers were measured after 12 weeks. The gastrocnemius muscle was stained with hematoxylin-eosin (H&E) and myogenin. The EX-CrM combination showed significant improvement in serum lipid profile, antioxidant markers, EMG, NUDT3 gene, myogenin expression, CK, and sarcopenic index markers from other groups. The NUDT3 gene and myogenin expression have proven efficient as diagnostic tools for sarcopenia. Concomitant treatment of CrM and EX is preferable to individual therapy because it reduces inflammation, improves the lipid serum profile, promotes muscle regeneration, and thus has the potential to improve sarcopenia.
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Affiliation(s)
- Eman I Elgizawy
- Medical Physiology Department, Faculty of Medicine, Menoufia University, Yassin Abd El Ghafar St., Shebin El Kom, Menoufia, 32511, Egypt.
| | - Ghada S Amer
- Medical Physiology Department, Faculty of Medicine, Menoufia University, Yassin Abd El Ghafar St., Shebin El Kom, Menoufia, 32511, Egypt
| | - Eman A Ali
- Clinical Pharmacology Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Menoufia, Egypt
| | - Fatma S Alqalashy
- Pathology Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Menoufia, Egypt
| | - Marwa M Ibrahim
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Menoufia, Egypt
| | - Asmaa A Abdel Latif
- Public Health and Community Medicine Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Menoufia, Egypt
| | - Anwar M Shaban
- Medical Physiology Department, Faculty of Medicine, Menoufia University, Yassin Abd El Ghafar St., Shebin El Kom, Menoufia, 32511, Egypt
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12
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Zhang Z, Samsa WE, Gong Z. NUDT16 regulates CtIP PARylation to dictate homologous recombination repair. Nucleic Acids Res 2024; 52:3761-3777. [PMID: 38324469 PMCID: PMC11039996 DOI: 10.1093/nar/gkae064] [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: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
CtIP initiates DNA end resection and mediates homologous recombination (HR) repair. However, the underlying mechanisms of CtIP regulation and how the control of its regulation affects DNA repair remain incompletely characterized. In this study, NUDT16 loss decreases CtIP protein levels and impairs CtIP recruitment to double-strand breaks (DSBs). Furthermore, overexpression of a catalytically inactive NUDT16 mutant is unable to rescue decreased CtIP protein and impaired CtIP recruitment to DSBs. In addition, we identified a novel posttranslational modification of CtIP by ADP-ribosylation that is targeted by a PAR-binding E3 ubiquitin ligase, RNF146, leading to CtIP ubiquitination and degradation. These data suggest that the hydrolase activity of NUDT16 plays a major role in controlling CtIP protein levels. Notably, ADP-ribosylation of CtIP is required for its interaction with NUDT16, its localization at DSBs, and for HR repair. Interestingly, NUDT16 can also be ADP-ribosylated. The ADP-ribosylated NUDT16 is critical for CtIP protein stability, CtIP recruitment to DSBs, and HR repair in response to DNA damage. In summary, we demonstrate that NUDT16 and its PARylation regulate CtIP stability and CtIP recruitment to DSBs, providing new insights into our understanding of the regulation of CtIP-mediated DNA end resection in the HR repair pathway.
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Affiliation(s)
- Zhen Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - William E Samsa
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
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13
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Andrilli LHS, Sebinelli HG, Cominal JG, Bolean M, Hayann L, Millán JL, Ramos AP, Ciancaglini P. Differential effects of the lipidic and ionic microenvironment on NPP1's phosphohydrolase and phosphodiesterase activities. Biochim Biophys Acta Biomembr 2024; 1866:184292. [PMID: 38342362 DOI: 10.1016/j.bbamem.2024.184292] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/30/2023] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
Abstract
Ecto-nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) is an enzyme present in matrix vesicles (MV). NPP1 participates on the regulation of bone formation by producing pyrophosphate (PPi) from adenosine triphosphate (ATP). Here, we have used liposomes bearing dipalmitoylphosphatidylcholine (DPPC), sphingomyelin (SM), and cholesterol (Chol) harboring NPP1 to mimic the composition of MV lipid rafts to investigate ionic and lipidic influence on NPP1 activity and mineral propagation. Atomic force microscopy (AFM) revealed that DPPC-liposomes had spherical and smooth surface. The presence of SM and Chol elicited rough and smooth surface, respectively. NPP1 insertion produced protrusions in all the liposome surface. Maximum phosphodiesterase activity emerged at 0.082 M ionic strength, whereas maximum phosphomonohydrolase activity arose at low ionic strength. Phosphoserine-Calcium Phosphate Complex (PS-CPLX) and amorphous calcium-phosphate (ACP) induced mineral propagation in DPPC- and DPPC:SM-liposomes and in DPPC:Chol-liposomes, respectively. Mineral characterization revealed the presence of bands assigned to HAp in the mineral propagated by NPP1 harbored in DPPC-liposomes without nucleators or in DPPC:Chol-liposomes with ACP nucleators. These data show that studying how the ionic and lipidic environment affects NPP1 properties is important, especially for HAp obtained under controlled conditions in vitro.
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Affiliation(s)
- Luiz H S Andrilli
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil; Sanford Children's Health Research Center, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Heitor G Sebinelli
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Juçara G Cominal
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Maytê Bolean
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Larwsk Hayann
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - José Luís Millán
- Sanford Children's Health Research Center, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Ana P Ramos
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil.
| | - Pietro Ciancaglini
- Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil.
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14
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Sun Y, Chen M, Han Y, Li W, Ma X, Shi Z, Zhou Y, Xu L, Yu L, Wang Y, Yu J, Diao X, Meng L, Xu S. Discovery of Pyrido[2,3- d]pyrimidin-7-one Derivatives as Highly Potent and Efficacious Ectonucleotide Pyrophosphatase/Phosphodiesterase 1 (ENPP1) Inhibitors for Cancer Treatment. J Med Chem 2024; 67:3986-4006. [PMID: 38387074 DOI: 10.1021/acs.jmedchem.3c02288] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) is an extracellular enzyme responsible for hydrolyzing cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), the endogenous agonist for the stimulator of interferon genes (STING) pathway. Inhibition of ENPP1 can trigger STING and promote antitumor immunity, offering an attractive therapeutic target for cancer immunotherapy. Despite progress in the discovery of ENPP1 inhibitors, the diversity in chemical structures and the efficacy of the agents are far from desirable, emphasizing the demand for novel inhibitors. Herein, we describe the design, synthesis, and biological evaluation of a series of ENPP1 inhibitors based on the pyrido[2,3-d]pyrimidin-7-one scaffold. Optimization efforts led to compound 31 with significant potency in both ENPP1 inhibition and STING pathway stimulation in vitro. Notably, 31 demonstrated in vivo efficacy in a syngeneic 4T1 mouse triple negative breast cancer model. These findings provide a promising lead compound with a novel scaffold for further drug development in cancer immunotherapy.
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Affiliation(s)
- Yaoliang Sun
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Manman Chen
- Division of Antitumor Pharmacology, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuyan Han
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqiang Li
- Center for Drug Metabolism and Pharmacokinetics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Ma
- Division of Antitumor Pharmacology, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihan Shi
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Lan Xu
- Division of Antitumor Pharmacology, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lei Yu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuxiang Wang
- Division of Antitumor Pharmacology, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinghua Yu
- Center for Drug Metabolism and Pharmacokinetics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xingxing Diao
- Center for Drug Metabolism and Pharmacokinetics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linghua Meng
- Division of Antitumor Pharmacology, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Wu W, Wu W, Zhou Y, Yang Q, Zhuang S, Zhong C, Li W, Li A, Zhao W, Yin X, Zu X, Chak-Lui Wong C, Yin D, Hu K, Cai M. The dePARylase NUDT16 promotes radiation resistance of cancer cells by blocking SETD3 for degradation via reversing its ADP-ribosylation. J Biol Chem 2024; 300:105671. [PMID: 38272222 PMCID: PMC10926213 DOI: 10.1016/j.jbc.2024.105671] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a critical posttranslational modification that plays a vital role in maintaining genomic stability via a variety of molecular mechanisms, including activation of replication stress and the DNA damage response. The nudix hydrolase NUDT16 was recently identified as a phosphodiesterase that is responsible for removing ADP-ribose units and that plays an important role in DNA repair. However, the roles of NUDT16 in coordinating replication stress and cell cycle progression remain elusive. Here, we report that SETD3, which is a member of the SET-domain containing protein (SETD) family, is a novel substrate for NUDT16, that its protein levels fluctuate during cell cycle progression, and that its stability is strictly regulated by NUDT16-mediated dePARylation. Moreover, our data indicated that the E3 ligase CHFR is responsible for the recognition and degradation of endogenous SETD3 in a PARP1-mediated PARylation-dependent manner. Mechanistically, we revealed that SETD3 associates with BRCA2 and promotes its recruitment to stalled replication fork and DNA damage sites upon replication stress or DNA double-strand breaks, respectively. Importantly, depletion of SETD3 in NUDT16-deficient cells did not further exacerbate DNA breaks or enhance the sensitivity of cancer cells to IR exposure, suggesting that the NUDT16-SETD3 pathway may play critical roles in the induction of tolerance to radiotherapy. Collectively, these data showed that NUDT16 functions as a key upstream regulator of SETD3 protein stability by reversing the ADP-ribosylation of SETD3, and NUDT16 participates in the resolution of replication stress and facilitates HR repair.
