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Scully TW, Jiao W, Mittelstädt G, Parker EJ. Structure, mechanism and inhibition of anthranilate phosphoribosyltransferase. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220039. [PMID: 36633281 PMCID: PMC9835598 DOI: 10.1098/rstb.2022.0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Anthranilate phosphoribosyltransferase catalyses the second reaction in the biosynthesis of tryptophan from chorismate in microorganisms and plants. The enzyme is homodimeric with the active site located in the hinge region between two domains. A range of structures in complex with the substrates, substrate analogues and inhibitors have been determined, and these have provided insights into the catalytic mechanism of this enzyme. Substrate 5-phospho-d-ribose 1-diphosphate (PRPP) binds to the C-terminal domain and coordinates to Mg2+, in a site completed by two flexible loops. Binding of the second substrate anthranilate is more complex, featuring multiple binding sites along an anthranilate channel. This multi-modal binding is consistent with the substrate inhibition observed at high concentrations of anthranilate. A series of structures predict a dissociative mechanism for the reaction, similar to the reaction mechanisms elucidated for other phosphoribosyltransferases. As this enzyme is essential for some pathogens, efforts have been made to develop inhibitors for this enzyme. To date, the best inhibitors exploit the multiple binding sites for anthranilate. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Thomas W. Scully
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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2
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The Role of CD38 in the Pathogenesis of Cardiorenal Metabolic Disease and Aging, an Approach from Basic Research. Cells 2023; 12:cells12040595. [PMID: 36831262 PMCID: PMC9954496 DOI: 10.3390/cells12040595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Aging is a major risk factor for the leading causes of mortality, and the incidence of age-related diseases including cardiovascular disease, kidney disease and metabolic disease increases with age. NAD+ is a classic coenzyme that exists in all species, and that plays a crucial role in oxidation-reduction reactions. It is also involved in the regulation of many cellular functions including inflammation, oxidative stress and differentiation. NAD+ declines with aging in various organs, and the reduction in NAD+ is possibly involved in the development of age-related cellular dysfunction in cardiorenal metabolic organs through the accumulation of inflammation and oxidative stress. Levels of NAD+ are regulated by the balance between its synthesis and degradation. CD38 is the main NAD+-degrading enzyme, and CD38 is activated in response to inflammation with aging, which is associated with the reduction in NAD+ levels. In this review, focusing on CD38, we discuss the role of CD38 in aging and the pathogenesis of age-related diseases, including cardiorenal metabolic disease.
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Zhou Z, Yang X, Huang T, Zheng J, Deng Z, Dai S, Lin S. Bifunctional NadC Homologue PyrZ Catalyzes Nicotinic Acid Formation in Pyridomycin Biosynthesis. ACS Chem Biol 2023; 18:141-150. [PMID: 36517246 DOI: 10.1021/acschembio.2c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pyridomycin is a potent antimycobacterial natural product by specifically inhibiting InhA, a clinically validated antituberculosis drug discovery target. Pyridyl moieties of pyridomycin play an essential role in inhibiting InhA by occupying the reduced form of the nicotinamide adenine dinucleotide (NADH) cofactor binding site. Herein, we biochemically characterize PyrZ that is a multifunctional NadC homologue and catalyzes the successive formation, dephosphorylation, and ribose hydrolysis of nicotinic acid mononucleotide (NAMN) to generate nicotinic acid (NA), a biosynthetic precursor for the pyridyl moiety of pyridomycin. Crystal structures of PyrZ in complex with substrate quinolinic acid (QA) and the final product NA revealed a specific salt bridge formed between K184 and the C3-carboxyl group of QA. This interaction positions QA for accepting the phosphoribosyl group to generate NAMN, retains NAMN within the active site, and mediates its translocation to nucleophile D296 for dephosphorylation. Combining kinetic and thermodynamic analysis with site-directed mutagenesis, the catalytic mechanism of PyrZ dephosphorylation was proposed. Our study discovered an alternative and concise NA biosynthetic pathway involving a unique multifunctional enzyme.
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Affiliation(s)
- Zihua Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shaobo Dai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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Morevati M, Fang EF, Mace ML, Kanbay M, Gravesen E, Nordholm A, Egstrand S, Hornum M. Roles of NAD + in Acute and Chronic Kidney Diseases. Int J Mol Sci 2022; 24:ijms24010137. [PMID: 36613582 PMCID: PMC9820289 DOI: 10.3390/ijms24010137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Nicotinamide adenine dinucleotide (oxidized form, NAD+) is a critical coenzyme, with functions ranging from redox reactions and energy metabolism in mitochondrial respiration and oxidative phosphorylation to being a central player in multiple cellular signaling pathways, organ resilience, health, and longevity. Many of its cellular functions are executed via serving as a co-substrate for sirtuins (SIRTs), poly (ADP-ribose) polymerases (PARPs), and CD38. Kidney damage and diseases are common in the general population, especially in elderly persons and diabetic patients. While NAD+ is reduced in acute kidney injury (AKI) and chronic kidney disease (CKD), mounting evidence indicates that NAD+ augmentation is beneficial to AKI, although conflicting results exist for cases of CKD. Here, we review recent progress in the field of NAD+, mainly focusing on compromised NAD+ levels in AKI and its effect on essential cellular pathways, such as mitochondrial dysfunction, compromised autophagy, and low expression of the aging biomarker αKlotho (Klotho) in the kidney. We also review the compromised NAD+ levels in renal fibrosis and senescence cells in the case of CKD. As there is an urgent need for more effective treatments for patients with injured kidneys, further studies on NAD+ in relation to AKI/CKD may shed light on novel therapeutics.
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Affiliation(s)
- Marya Morevati
- Department of Nephrology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
- Correspondence:
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway
| | - Maria L. Mace
- Department of Nephrology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mehmet Kanbay
- Division of Nephrology, Department of Medicine, Koç University School of Medicine, Istanbul 34010, Turkey
| | - Eva Gravesen
- Department of Pathology, Herlev Hospital, University of Copenhagen, 2730 Copenhagen, Denmark
| | - Anders Nordholm
- Department of Nephrology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Egstrand
- Department of Nephrology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mads Hornum
- Department of Nephrology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
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Ren Z, Xu Y, Li T, Sun W, Tang Z, Wang Y, Zhou K, Li J, Ding Q, Liang K, Wu L, Yin Y, Sun Z. NAD+ and its possible role in gut microbiota: Insights on the mechanisms by which gut microbes influence host metabolism. ANIMAL NUTRITION 2022; 10:360-371. [PMID: 35949199 PMCID: PMC9356074 DOI: 10.1016/j.aninu.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/01/2022] [Accepted: 06/15/2022] [Indexed: 11/26/2022]
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Raman H, Raman R, Pirathiban R, McVittie B, Sharma N, Liu S, Qiu Y, Zhu A, Kilian A, Cullis B, Farquhar GD, Stuart‐Williams H, White R, Tabah D, Easton A, Zhang Y. Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola. PLANT, CELL & ENVIRONMENT 2022; 45:2019-2036. [PMID: 35445756 PMCID: PMC9325393 DOI: 10.1111/pce.14337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/06/2022] [Indexed: 05/29/2023]
Abstract
Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ13 C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ13 C QTL. QTL contributing to main and QTL × environment interaction effects for Δ13 C and yield were identified. One multiple-trait QTL for Δ13 C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ13 C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Rosy Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Ramethaa Pirathiban
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research AustraliaUniversity of WollongongWollongongNew South WalesAustralia
| | - Brett McVittie
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Niharika Sharma
- NSW Department