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Affiliation(s)
- Weijun Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wenjing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Breast Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yingshi Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Qiao Yang
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shuting Zhuang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Caixia Zhong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjia Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Aixin Li
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wanzhen Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xiaomin Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Carmen Chak-Lui Wong
- Li Ka Shing Faculty of Medicine, Department of Pathology, The University of Hong Kong, Hong Kong, Guangdong, China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Manbo Cai
- Department of Oncology Radiotherapy, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
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16
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Okamoto H, Tanaka Y, Shibagaki Y, Kuronuma S, Miyatani Y, Umeda S, Mishiro-Sato E, Takeuchi O, Hattori S, Kobayashi T, Okuwaki M. Measurement of the intracellular active metabolites of thiopurine drugs to evaluate the enzymatic activity of nudix hydrolase 15 in human blood samples. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1234:123993. [PMID: 38246006 DOI: 10.1016/j.jchromb.2024.123993] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 12/13/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Thiopurine is metabolized to 6-thio-(deoxy) guanosine triphosphate (6-thio-(d) GTP), which is then incorporated into DNA or RNA and causes cytotoxicity. Nudix hydrolase 15 (NUDT15) reduces the cytotoxic effects of thiopurine by converting 6-thio-(d) GTP to 6-thio-(d) guanosine monophosphate (6-thio-(d) GMP). NUDT15 polymorphisms like the Arg139Cys variant are strongly linked to thiopurine-induced severe leukocytopenia and alopecia. Therefore, measurement of NUDT15 enzymatic activity in individual patients can help predict thiopurine tolerability and adjust the dosage. We aimed to develop a quantitative assay for NUDT15 enzymatic activity in human blood samples. Blood samples were collected from donors whose NUDT15 genetic status was determined. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to assess the 6-thio-GTP metabolic activity in cell extracts. Because 6-thio-guanosine diphosphate (6-thio-GDP) and 6-thio-GMP were generated upon incubation of 6-thio-GTP with human blood cell extracts, the method detecting 6-thio-GTP, 6-thio-GDP, and 6-thio-GMP was validated. All three metabolites were linearly detected, and the lower limit of quantification (LLOQ) of 6-thio-GTP, 6-thio-GDP, and 6-thio-GMP were 5 μM, 1 μM, and 2 μM, respectively. Matrix effects of human blood cell extracts to detect 6-thio-GTP, 6-thio-GDP, and 6-thio-GMP were 99.0 %, 100.5 %, and 101.4 %, respectively, relative to the signals in the absence of blood cell extracts. The accuracy and precision of the method and the stability of the samples were also assessed. Using this established method, the genotype-dependent differences in NUDT15 activities were successfully determined using cell extracts derived from human blood cells with NUDT15 wild-type (WT) or Arg139Cys variant and 6-thio-GTP (100 μM) as a substrate (18.1, 14.9, and 6.43 μM/h/106 cells for WT, Arg139Cys heterozygous, and homozygous variant, respectively). We developed a method for quantifying intracellular NUDT15 activity in peripheral blood mononuclear cells (PBMCs), which we defined as the conversion of 6-thio-GTP to 6-thio-GMP. Although PBMCs preparation takes some time, its reproducibility in experiments makes it a promising candidate for clinical application. This method can tell the difference between WT and Arg139Cys homozygous blood samples. Even in patients with WT NUDT15, WT samples showed variations in NUDT15 activity, which may correlate with variations in thiopurine dosage.
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Affiliation(s)
- Hitomi Okamoto
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan; Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yoichi Tanaka
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan; Division of Medicinal Safety Science, National Institute of Health Sciences, Kanagawa, Japan.
| | - Yoshio Shibagaki
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yusuke Miyatani
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan; Department of Gastroenterology and Hepatology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Satoko Umeda
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan; Department of Gastroenterology and Hepatology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Emi Mishiro-Sato
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Seisuke Hattori
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan
| | - Taku Kobayashi
- Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan; Department of Gastroenterology and Hepatology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Mitsuru Okuwaki
- Laboratory of Biochemistry, Graduate School of Pharmaceutical Sciences, Japan.
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17
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Bednor L, Sanchez AM, Garg A, Shuman S, Schwer B. Genetic suppressor screen identifies Tgp1 (glycerophosphocholine transporter), Kcs1 (IP 6 kinase), and Plc1 (phospholipase C) as determinants of inositol pyrophosphate toxicosis in fission yeast. mBio 2024; 15:e0306223. [PMID: 38133430 PMCID: PMC10865970 DOI: 10.1128/mbio.03062-23] [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: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The inositol pyrophosphate signaling molecule 1,5-IP8 is an agonist of RNA 3'-processing and transcription termination in fission yeast that regulates the expression of phosphate acquisition genes pho1, pho84, and tgp1. IP8 is synthesized from 5-IP7 by the Asp1 N-terminal kinase domain and catabolized by the Asp1 C-terminal pyrophosphatase domain. asp1-STF mutations that delete or inactivate the Asp1 pyrophosphatase domain elicit growth defects in yeast extract with supplements (YES) medium ranging from severe sickness to lethality. We now find that the toxicity of asp1-STF mutants is caused by a titratable constituent of yeast extract. Via a genetic screen for spontaneous suppressors, we identified a null mutation of glycerophosphodiester transporter tgp1 that abolishes asp1-STF toxicity in YES medium. This result, and the fact that tgp1 mRNA expression is increased by >40-fold in asp1-STF cells, prompted discovery that: (i) glycerophosphocholine (GPC) recapitulates the toxicity of yeast extract to asp1-STF cells in a Tgp1-dependent manner, and (ii) induced overexpression of tgp1 in asp1+ cells also elicits toxicity dependent on GPC. asp1-STF suppressor screens yielded a suite of single missense mutations in the essential IP6 kinase Kcs1 that generates 5-IP7, the immediate precursor to IP8. Transcription profiling of the kcs1 mutants in an asp1+ background revealed the downregulation of the same phosphate acquisition genes that were upregulated in asp1-STF cells. The suppressor screen also returned single missense mutations in Plc1, the fission yeast phospholipase C enzyme that generates IP3, an upstream precursor for the synthesis of inositol pyrophosphates.IMPORTANCEThe inositol pyrophosphate metabolite 1,5-IP8 governs repression of fission yeast phosphate homeostasis genes pho1, pho84, and tgp1 by lncRNA-mediated transcriptional interference. Asp1 pyrophosphatase mutations that increase IP8 levels elicit precocious lncRNA termination, leading to derepression of the PHO genes. Deletions of the Asp1 pyrophosphatase domain result in growth impairment or lethality via IP8 agonism of transcription termination. It was assumed that IP8 toxicity ensues from dysregulation of essential genes. In this study, a suppressor screen revealed that IP8 toxicosis of Asp1 pyrophosphatase mutants is caused by: (i) a >40-fold increase in the expression of the inessential tgp1 gene encoding a glycerophosphodiester transporter and (ii) the presence of glycerophosphocholine in the growth medium. The suppressor screen yielded missense mutations in two upstream enzymes of inositol polyphosphate metabolism: the phospholipase C enzyme Plc1 that generates IP3 and the essential Kcs1 kinase that converts IP6 to 5-IP7, the immediate precursor of IP8.
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Affiliation(s)
- Lauren Bednor
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
- Weill Cornell Graduate School of Medical Sciences, New York, USA
| | - Ana M. Sanchez
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, USA
| | - Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
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18
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Strauss J, Wilkinson C, Vidilaseris K, de Castro Ribeiro OM, Liu J, Hillier J, Wichert M, Malinen AM, Gehl B, Jeuken LJ, Pearson AR, Goldman A. Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases. EMBO Rep 2024; 25:853-875. [PMID: 38182815 PMCID: PMC10897367 DOI: 10.1038/s44319-023-00037-x] [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: 08/24/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that couple the transport of Na+- and/or H+ across membranes to the hydrolysis of pyrophosphate. Their role in the virulence of protist pathogens like Plasmodium falciparum makes them an intriguing target for structural and functional studies. Here, we show the first structure of a K+-independent M-PPase, asymmetric and time-dependent substrate binding in time-resolved structures of a K+-dependent M-PPase and demonstrate pumping-before-hydrolysis by electrometric studies. We suggest how key residues in helix 12, 13, and the exit channel loops affect ion selectivity and K+-activation due to a complex interplay of residues that are involved in subunit-subunit communication. Our findings not only explain ion selectivity in M-PPases but also why they display half-of-the-sites reactivity. Based on this, we propose, for the first time, a unified model for ion-pumping, hydrolysis, and energy coupling in all M-PPases, including those that pump both Na+ and H+.
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Affiliation(s)
- Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Numaferm GmbH, Düsseldorf, Germany
| | - Craig Wilkinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Keni Vidilaseris
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Orquidea M de Castro Ribeiro
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Jianing Liu
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - James Hillier
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Bio-Rad Laboratories Ltd., Watford, UK
| | - Maximilian Wichert
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Anssi M Malinen
- Department of Life Technologies, University of Turku, FIN-20014, Turku, Finland
| | - Bernadette Gehl
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
- Department of Applied Physics, Aalto University, FI-00076, AALTO, Espoo, Finland
| | - Lars Jc Jeuken
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany
| | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland.
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Suito H, Fujikawa K, Ohsako M. ENPP1 downregulation and FGF23 upregulation in growth-related calcification of the tibial tuberosity in rats. J Anat 2024; 244:333-342. [PMID: 37814911 PMCID: PMC10780148 DOI: 10.1111/joa.13958] [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: 03/24/2023] [Revised: 08/15/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023] Open
Abstract
During tibial tuberosity growth, superficial and deep portions can be observed; however, the deep portion is not observed after the growth period, as it develops into bone tissues. Calcification in vivo is known to be constitutively suppressed by ectonucleotide pyrophosphatase/phosphodiesterase-1 (ENPP1) but promoted by tissue-nonspecific alkaline phosphatase (TNAP). FGF23 promotes calcification of enthesis. Gene expression of FGF23 increased rapidly at 13W in this study. Therefore, the tibial tuberosity is speculated to develop via Enpp1 downregulation and Tnap upregulation; however, the understanding of these processes remains unclear. Hence, in the present study, we aimed to explore the age-related structural changes and underlying gene expression changes in the tibial tuberosity of rats. Male Wistar rats were divided into three groups (3-, 7-, and 13-week-old; eight each). The tibial tuberosity superficial and deep portions were clearly observed in 3- and 7-week-old rats, but the presence of the deep portion was not confirmed in 13-week-old rats. The extracellular matrix of hypertrophic chondrocytes was calcified. Furthermore, the Enpp1 expression was the highest in 3-week-old rats and decreased with growth. The TNAP expression did not differ significantly among the groups. The deep portion area was significantly lower in 3-week-old rats than in 7-week-old rats. Generally, the extracellular matrix of the immature chondrocytes is not calcified. Therefore, we speculated that the cartilaginous tibial tuberosity calcifies and ossifies with growth. The Enpp1 expression decreased with growth, whereas the Tnap expression remained unchanged. Thus, we surmise that the tibial tuberosity calcifies with growth and that this process involves Enpp1 downregulation and FGF23 upregulation. As Osgood-Schlatter disease is closely related to the calcification of the tibial tuberosity, these findings may help clarify the pathogenesis of this disease.
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Affiliation(s)
- Hirai Suito
- Graduate School of Human Life Design, Toyo University, Tokyo, Japan
- Japan Society for the Promotion of Science Research Fellowships DC, Tokyo, Japan
| | - Kaoru Fujikawa
- Department of Oral Anatomy and Developmental Biology, Showa University School of Dentistry, Tokyo, Japan
| | - Masafumi Ohsako
- Graduate School of Health and Sports Science, Toyo University, Tokyo, Japan
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20
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Ferreira CR, Carpenter TO, Braddock DT. ENPP1 in Blood and Bone: Skeletal and Soft Tissue Diseases Induced by ENPP1 Deficiency. Annu Rev Pathol 2024; 19:507-540. [PMID: 37871131 PMCID: PMC11062289 DOI: 10.1146/annurev-pathmechdis-051222-121126] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The enzyme ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) codes for a type 2 transmembrane glycoprotein that hydrolyzes extracellular ATP to generate pyrophosphate (PPi) and adenosine monophosphate, thereby contributing to downstream purinergic signaling pathways. The clinical phenotypes induced by ENPP1 deficiency are seemingly contradictory and include early-onset osteoporosis in middle-aged adults and life-threatening vascular calcifications in the large arteries of infants with generalized arterial calcification of infancy. The progressive overmineralization of soft tissue and concurrent undermineralization of skeleton also occur in the general medical population, where it is referred to as paradoxical mineralization to highlight the confusing pathophysiology. This review summarizes the clinical presentation and pathophysiology of paradoxical mineralization unveiled by ENPP1 deficiency and the bench-to-bedside development of a novel ENPP1 biologics designed to treat mineralization disorders in the rare disease and general medical population.
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Affiliation(s)
- Carlos R Ferreira
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas O Carpenter
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Demetrios T Braddock
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA;
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21
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Duangiad P, Nutho B, Chaijarasphong T, Morales NP, Pongtharangkul T, Hamachi I, Ojida A, Wongkongkatep J. Naturally occurring quercetin and myricetin as potent inhibitors for human ectonucleotide pyrophosphatase/phosphodiesterase 1. Sci Rep 2024; 14:125. [PMID: 38167594 PMCID: PMC10761680 DOI: 10.1038/s41598-023-50590-7] [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: 06/27/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto Green, a rapid chemical sensor of pyrophosphate, was employed to screen for effective ENPP1 inhibitors among five representative flavonoids (quercetin, myricetin, morin, kaempferol, and quercetin-3-glucoside), five nucleosides (adenosine, guanosine, inosine, uridine, and cytidine), and five deoxynucleosides (2'- and 3'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxyinosine, and 2'-deoxyuridine). Conventional colorimetric, fluorescence, and bioluminescence assays revealed that ENPP1 was effectively inhibited by quercetin (Ki ~ 4 nM) and myricetin (Ki ~ 32 nM) when ATP was used as a substrate at pH 7.4. In silico analysis indicated that the presence of a chromone scaffold, particularly one containing a hydroxyl group at the 3' position on the B ring, may promote binding to the active site pocket of ENPP1 and enhance inhibition. This study demonstrated that the naturally derived quercetin and myricetin could effectively inhibit ENPP1 enzymatic activity and may offer health benefits in arthritis management.
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Affiliation(s)
- Peeradon Duangiad
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Thawatchai Chaijarasphong
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Noppawan Phumala Morales
- Department of Pharmacology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Thunyarat Pongtharangkul
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Jirarut Wongkongkatep
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
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22
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Backer N, Kumar A, Singh AK, Singh H, Narasimhan B, Kumar P. Medicinal chemistry aspects of uracil containing dUTPase inhibitors targeting colorectal cancer. Drug Discov Today 2024; 29:103853. [PMID: 38070703 DOI: 10.1016/j.drudis.2023.103853] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Deoxyuridine-5'-triphosphate nucleotidohydrolase (dUTPase), a vital enzyme in pyrimidine metabolism, is a prime target for treating colorectal cancer. Uracil shares structural traits with DNA/RNA bases, prompting exploration by medicinal chemists for pharmacological modifications. Some existing drugs, including thymidylate synthase (TS) and dUTPase inhibitors, incorporate uracil moieties. These derivatives hinder crucial cell proliferation pathways encompassing TS, dUTPases, dihydropyrimidine dehydrogenase, and uracil-DNA glycosylase. This review compiles uracil derivatives that have served as dUTPase inhibitors across various organisms, forming a library for targeting human dUTPase. Insights into their structural requisites for human applications and comparative analyses of binding pockets are provided for analyzing the compounds against human dUTPase.
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Affiliation(s)
- Nabeel Backer
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | - Harshwardhan Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India
| | | | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151401, India.
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23
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Arima T, Sugimoto K, Taniwaki T, Maeda K, Shibata Y, Tateyama M, Karasugi T, Tokunaga T, Sueyoshi T, Hisanaga S, Masuda T, Uehara Y, Yugami M, Matsushita K, Yonemitsu R, Kawakami J, Yoshimura N, Tanimura S, Kato H, Ito N, Inoue K, Bando K, Nakamura T, Miyamoto T. Cartilage tissues regulate systemic aging via ectonucleotide pyrophosphatase/phosphodiesterase 1 in mice. J Biol Chem 2024; 300:105512. [PMID: 38042486 PMCID: PMC10777000 DOI: 10.1016/j.jbc.2023.105512] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Aging presents fundamental health concerns worldwide; however, mechanisms underlying how aging is regulated are not fully understood. Here, we show that cartilage regulates aging by controlling phosphate metabolism via ectonucleotide pyrophosphatase/phosphodiesterase 1 (Enpp1). We newly established an Enpp1 reporter mouse, in which an EGFP-luciferase sequence was knocked-in at the Enpp1 gene start codon (Enpp1/EGFP-luciferase), enabling detection of Enpp1 expression in cartilage tissues of resultant mice. We then established a cartilage-specific Enpp1 conditional knockout mouse (Enpp1 cKO) by generating Enpp1 flox mice and crossing them with cartilage-specific type 2 collagen Cre mice. Relative to WT controls, Enpp1 cKO mice exhibited phenotypes resembling human aging, such as short life span, ectopic calcifications, and osteoporosis, as well as significantly lower serum pyrophosphate levels. We also observed significant weight loss and worsening of osteoporosis in Enpp1 cKO mice under phosphate overload conditions, similar to global Enpp1-deficient mice. Aging phenotypes seen in Enpp1 cKO mice under phosphate overload conditions were rescued by a low vitamin D diet, even under high phosphate conditions. These findings suggest overall that cartilage tissue plays an important role in regulating systemic aging via Enpp1.
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Affiliation(s)
- Takahiro Arima
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuki Sugimoto
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takuya Taniwaki
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Maeda
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuto Shibata
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Makoto Tateyama
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tatsuki Karasugi
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takuya Tokunaga
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takanao Sueyoshi
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoshi Hisanaga
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tetsuro Masuda
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yusuke Uehara
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masaki Yugami
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kozo Matsushita
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryuji Yonemitsu
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Junki Kawakami
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoto Yoshimura
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shuntaro Tanimura
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hajime Kato
- Division of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan
| | - Nobuaki Ito
- Division of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Kana Bando
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Takayuki Nakamura
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
| | - Takeshi Miyamoto
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
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Wang S, Böhnert V, Joseph AJ, Sudaryo V, Skariah G, Swinderman JT, Yu FB, Subramanyam V, Wolf DM, Lyu X, Gilbert LA, van’t Veer LJ, Goodarzi H, Li L. ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway in breast cancer. Proc Natl Acad Sci U S A 2023; 120:e2313693120. [PMID: 38117852 PMCID: PMC10756298 DOI: 10.1073/pnas.2313693120] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 12/22/2023] Open
Abstract
Ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) expression correlates with poor prognosis in many cancers, and we previously discovered that ENPP1 is the dominant hydrolase of extracellular cGAMP: a cancer-cell-produced immunotransmitter that activates the anticancer stimulator of interferon genes (STING) pathway. However, ENPP1 has other catalytic activities and the molecular and cellular mechanisms contributing to its tumorigenic effects remain unclear. Here, using single-cell RNA-seq, we show that ENPP1 in both cancer and normal tissues drives primary breast tumor growth and metastasis by dampening extracellular 2'3'-cyclic-GMP-AMP (cGAMP)-STING-mediated antitumoral immunity. ENPP1 loss-of-function in both cancer cells and normal tissues slowed primary tumor growth and abolished metastasis. Selectively abolishing the cGAMP hydrolysis activity of ENPP1 phenocopied ENPP1 knockout in a STING-dependent manner, demonstrating that restoration of paracrine cGAMP-STING signaling is the dominant anti-cancer mechanism of ENPP1 inhibition. Finally, ENPP1 expression in breast tumors deterministically predicated whether patients would remain free of distant metastasis after pembrolizumab (anti-PD-1) treatment followed by surgery. Altogether, ENPP1 blockade represents a strategy to exploit cancer-produced extracellular cGAMP for controlled local activation of STING and is therefore a promising therapeutic approach against breast cancer.
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Affiliation(s)
- Songnan Wang
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
| | - Volker Böhnert
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
| | - Alby J. Joseph
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
| | - Valentino Sudaryo
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
| | - Gemini Skariah
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
| | - Jason T. Swinderman
- Arc Institute, Palo Alto, CA94304
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
| | | | - Vishvak Subramanyam
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
- Department of Biophysics & Biochemistry, University of California, San Francisco, CA94143
- Baker Computational Health Science Institute, University of California, San Francisco, CA94143
| | - Denise M. Wolf
- Department of Laboratory Medicine, University of California, San Francisco, CA94115
| | - Xuchao Lyu
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Luke A. Gilbert
- Arc Institute, Palo Alto, CA94304
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
| | - Laura J. van’t Veer
- Department of Laboratory Medicine, University of California, San Francisco, CA94115
| | - Hani Goodarzi
- Department of Urology, University of California, San Francisco, CA94143
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA94158
- Department of Biophysics & Biochemistry, University of California, San Francisco, CA94143
- Baker Computational Health Science Institute, University of California, San Francisco, CA94143
| | - Lingyin Li
- Department of Biochemistry, Stanford University, Stanford, CA94305
- ChEM-H Institute, Stanford University, Stanford, CA94305
- Arc Institute, Palo Alto, CA94304
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Port H, Hausgaard CM, He Y, Maksymowych WP, Wichuk S, Sinkeviciute D, Bay-Jensen AC, Holm Nielsen S. A novel biomarker of MMP-cleaved cartilage intermediate layer protein-1 is elevated in patients with rheumatoid arthritis, ankylosing spondylitis and osteoarthritis. Sci Rep 2023; 13:21717. [PMID: 38066013 PMCID: PMC10709337 DOI: 10.1038/s41598-023-48787-x] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Rheumatic joints have an altered cartilage turnover. Cartilage intermediate layer protein 1 (CILP-1) is secreted from articular chondrocytes and deposited into the cartilage extracellular matrix. We developed an immunoassay targeting a Matrix Metalloproteinase (MMP)-generated neo-epitope of CILP-1, named CILP-M. Human articular cartilage was cleaved with proteolytic enzymes and CILP-M levels were measured. We also quantified CILP-M in two studies from patients with rheumatoid arthritis (RA), ankylosing spondylitis (AS) and osteoarthritis (OA) and explored the monitoring and prognostic potential of CILP-M in TNF-α inhibitory treatment and modified Stoke AS Spine Score (mSASSS) progression. CILP-M was generated by MMP-1, -8 and -12. In the discovery study, CILP-M was significantly higher in patients with RA, AS and OA than healthy donors (p < 0.01, p < 0.001, p < 0.05) with an area under the curve (AUC) between the diseased groups and healthy donors > 0.95 (p < 0.001). In the validation study, patients with RA and AS had significantly higher CILP-M levels than healthy controls (p < 0.001) and AUC > 0.90 (p < 0.001). Patients with AS treated with TNF- α inhibitory treatment in the validation study had significantly lower CILP-M levels after treatment (p = 0.004). CILP-M may provide useful insights into cartilage degradation processes in rheumatic diseases.
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Affiliation(s)
- Helena Port
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
- Immunoscience, Nordic Bioscience, Herlev Hovedgade 205-207, 2730, Herlev, Denmark.
| | | | - Yi He
- Immunoscience, Nordic Bioscience, Herlev Hovedgade 205-207, 2730, Herlev, Denmark
| | | | - Stephanie Wichuk
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Dovile Sinkeviciute
- Immunoscience, Nordic Bioscience, Herlev Hovedgade 205-207, 2730, Herlev, Denmark
| | | | - Signe Holm Nielsen
- Immunoscience, Nordic Bioscience, Herlev Hovedgade 205-207, 2730, Herlev, Denmark
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Zamakhov IM, Anashkin VA, Moiseenko AV, Orlov VN, Vorobyeva NN, Sokolova OS, Baykov AA. The Structure and Nucleotide-Binding Characteristics of Regulated Cystathionine β-Synthase Domain-Containing Pyrophosphatase without One Catalytic Domain. Int J Mol Sci 2023; 24:17160. [PMID: 38138989 PMCID: PMC10742508 DOI: 10.3390/ijms242417160] [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: 10/31/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Regulatory adenine nucleotide-binding cystathionine β-synthase (CBS) domains are widespread in proteins; however, information on the mechanism of their modulating effects on protein function is scarce. The difficulty in obtaining structural data for such proteins is ascribed to their unusual flexibility and propensity to form higher-order oligomeric structures. In this study, we deleted the most movable domain from the catalytic part of a CBS domain-containing bacterial inorganic pyrophosphatase (CBS-PPase) and characterized the deletion variant both structurally and functionally. The truncated CBS-PPase was inactive but retained the homotetrameric structure of the full-size enzyme and its ability to bind a fluorescent AMP analog (inhibitor) and diadenosine tetraphosphate (activator) with the same or greater affinity. The deletion stabilized the protein structure against thermal unfolding, suggesting that the deleted domain destabilizes the structure in the full-size protein. A "linear" 3D structure with an unusual type of domain swapping predicted for the truncated CBS-PPase by Alphafold2 was confirmed by single-particle electron microscopy. The results suggest a dual role for the CBS domains in CBS-PPase regulation: they allow for enzyme tetramerization, which impedes the motion of one catalytic domain, and bind adenine nucleotides to mitigate or aggravate this effect.
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Affiliation(s)
- Ilya M. Zamakhov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
- Department of Chemistry, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Viktor A. Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Andrey V. Moiseenko
- Department of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (O.S.S.)
| | - Victor N. Orlov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Natalia N. Vorobyeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Olga S. Sokolova
- Department of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (O.S.S.)
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Alexander A. Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
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27
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Solebo O, Ling L, Nwankwo I, Zhou J, Fu TM, Ke H. Plasmodium falciparum utilizes pyrophosphate to fuel an essential proton pump in the ring stage and the transition to trophozoite stage. PLoS Pathog 2023; 19:e1011818. [PMID: 38048362 PMCID: PMC10732439 DOI: 10.1371/journal.ppat.1011818] [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: 05/25/2023] [Revised: 12/20/2023] [Accepted: 11/10/2023] [Indexed: 12/06/2023] Open
Abstract
During asexual growth and replication cycles inside red blood cells, the malaria parasite Plasmodium falciparum primarily relies on glycolysis for energy supply, as its single mitochondrion performs little or no oxidative phosphorylation. Post merozoite invasion of a host red blood cell, the ring stage lasts approximately 20 hours and was traditionally thought to be metabolically quiescent. However, recent studies have shown that the ring stage is active in several energy-costly processes, including gene transcription, protein translation, protein export, and movement inside the host cell. It has remained unclear whether a low glycolytic flux alone can meet the energy demand of the ring stage over a long period post invasion. Here, we demonstrate that the metabolic by-product pyrophosphate (PPi) is a critical energy source for the development of the ring stage and its transition to the trophozoite stage. During early phases of the asexual development, the parasite utilizes Plasmodium falciparum vacuolar pyrophosphatase 1 (PfVP1), an ancient pyrophosphate-driven proton pump, to export protons across the parasite plasma membrane. Conditional deletion of PfVP1 leads to a delayed ring stage that lasts nearly 48 hours and a complete blockage of the ring-to-trophozoite transition before the onset of parasite death. This developmental arrest can be partially rescued by an orthologous vacuolar pyrophosphatase from Arabidopsis thaliana, but not by the soluble pyrophosphatase from Saccharomyces cerevisiae, which lacks proton pumping activities. Since proton-pumping pyrophosphatases have been evolutionarily lost in human hosts, the essentiality of PfVP1 suggests its potential as an antimalarial drug target. A drug target of the ring stage is highly desired, as current antimalarials have limited efficacy against this stage.
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Affiliation(s)
- Omobukola Solebo
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Liqin Ling
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ikechukwu Nwankwo
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- The Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Hangjun Ke
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
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28
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Sanchez AM, Schwer B, Jork N, Jessen HJ, Shuman S. Activities, substrate specificity, and genetic interactions of fission yeast Siw14, a cysteinyl-phosphatase-type inositol pyrophosphatase. mBio 2023; 14:e0205623. [PMID: 37772819 PMCID: PMC10653929 DOI: 10.1128/mbio.02056-23] [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: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE The inositol pyrophosphate signaling molecule 1,5-IP8 modulates fission yeast phosphate homeostasis via its action as an agonist of RNA 3'-processing and transcription termination. Cellular 1,5-IP8 levels are determined by a balance between the activities of the inositol polyphosphate kinase Asp1 and several inositol pyrophosphatase enzymes. Here, we characterize Schizosaccharomyces pombe Siw14 (SpSiw14) as a cysteinyl-phosphatase-family pyrophosphatase enzyme capable of hydrolyzing the phosphoanhydride substrates inorganic pyrophosphate, inorganic polyphosphate, and inositol pyrophosphates 5-IP7, 1-IP7, and 1,5-IP8. Genetic analyses implicate SpSiw14 in 1,5-IP8 catabolism in vivo, insofar as: loss of SpSiw14 activity is lethal in the absence of the Nudix-type inositol pyrophosphatase enzyme Aps1; and siw14∆ aps1∆ lethality depends on synthesis of 1,5-IP8 by the Asp1 kinase. Suppression of siw14∆ aps1∆ lethality by loss-of-function mutations of 3'-processing/termination factors points to precocious transcription termination as the cause of 1,5-IP8 toxicosis.
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Affiliation(s)
- Ana M. Sanchez
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry and Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry and Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, New York, USA
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29
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Lukaszewicz M, Ferenc-Mrozek A, Kokosza J, Stefaniuk A, Stepinski J, Bojarska E, Darzynkiewicz E. Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides. Eur Biophys J 2023; 52:487-495. [PMID: 37644211 PMCID: PMC10618335 DOI: 10.1007/s00249-023-01678-5] [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] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5'RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Aleksandra Ferenc-Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Julia Kokosza
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Anna Stefaniuk
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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30
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Schroader JH, Handley MT, Reddy K. Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function. Wiley Interdiscip Rev RNA 2023; 14:e1790. [PMID: 37092460 DOI: 10.1002/wrna.1790] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Inosine triphosphate pyrophosphatase (ITPase), encoded by the ITPA gene in humans, is an important enzyme that preserves the integrity of cellular nucleotide pools by hydrolyzing the noncanonical purine nucleotides (deoxy)inosine and (deoxy)xanthosine triphosphate into monophosphates and pyrophosphate. Variants in the ITPA gene can cause partial or complete ITPase deficiency. Partial ITPase deficiency is benign but clinically relevant as it is linked to altered drug responses. Complete ITPase deficiency causes a severe multisystem disorder characterized by seizures and encephalopathy that is frequently associated with fatal infantile dilated cardiomyopathy. In the absence of ITPase activity, its substrate noncanonical nucleotides have the potential to accumulate and become aberrantly incorporated into DNA and RNA. Hence, the pathophysiology of ITPase deficiency could arise from metabolic imbalance, altered DNA or RNA regulation, or from a combination of these factors. Here, we review the known functions of ITPase and highlight recent work aimed at determining the molecular basis for ITPA-associated pathogenesis which provides evidence for RNA dysfunction. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jacob H Schroader
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Mark T Handley
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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31
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Wang S, Zhan C, Nie S, Tian D, Lu J, Wen M, Qiao J, Zhu H, Caiyin Q. Enzyme and Metabolic Engineering Strategies for Biosynthesis of α-Farnesene in Saccharomyces cerevisiae. J Agric Food Chem 2023; 71:12452-12461. [PMID: 37574876 DOI: 10.1021/acs.jafc.3c03677] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
α-Farnesene, a type of acyclic sesquiterpene, is an important raw material in agriculture, aircraft fuel, and the chemical industry. In this study, we constructed an efficient α-farnesene-producing yeast cell factory by combining enzyme and metabolic engineering strategies. First, we screened different plants for α-farnesene synthase (AFS) with the best activity and found that AFS from Camellia sinensis (CsAFS) exhibited the most efficient α-farnesene production in Saccharomyces cerevisiae 4741. Second, the metabolic flux of the mevalonate pathway was increased to improve the supply of the precursor farnesyl pyrophosphate. Third, inducing site-directed mutagenesis in CsAFS, the CsAFSW281C variant was obtained, which considerably increased α-farnesene production. Fourth, the N-terminal serine-lysine-isoleucine-lysine (SKIK) tag was introduced to construct the SKIK∼CsAFSW281C variant, which further increased α-farnesene production to 2.8 g/L in shake-flask cultures. Finally, the α-farnesene titer of 28.3 g/L in S. cerevisiae was obtained by fed-batch fermentation in a 5 L bioreactor.
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Affiliation(s)
- Shengli Wang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Chuanling Zhan
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Shengxin Nie
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Daoguang Tian
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Juane Lu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Mingzhang Wen
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing 312300, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
| | - Qinggele Caiyin
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, People's Republic of China
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32
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Pavlakis E, Neumann M, Merle N, Wieboldt R, Wanzel M, Ponath V, Pogge von Strandmann E, Elmshäuser S, Stiewe T. Mutant p53-ENTPD5 control of the calnexin/calreticulin cycle: a druggable target for inhibiting integrin-α5-driven metastasis. J Exp Clin Cancer Res 2023; 42:203. [PMID: 37563605 PMCID: PMC10413714 DOI: 10.1186/s13046-023-02785-z] [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: 04/17/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND TP53, encoding the tumor suppressor p53, is frequently mutated in various cancers, producing mutant p53 proteins (mutp53) which can exhibit neomorphic, gain-of-function properties. The latter transform p53 into an oncoprotein that promotes metastatic tumor progression via downstream effectors such as ENTPD5, an endoplasmic reticulum UDPase involved in the calnexin/calreticulin cycle of N-glycoprotein biosynthesis. Elucidating the mechanisms underlying the pro-metastatic functions of the mutp53-ENTPD5 axis is crucial for developing targeted therapies for aggressive metastatic cancer. METHODS We analyzed pancreatic, lung, and breast adenocarcinoma cells with p53 missense mutations to study the impact of mutp53 and ENTPD5 on the N-glycoproteins integrin-α5 (ITGA5) and integrin-β1 (ITGB1), which heterodimerize to form the key fibronectin receptor. We assessed the role of the mutp53-ENTPD5 axis in integrin-dependent tumor-stroma interactions and tumor cell motility using adhesion, migration, and invasion assays, identifying and validating therapeutic intervention targets. We employed an orthotopic xenograft model of pancreatic ductal adenocarcinoma to examine in vivo targeting of mutp53-ENTPD5-mediated ITGA5 regulation for cancer therapy. RESULTS Mutp53 depletion diminished ITGA5 and ITGB1 expression and impaired tumor cell adhesion, migration, and invasion, rescued by ENTPD5. The mutp53-ENTPD5 axis maintained ITGA5 expression and function via the calnexin/calreticulin cycle. Targeting this axis using ITGA5-blocking antibodies, α-glucosidase inhibitors, or pharmacological degradation of mutp53 by HSP90 inhibitors, such as Ganetespib, effectively inhibited ITGA5-mediated cancer cell motility in vitro. In the orthotopic xenograft model, Ganetespib reduced ITGA5 expression and metastasis in an ENTPD5-dependent manner. CONCLUSIONS The mutp53-ENTPD5 axis fosters ITGA5 and ITGB1 expression and tumor cell motility through the calnexin/calreticulin cycle, contributing to cancer metastasis. ITGA5-blocking antibodies or α-glucosidase inhibitors target this axis and represent potential therapeutic options worth exploring in preclinical models. The pharmacologic degradation of mutp53 by HSP90 inhibitors effectively blocks ENTPD5-ITGA5-mediated cancer cell motility and metastasis in vivo, warranting further clinical evaluation in p53-mutant cancers. This research underscores the significance of understanding the complex interplay between mutp53, ENTPD5, and the calnexin/calreticulin cycle in integrin-mediated metastatic tumor progression, offering valuable insights for the development of potential therapeutic strategies.
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Affiliation(s)
- Evangelos Pavlakis
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
| | - Michelle Neumann
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
| | - Nastasja Merle
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
| | - Ronja Wieboldt
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
| | - Michael Wanzel
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Marburg, 35043, Germany
| | - Viviane Ponath
- Institute for Tumor Immunology, Philipps-University, 35043, Marburg, Germany
| | | | - Sabrina Elmshäuser
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany.
- Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Marburg, 35043, Germany.
- Genomics Core Facility, Philipps-University, 35043, Marburg, Germany.
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany.
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33
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Burgis NE, April C, VanWormer K. Arginine-178 is an essential residue for ITPA function. Arch Biochem Biophys 2023; 744:109700. [PMID: 37506994 PMCID: PMC10530447 DOI: 10.1016/j.abb.2023.109700] [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: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023]
Abstract
The inosine triphosphate pyrophosphatase (ITPA) enzyme plays a critical cellular role by removing noncanonical nucleoside triphosphates from nucleotide pools. One of the first pathological ITPA mutants identified is R178C (rs746930990), which causes a fatal infantile encephalopathy, termed developmental and epileptic encephalopathy 35 (DEE 35). The accumulation of noncanonical nucleotides such as inosine triphosphate (ITP), is suspected to affect RNA and/or interfere with normal nucleotide function, leading to development of DEE 35. Molecular dynamics simulations have shown that the very rare R178C mutation does not significantly perturb the overall structure of the protein, but results in a high level of structural flexibility and disrupts active-site hydrogen bond networks, while preliminary biochemical data indicate that ITP hydrolyzing activity is significantly reduced for the R178C mutant. Here we report Michaelis-Menten enzyme kinetics data for the R178C ITPA mutant and three other position 178 ITPA mutants. These data confirm that position 178 is essential for ITPA activity and even conservative mutation at this site (R178K) results in significantly reduced enzyme activity. Our data support that disruption of the active-site hydrogen bond network is a major cause of diminished ITP hydrolyzing activity for the R178C mutation. These results suggest an avenue for developing therapies to address DEE 35.
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Affiliation(s)
- Nicholas E Burgis
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA.
| | - Caitlin April
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA
| | - Kandise VanWormer
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA
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34
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Gómez-Rubio E, Garcia-Marin J. Molecular dynamics simulations reveal the impact of NUDT15 R139C and R139H variants in structural conformation and dynamics. J Biomol Struct Dyn 2023; 41:14812-14821. [PMID: 36907600 DOI: 10.1080/07391102.2023.2187626] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/22/2023] [Indexed: 03/14/2023]
Abstract
NUDT15, also known as MTH2, is a member of the NUDIX protein family that catalyzes the hydrolysis of nucleotides and deoxynucleotides, as well as thioguanine analogues. NUDT15 has been reported as a DNA sanitizer in humans, and more recent studies have shown that some genetic variants are related to a poor prognosis in neoplastic and immunologic diseases treated with thioguanine drugs. Despite this, the role of NUDT15 in physiology and molecular biology is quite unclear, as is the mechanism of action of this enzyme. The existence of clinically relevant variants has prompted the study of these enzymes, whose capacity to bind and hydrolyze thioguanine nucleotides is still poorly understood. By using a combination of biomolecular modeling techniques and molecular dynamics, we have studied the monomeric wild type NUDT15 as well as two important variants, R139C and R139H. Our findings reveal not only how nucleotide binding stabilizes the enzyme but also how two loops are responsible for keeping the enzyme in a packed, close conformation. Mutations in α2 helix affect a network of hydrophobic and π-interactions that enclose the active site. This knowledge contributes to the understanding of NUDT15 structural dynamics and will be valuable for the design of new chemical probes and drugs targeting this protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elena Gómez-Rubio
- Departamento de Biología Estructural y Química, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Javier Garcia-Marin
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá (IRYCIS), Madrid, Spain
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35
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Zhang N, Zhao L, He M, Luo P, Tan L. Assay of inorganic pyrophosphatase activity based on a fluorescence "turn-off" strategy using carbon quantum dots@Cu-MOF nanotubes. Spectrochim Acta A Mol Biomol Spectrosc 2023; 284:121771. [PMID: 36027790 DOI: 10.1016/j.saa.2022.121771] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
A highly sensitive and selective sensor for the quantitative assay of inorganic pyrophosphatase (PPase) activity was developed based on a fluorescence "turn-off" strategy. Carbon quantum dots@Cu(II)-based metal-organic framework nanotubes (CQDs@Cu-MOF) with length less than 300 nm and width less than 20 nm were synthesized. CQDs in the nanotubes exhibited weak fluorescence owing to static quenching. The coordination reaction between pyrophosphate ion (PPi) and Cu(II) decomposed CQDs@Cu-MOF and led to the release of CQDs, of which the fluorescence recovered. In the presence of PPase, the hydrolysis of PPi generated phosphate ion (Pi). CQDs@Cu-MOF remained their structural stability and the fluorescence turned off. The fluorescence intensity difference of the mixture of CQDs@Cu-MOF and PPi in the absence and presence of PPase (-ΔF) was proportional to the PPase concentration from 0.1 to 5 mU mL-1 and that from 5 to 50 mU mL-1, and a limit of detection at 0.03 mU mL-1 was obtained. PPase activity in human serum was analyzed using the proposed fluorescence sensor and the recovery values were found to vary from 95.0% to 104 %.
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Affiliation(s)
- Ningning Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Lixin Zhao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Mengting He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Peng Luo
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Liang Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China.
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36
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Benjamin B, Goldgur Y, Jork N, Jessen HJ, Schwer B, Shuman S. Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States. mBio 2022; 13:e0308722. [PMID: 36468882 PMCID: PMC9765450 DOI: 10.1128/mbio.03087-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Expression of the fission yeast Schizosaccharomyces pombe phosphate regulon is sensitive to the intracellular level of the inositol pyrophosphate signaling molecule 1,5-IP8. IP8 dynamics are determined by Asp1, a bifunctional enzyme consisting of an N-terminal kinase domain and a C-terminal pyrophosphatase domain that catalyze IP8 synthesis and catabolism, respectively. Here, we report structures of the Asp1 kinase domain, crystallized with two protomers in the asymmetric unit, one of which was complexed with ligands (ADPNP, ADP, or ATP; Mg2+ or Mn2+; IP6, 5-IP7, or 1,5-IP8) and the other which was ligand-free. The ligand-free enzyme adopts an "open" conformation that allows ingress of substrates and egress of products. ADPNP, ADP, and ATP and associated metal ions occupy a deep phospho-donor pocket in the active site. IP6 or 5-IP7 engagement above the nucleotide favors adoption of a "closed" conformation, in which surface protein segments undergo movement and a disordered-to-ordered transition to form an inositol polyphosphate-binding site. In a structure mimetic of the kinase Michaelis complex, the anionic 5-IP7 phosphates are encaged by an ensemble of nine cationic amino acids: Lys43, Arg223, Lys224, Lys260, Arg274, Arg285, Lys290, Arg293, and Lys341. Alanine mutagenesis of amino acids that contact the adenosine nucleoside of the ATP donor underscored the contributions of Asp258 interaction with the ribose 3'-OH and of Glu248 with adenine-N6. Changing Glu248 to Gln elicited a gain of function whereby the kinase became adept at using GTP as phosphate donor. Wild-type Asp1 kinase can utilize N6-benzyl-ATP as phosphate donor. IMPORTANCE The inositol pyrophosphate signaling molecule 1,5-IP8 modulates fission yeast phosphate homeostasis via its action as an agonist of RNA 3'-processing and transcription termination. Cellular IP8 levels are determined by Asp1, a bifunctional enzyme composed of an N-terminal kinase and a C-terminal pyrophosphatase domain. Here, we present a series of crystal structures of the Asp1 kinase domain, in a ligand-free state and in complexes with nucleotides ADPNP, ADP, and ATP, divalent cations magnesium and manganese, and inositol polyphosphates IP6, 5-IP7, and 1,5-IP8. Substrate binding elicits a switch from open to closed conformations, entailing a disordered-to-ordered transition and a rearrangement or movement of two peptide segments that form a binding site for the phospho-acceptor. Our structures, along with structure-guided mutagenesis, fortify understanding of the mechanism and substrate specificity of Asp1 kinase, and they extend and complement structural and functional studies of the orthologous human kinase PPIP5K2.
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Affiliation(s)
- Bradley Benjamin
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Yehuda Goldgur
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikolaus Jork
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, Freiburg, Germany
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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37
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Li Y, Yang X, Gao R. Thermophilic Inorganic Pyrophosphatase Ton1914 from Thermococcus onnurineus NA1 Removes the Inhibitory Effect of Pyrophosphate. Int J Mol Sci 2022; 23:ijms232112735. [PMID: 36361526 PMCID: PMC9653972 DOI: 10.3390/ijms232112735] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 01/25/2023] Open
Abstract
Pyrophosphate (PPi) is a byproduct of over 120 biosynthetic reactions, and an overabundance of PPi can inhibit industrial synthesis. Pyrophosphatases (PPases) can effectively hydrolyze pyrophosphate to remove the inhibitory effect of pyrophosphate. In the present work, a thermophilic alkaline inorganic pyrophosphatase from Thermococcus onnurineus NA1 was studied. The optimum pH and temperature of Ton1914 were 9.0 and 80 °C, respectively, and the half-life was 52 h at 70 °C and 2.5 h at 90 °C. Ton1914 showed excellent thermal stability, and its relative enzyme activity, when incubated in Tris-HCl 9.0 containing 1.6 mM Mg2+ at 90 °C for 5 h, was still 100%, which was much higher than the control, whose relative activity was only 37%. Real-time quantitative PCR (qPCR) results showed that the promotion of Ton1914 on long-chain DNA was more efficient than that on short-chain DNA when the same concentration of templates was supplemented. The yield of long-chain products was increased by 32-41%, while that of short-chain DNA was only improved by 9.5-15%. Ton1914 also increased the yields of UDP-glucose and UDP-galactose enzymatic synthesis from 40.1% to 84.8% and 20.9% to 35.4%, respectively. These findings suggested that Ton1914 has considerable potential for industrial applications.
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Affiliation(s)
| | | | - Renjun Gao
- Correspondence: ; Tel.: +86-186-0431-3058
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38
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Holmes AOM, Goldman A, Kalli AC. mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations. PLoS Comput Biol 2022; 18:e1010578. [PMID: 36191052 PMCID: PMC9560603 DOI: 10.1371/journal.pcbi.1010578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/08/2022] [Revised: 10/13/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022] Open
Abstract
Membrane-integral pyrophosphatases (mPPases) are membrane-bound enzymes responsible for hydrolysing inorganic pyrophosphate and translocating a cation across the membrane. Their function is essential for the infectivity of clinically relevant protozoan parasites and plant maturation. Recent developments have indicated that their mechanism is more complicated than previously thought and that the membrane environment may be important for their function. In this work, we use multiscale molecular dynamics simulations to demonstrate for the first time that mPPases form specific anionic lipid interactions at 4 sites at the distal and interfacial regions of the protein. These interactions are conserved in simulations of the mPPases from Thermotoga maritima, Vigna radiata and Clostridium leptum and characterised by interactions with positive residues on helices 1, 2, 3 and 4 for the distal site, or 9, 10, 13 and 14 for the interfacial site. Due to the importance of these helices in protein stability and function, these lipid interactions may play a crucial role in the mPPase mechanism and enable future structural and functional studies.
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Affiliation(s)
- Alexandra O. M. Holmes
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Goldman
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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39
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Niehaus M, Straube H, Specht A, Baccolini C, Witte CP, Herde M. The nucleotide metabolome of germinating Arabidopsis thaliana seeds reveals a central role for thymidine phosphorylation in chloroplast development. Plant Cell 2022; 34:3790-3813. [PMID: 35861422 PMCID: PMC9516053 DOI: 10.1093/plcell/koac207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/13/2022] [Indexed: 05/29/2023]
Abstract
Thymidylates are generated by several partially overlapping metabolic pathways in different subcellular locations. This interconnectedness complicates an understanding of how thymidylates are formed in vivo. Analyzing a comprehensive collection of mutants and double mutants on the phenotypic and metabolic level, we report the effect of de novo thymidylate synthesis, salvage of thymidine, and conversion of cytidylates to thymidylates on thymidylate homeostasis during seed germination and seedling establishment in Arabidopsis (Arabidopsis thaliana). During germination, the salvage of thymidine in organelles contributes predominantly to the thymidylate pools and a mutant lacking organellar (mitochondrial and plastidic) thymidine kinase has severely altered deoxyribonucleotide levels, less chloroplast DNA, and chlorotic cotyledons. This phenotype is aggravated when mitochondrial thymidylate de novo synthesis is additionally compromised. We also discovered an organellar deoxyuridine-triphosphate pyrophosphatase and show that its main function is not thymidylate synthesis but probably the removal of noncanonical nucleotide triphosphates. Interestingly, cytosolic thymidylate synthesis can only compensate defective organellar thymidine salvage in seedlings but not during germination. This study provides a comprehensive insight into the nucleotide metabolome of germinating seeds and demonstrates the unique role of enzymes that seem redundant at first glance.
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Affiliation(s)
- Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - André Specht
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | | | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
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40
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Zimmerman K, Li X, von Kroge S, Stabach P, Lester ER, Chu EY, Srivastava S, Somerman MJ, Tommasini SM, Busse B, Schinke T, Carpenter TO, Oheim R, Braddock DT. Catalysis-Independent ENPP1 Protein Signaling Regulates Mammalian Bone Mass. J Bone Miner Res 2022; 37:1733-1749. [PMID: 35773783 PMCID: PMC9709593 DOI: 10.1002/jbmr.4640] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022]
Abstract
Biallelic ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) deficiency induces vascular/soft tissue calcifications in generalized arterial calcification of infancy (GACI), and low bone mass with phosphate-wasting rickets in GACI survivors (autosomal hypophosphatemic rickets type-2). ENPP1 haploinsufficiency induces early-onset osteoporosis and mild phosphate wasting in adults. Both conditions demonstrate the unusual combination of reduced accrual of skeletal mineral, yet excess and progressive heterotopic mineralization. ENPP1 is the only enzyme that generates extracellular pyrophosphate (PPi), a potent inhibitor of both bone and heterotopic mineralization. Life-threatening vascular calcification in ENPP1 deficiency is due to decreased plasma PPi; however, the mechanism by which osteopenia results is not apparent from an understanding of the enzyme's catalytic activity. To probe for catalysis-independent ENPP1 pathways regulating bone, we developed a murine model uncoupling ENPP1 protein signaling from ENPP1 catalysis, Enpp1T238A mice. In contrast to Enpp1asj mice, which lack ENPP1, Enpp1T238A mice have normal trabecular bone microarchitecture and favorable biomechanical properties. However, both models demonstrate low plasma Pi and PPi, increased fibroblast growth factor 23 (FGF23), and by 23 weeks, osteomalacia demonstrating equivalent phosphate wasting in both models. Reflecting findings in whole bone, calvarial cell cultures from Enpp1asj mice demonstrated markedly decreased calcification, elevated transcription of Sfrp1, and decreased nuclear β-catenin signaling compared to wild-type (WT) and Enpp1T238A cultures. Finally, the decreased calcification and nuclear β-catenin signaling observed in Enpp1asj cultures was restored to WT levels by knockout of Sfrp1. Collectively, our findings demonstrate that catalysis-independent ENPP1 signaling pathways regulate bone mass via the expression of soluble Wnt inhibitors such as secreted frizzled-related protein 1 (SFRP1), whereas catalysis dependent pathways regulate phosphate homeostasis through the regulation of plasma FGF23. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Kristin Zimmerman
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut, 06510
| | - Xiaochen Li
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut, 06510
| | - Simon von Kroge
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany
| | - Paul Stabach
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut, 06510
| | - Ethan R. Lester
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut, 06510
| | - Emily Y. Chu
- National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of General Dentistry, Operative Division, University of Maryland School of Dentistry, Baltimore, Maryland, 21202
| | - Shivani Srivastava
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut, 06510
| | - Martha J. Somerman
- National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Steven M. Tommasini
- Department of Orthopædics and Rehabilitation, Yale University School of Medicine, New Haven Connecticut, 06510
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany
| | - Thomas O. Carpenter
- Department of Pediatrics at Yale University School of Medicine, New Haven Connecticut, 06510
| | - Ralf Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany
| | - Demetrios T. Braddock
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut, 06510
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41
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Luo X, Yan S, Jin L, Zhu H, Zhang X, Ge W. Inosine Triphosphate Pyrophosphatase and NUDT15 are Good Predictors of Clinical Outcomes in Thiopurine-Treated Chinese Patients with Inflammatory Bowel Disease. Ther Drug Monit 2022; 44:391-395. [PMID: 35067667 DOI: 10.1097/ftd.0000000000000965] [Citation(s) in RCA: 2] [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: 07/06/2021] [Accepted: 09/07/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Although the relationship between NUDT15 and thiopurine-induced leukopenia has been proven in previous studies, no prominent factors explaining interindividual variations in its active metabolite, 6-thioguanine nucleotide (6-TGN), and clinical efficacy have been identified. In this study, the correlation between genotypes (thiopurine S-methyltransferase, NUDT15, and ITPA polymorphisms), 6-TGN concentrations, and clinical outcomes (efficacy and side effects) in patients with inflammatory bowel disease were investigated. METHODS In total, 160 patients with inflammatory bowel disease were included, and the 3 genotyped genes and 6-TGN levels were measured by high-performance liquid chromatography. Statistical analyses and calculations were performed to determine their relationships. RESULTS ITPA genotypes and 6-TGN concentration were both associated with the clinical effectiveness of azathioprine (P = 0.036 and P = 4.6 × 10-7), with a significant correlation also detected between them (P = 0.042). Patients with ITPA variant alleles exhibited higher 6-TGN levels than those with the wild-type allele. In addition, the relationship between NUDT15 and leukopenia and neutropenia was confirmed (P = 1.79 × 10-7 and 0.002). CONCLUSIONS In summary, it is recommended that both ITPA and NUDT15 genotyping should be performed before azathioprine initiation. Moreover, the 6-TGN concentration should be routinely monitored during the later period of treatment.
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Affiliation(s)
- Xuemei Luo
- Department of Medication, The Affiliated Drum Tower Hospital of Nanjing University Medical School; and
- Nanjing Medical Center for Clinical Pharmacy, and
| | - Simin Yan
- Department of Medication, The Affiliated Drum Tower Hospital of Nanjing University Medical School; and
- Nanjing Medical Center for Clinical Pharmacy, and
| | - Lu Jin
- Department of Medication, The Affiliated Drum Tower Hospital of Nanjing University Medical School; and
- Nanjing Medical Center for Clinical Pharmacy, and
| | - Huaijun Zhu
- Department of Medication, The Affiliated Drum Tower Hospital of Nanjing University Medical School; and
- Nanjing Medical Center for Clinical Pharmacy, and
| | - Xiaoqi Zhang
- Department of Medication, The Affiliated Drum Tower Hospital of Nanjing University Medical School; and
- Nanjing Medical Center for Clinical Pharmacy, and
| | - Weihong Ge
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
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Görigk S, Ouwens DM, Kuhn T, Altenhofen D, Binsch C, Damen M, Khuong JMA, Kaiser K, Knebel B, Vogel H, Schürmann A, Chadt A, Al-Hasani H. Nudix hydrolase NUDT19 regulates mitochondrial function and ATP production in murine hepatocytes. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159153. [PMID: 35367353 DOI: 10.1016/j.bbalip.2022.159153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/24/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023]
Abstract
Changes in intracellular CoA levels are known to contribute to the development of non-alcoholic fatty liver disease (NAFLD) in type 2 diabetes (T2D) in human and rodents. However, the underlying genetic basis is still poorly understood. Due to their diverse susceptibility towards metabolic diseases, mouse inbred strains have been proven to serve as powerful tools for the identification of novel genetic factors that underlie the pathophysiology of NAFLD and diabetes. Transcriptome analysis of mouse liver samples revealed the nucleoside diphosphate linked moiety X-type motif Nudt19 as novel candidate gene responsible for NAFLD and T2D development. Knockdown (KD) of Nudt19 increased mitochondrial and glycolytic ATP production rates in Hepa 1-6 cells by 41% and 10%, respectively. The enforced utilization of glutamine or fatty acids as energy substrate reduced uncoupled respiration by 41% and 47%, respectively, in non-target (NT) siRNA transfected cells. This reduction was prevented upon Nudt19 KD. Furthermore, incubation with palmitate or oleate respectively increased mitochondrial ATP production by 31% and 20%, and uncoupled respiration by 23% and 30% in Nudt19 KD cells, but not in NT cells. The enhanced fatty acid oxidation in Nudt19 KD cells was accompanied by a 1.3-fold increased abundance of Pdk4. This study is the first to describe Nudt19 as regulator of hepatic lipid metabolism and potential mediator of NAFLD and T2D development.
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Affiliation(s)
- Sarah Görigk
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany
| | - D Margriet Ouwens
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany; Department of Endocrinology, Ghent University Hospital, Ghent, Belgium
| | - Tanja Kuhn
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany
| | - Delsi Altenhofen
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany
| | - Christian Binsch
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - Mareike Damen
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
| | - Jenny Minh-An Khuong
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany
| | - Katharina Kaiser
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany
| | - Birgit Knebel
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany
| | - Heike Vogel
- German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany; Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, D-14558 Nuthetal, Germany; Research Group Genetics of Obesity, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), 14558 Nuthetal, Germany; Research Group Molecular and Clinical Life Science of Metabolic Diseases, Faculty of Health Sciences Brandenburg, University of Potsdam, Brandenburg, Germany
| | - Annette Schürmann
- German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany; Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, D-14558 Nuthetal, Germany
| | - Alexandra Chadt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany; Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
| | - Hadi Al-Hasani
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany; German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany; Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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Carozza JA, Cordova AF, Brown JA, AlSaif Y, Böhnert V, Cao X, Mardjuki RE, Skariah G, Fernandez D, Li L. ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling. Proc Natl Acad Sci U S A 2022; 119:e2119189119. [PMID: 35588451 PMCID: PMC9173814 DOI: 10.1073/pnas.2119189119] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/01/2022] [Indexed: 11/18/2022] Open
Abstract
The metazoan innate immune second messenger 2′3′-cGAMP is present both inside and outside cells. However, only extracellular cGAMP can be negatively regulated by the extracellular hydrolase ENPP1. Here, we determine whether ENPP1’s regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating stimulator of interferon genes (STING) signaling. We identified ENPP1H362A, a point mutation that cannot degrade the 2′-5′ linkage in cGAMP while maintaining otherwise normal function. The selectivity of this histidine is conserved down to bacterial nucleotide pyrophosphatase/phosphodiesterase (NPP), allowing structural analysis and suggesting an unexplored ancient history of 2′-5′ cyclic dinucleotides. Enpp1H362A mice demonstrated that extracellular cGAMP is not responsible for the devastating phenotype in ENPP1-null humans and mice but is responsible for antiviral immunity and systemic inflammation. Our data define extracellular cGAMP as a pivotal STING activator, identify an evolutionarily critical role for ENPP1 in regulating inflammation, and suggest a therapeutic strategy for viral and inflammatory conditions by manipulating ENPP1 activity.
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Affiliation(s)
- Jacqueline A. Carozza
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Chemistry, Stanford University, Stanford, CA 94301
| | - Anthony F. Cordova
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Cancer Biology Program, Stanford University, Stanford, CA 94301
| | - Jenifer A. Brown
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Biophysics, Stanford University, Stanford, CA 94301
| | - Yasmeen AlSaif
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Biology, Stanford University, Stanford, CA 94301
| | - Volker Böhnert
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Biochemistry, Stanford University, Stanford, CA 94301
| | - Xujun Cao
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Chemistry, Stanford University, Stanford, CA 94301
| | - Rachel E. Mardjuki
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Chemistry, Stanford University, Stanford, CA 94301
| | - Gemini Skariah
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Biochemistry, Stanford University, Stanford, CA 94301
| | - Daniel Fernandez
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Biochemistry, Stanford University, Stanford, CA 94301
- Macromolecular Structural Knowledge Center, Stanford University, Stanford, CA 94301
| | - Lingyin Li
- ChEM-H Institute, Stanford University, Stanford, CA 94301
- Department of Biochemistry, Stanford University, Stanford, CA 94301
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Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A 2022; 119:e2203118119. [PMID: 35594391 PMCID: PMC9173781 DOI: 10.1073/pnas.2203118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/21/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto, 862-8678, Japan
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Ralph D, Nitschke Y, Levine MA, Caffet M, Wurst T, Saeidian AH, Youssefian L, Vahidnezhad H, Terry SF, Rutsch F, Uitto J, Li Q. ENPP1 variants in patients with GACI and PXE expand the clinical and genetic heterogeneity of heritable disorders of ectopic calcification. PLoS Genet 2022; 18:e1010192. [PMID: 35482848 PMCID: PMC9089899 DOI: 10.1371/journal.pgen.1010192] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 11/26/2021] [Revised: 05/10/2022] [Accepted: 04/05/2022] [Indexed: 12/17/2022] Open
Abstract
Pseudoxanthoma elasticum (PXE) and generalized arterial calcification of infancy (GACI) are clinically distinct genetic entities of ectopic calcification associated with differentially reduced circulating levels of inorganic pyrophosphate (PPi), a potent endogenous inhibitor of calcification. Variants in ENPP1, the gene mutated in GACI, have not been associated with classic PXE. Here we report the clinical, laboratory, and molecular evaluations of ten GACI and two PXE patients from five and two unrelated families registered in GACI Global and PXE International databases, respectively. All patients were found to carry biallelic variants in ENPP1. Among ten ENPP1 variants, one homozygous variant demonstrated uniparental disomy inheritance. Functional assessment of five previously unreported ENPP1 variants suggested pathogenicity. The two PXE patients, currently 57 and 27 years of age, had diagnostic features of PXE and had not manifested the GACI phenotype. The similarly reduced PPi plasma concentrations in the PXE and GACI patients in our study correlate poorly with their disease severity. This study demonstrates that in addition to GACI, ENPP1 variants can cause classic PXE, expanding the clinical and genetic heterogeneity of heritable ectopic calcification disorders. Furthermore, the results challenge the current prevailing concept that plasma PPi is the only factor governing the severity of ectopic calcification. Biallelic inactivating mutations in the ENPP1 gene cause generalized arterial calcification of infancy (GACI), a frequently fatal disease characterized by infantile onset of widespread arterial calcification and/or narrowing of large and medium-sized vessels often resulting in the early demise of affected individuals. Significantly reduced, almost zero plasma levels of a potent and endogenous calcification inhibitor, inorganic pyrophosphate (PPi), is thought to be the underlying cause of vascular calcification in GACI. Mutations in ENPP1 have not been found in patients with pseudoxanthoma elasticum (PXE), another genetic multisystem ectopic calcification disorder caused by mutations in the ABCC6 gene. This study reports that ENPP1 mutations can also cause PXE with more favorable clinical outcomes. In addition, it was previously thought that plasma PPi levels correlate with vascular calcification severity. However, we here show that vascular calcification severity does not correlate with plasma PPi levels. The results suggest that in addition to PPi, the long-believed determinant of ectopic calcification, additional mechanisms may be at play in regulating ectopic calcification.
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Affiliation(s)
- Douglas Ralph
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Genetics, Genomics and Cancer Biology Ph.D. Program, Jefferson College of Life Sciences, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- PXE International Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | | | - Michael A. Levine
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Matthew Caffet
- PXE International, Inc., Damascus, Maryland, United States of America
| | - Tamara Wurst
- PXE International, Inc., Damascus, Maryland, United States of America
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Genetics, Genomics and Cancer Biology Ph.D. Program, Jefferson College of Life Sciences, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Sharon F. Terry
- PXE International, Inc., Damascus, Maryland, United States of America
| | - Frank Rutsch
- Münster University Children’s Hospital, Münster, Germany
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- PXE International Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Qiaoli Li
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- PXE International Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Chang CC, Lee KL, Chan TS, Chung CC, Liang YC. Histone Deacetylase Inhibitors Downregulate Calcium Pyrophosphate Crystal Formation in Human Articular Chondrocytes. Int J Mol Sci 2022; 23:ijms23052604. [PMID: 35269745 PMCID: PMC8910507 DOI: 10.3390/ijms23052604] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Calcium pyrophosphate (CPP) deposition disease (CPPD) is a form of CPP crystal-induced arthritis. A high concentration of extracellular pyrophosphate (ePPi) in synovial fluid is positively correlated with the formation of CPP crystals, and ePPi can be upregulated by ankylosis human (ANKH) and ectonucleotide pyrophosphatase 1 (ENPP1) and downregulated by tissue non-specific alkaline phosphatase (TNAP). However, there is currently no drug that eliminates CPP crystals. We explored the effects of the histone deacetylase (HDAC) inhibitors (HDACis) trichostatin A (TSA) and vorinostat (SAHA) on CPP formation. Transforming growth factor (TGF)-β1-treated human primary cultured articular chondrocytes (HC-a cells) were used to increase ePPi and CPP formation, which were determined by pyrophosphate assay and CPP crystal staining assay, respectively. Artificial substrates thymidine 5′-monophosphate p-nitrophenyl ester (p-NpTMP) and p-nitrophenyl phosphate (p-NPP) were used to estimate ENPP1 and TNAP activities, respectively. The HDACis TSA and SAHA significantly reduced mRNA and protein expressions of ANKH and ENPP1 but increased TNAP expression in a dose-dependent manner in HC-a cells. Further results demonstrated that TSA and SAHA decreased ENPP1 activity, increased TNAP activity, and limited levels of ePPi and CPP. As expected, both TSA and SAHA significantly increased the acetylation of histones 3 and 4 but failed to block Smad-2 phosphorylation induced by TGF-β1. These results suggest that HDACis prevented the formation of CPP by regulating ANKH, ENPP1, and TNAP expressions and can possibly be developed as a potential drug to treat or prevent CPPD.
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Affiliation(s)
- Chi-Ching Chang
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Kun-Lin Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (K.-L.L.); (C.-C.C.)
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Tze-Sian Chan
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Gastroenterology, Department of Internal Medicine, Wan Fang Hospital, Taipei 11696, Taiwan
| | - Chia-Chen Chung
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (K.-L.L.); (C.-C.C.)
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Chih Liang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (K.-L.L.); (C.-C.C.)
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Correspondence:
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Zamzami MA. Inosine Triphosphate Pyrophosphatase (ITPase): Functions, Mutations, Polymorphisms and Its Impact on Cancer Therapies. Cells 2022; 11:384. [PMID: 35159194 PMCID: PMC8833965 DOI: 10.3390/cells11030384] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Inosine triphosphate pyrophosphatase (ITPase) is an enzyme encoded by the ITPA gene and functions to prevent the incorporation of noncanonical purine nucleotides into DNA and RNA. Specifically, the ITPase catalyzed the hydrolysis of (deoxy) nucleoside triphosphates ((d) NTPs) into the corresponding nucleoside monophosphate with the concomitant release of pyrophosphate. Recently, thiopurine drug metabolites such as azathioprine have been included in the lists of ITPase substrates. Interestingly, inosine or xanthosine triphosphate (ITP/XTP) and their deoxy analogs, deoxy inosine or xanthosine triphosphate (dITP/dXTP), are products of important biological reactions such as deamination that take place within the cellular compartments. However, the incorporation of ITP/XTP, dITP/dXTP, or the genetic deficiency or polymorphism of the ITPA gene have been implicated in many human diseases, including infantile epileptic encephalopathy, early onset of tuberculosis, and the responsiveness of patients to cancer therapy. This review provides an up-to-date report on the ITPase enzyme, including information regarding its discovery, analysis, and cellular localization, its implication in human diseases including cancer, and its therapeutic potential, amongst others.
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Affiliation(s)
- Mazin A. Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Hoyle DJ, Dranow DB, Schilling TF. Pthlha and mechanical force control early patterning of growth zones in the zebrafish craniofacial skeleton. Development 2022; 149:dev199826. [PMID: 34919126 PMCID: PMC8917414 DOI: 10.1242/dev.199826] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022]
Abstract
Secreted signals in patterning systems often induce repressive signals that shape their distributions in space and time. In developing growth plates (GPs) of endochondral long bones, Parathyroid hormone-like hormone (Pthlh) inhibits Indian hedgehog (Ihh) to form a negative-feedback loop that controls GP progression and bone size. Whether similar systems operate in other bones and how they arise during embryogenesis remain unclear. We show that Pthlha expression in the zebrafish craniofacial skeleton precedes chondrocyte differentiation and restricts where cells undergo hypertrophy, thereby initiating a future GP. Loss of Pthlha leads to an expansion of cells expressing a novel early marker of the hypertrophic zone (HZ), entpd5a, and later HZ markers, such as ihha, whereas local Pthlha misexpression induces ectopic entpd5a expression. Formation of this early pre-HZ correlates with onset of muscle contraction and requires mechanical force; paralysis leads to loss of entpd5a and ihha expression in the pre-HZ, mislocalized pthlha expression and no subsequent ossification. These results suggest that local Pthlh sources combined with force determine HZ locations, establishing the negative-feedback loop that later maintains GPs.
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Affiliation(s)
| | | | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92693, USA
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Bernhard E, Nitschke Y, Khursigara G, Sabbagh Y, Wang Y, Rutsch F. A Reference Range for Plasma Levels of Inorganic Pyrophosphate in Children Using the ATP Sulfurylase Method. J Clin Endocrinol Metab 2022; 107:109-118. [PMID: 34498693 PMCID: PMC8684482 DOI: 10.1210/clinem/dgab615] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Indexed: 11/19/2022]
Abstract
PURPOSE Generalized arterial calcification of infancy, pseudoxanthoma elasticum, autosomal recessive hypophosphatemic rickets type 2, and hypophosphatasia are rare inherited disorders associated with altered plasma levels of inorganic pyrophosphate (PPi). In this study, we aimed to establish a reference range for plasma PPi in the pediatric population, which would be essential to support its use as a biomarker in children with mineralization disorders. METHODS Plasma samples were collected from 200 children aged 1 day to 18 years who underwent blood testing for medical conditions not affecting plasma PPi levels. PPi was measured in proband plasma utilizing a validated adenosine triphosphate (ATP) sulfurylase method. RESULTS The analytical sensitivity of the ATP sulfurylase assay consisted of 0.15 to 10 µM PPi. Inter- and intra-assay coefficients of variability on identical samples were below 10%. The standard range of PPi in the blood plasma of children and adolescents aged 0 to 18 years was calculated as 2.36 to 4.44 µM, with a median of 3.17 µM, with no difference between male and female probands. PPi plasma levels did not differ significantly in different pediatric age groups. MAIN CONCLUSIONS Our results yielded no noteworthy discrepancy to the reported standard range of plasma PPi in adults (2-5 µM). We propose the described ATP sulfurylase method as a diagnostic tool to measure PPi levels in plasma as a biomarker in the pediatric population.
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Affiliation(s)
- Eva Bernhard
- Department of General Pediatrics, Muenster University Children’s Hospital, Muenster, Germany
| | - Yvonne Nitschke
- Department of General Pediatrics, Muenster University Children’s Hospital, Muenster, Germany
| | | | | | - Yongbao Wang
- National Jewish Health Advanced Diagnostic Laboratories, Denver, CO, USA
| | - Frank Rutsch
- Department of General Pediatrics, Muenster University Children’s Hospital, Muenster, Germany
- Correspondence: Frank Rutsch, MD, Department of General Pediatrics, Muenster University Children’s Hospital, Albert-Schweitzer-Campus 1, Gebäude A1, D-48149 Muenster, Germany.
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50
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Johansson NG, Dreano L, Vidilaseris K, Khattab A, Liu J, Lasbleiz A, Ribeiro O, Kiriazis A, Boije af Gennäs G, Meri S, Goldman A, Yli‐Kauhaluoma J, Xhaard H. Exploration of Pyrazolo[1,5-a]pyrimidines as Membrane-Bound Pyrophosphatase Inhibitors. ChemMedChem 2021; 16:3360-3367. [PMID: 34459148 PMCID: PMC8597055 DOI: 10.1002/cmdc.202100392] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Inhibition of membrane-bound pyrophosphatase (mPPase) with small molecules offer a new approach in the fight against pathogenic protozoan parasites. mPPases are absent in humans, but essential for many protists as they couple pyrophosphate hydrolysis to the active transport of protons or sodium ions across acidocalcisomal membranes. So far, only few nonphosphorus inhibitors have been reported. Here, we explore the chemical space around previous hits using a combination of screening and synthetic medicinal chemistry, identifying compounds with low micromolar inhibitory activities in the Thermotoga maritima mPPase test system. We furthermore provide early structure-activity relationships around a new scaffold having a pyrazolo[1,5-a]pyrimidine core. The most promising pyrazolo[1,5-a]pyrimidine congener was further investigated and found to inhibit Plasmodium falciparum mPPase in membranes as well as the growth of P. falciparum in an ex vivo survival assay.
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Affiliation(s)
- Niklas G. Johansson
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Loïc Dreano
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Keni Vidilaseris
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
| | - Ayman Khattab
- Malaria Research Laboratory, Translational Immunology Research Program, Department of Bacteriology and Immunology, Haartman InstituteUniversity of HelsinkiP.O. Box 21 (Haartmaninkatu 3)00014HelsinkiFinland
| | - Jianing Liu
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
| | - Arthur Lasbleiz
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Orquidea Ribeiro
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
| | - Alexandros Kiriazis
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Gustav Boije af Gennäs
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Seppo Meri
- Malaria Research Laboratory, Translational Immunology Research Program, Department of Bacteriology and Immunology, Haartman InstituteUniversity of HelsinkiP.O. Box 21 (Haartmaninkatu 3)00014HelsinkiFinland
| | - Adrian Goldman
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
- School of Biomedical Sciences and Astbury Centre for Structural Molecular BiologyUniversity of Leeds, Clarendon WayLeeds LS2 9JTUK
| | - Jari Yli‐Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
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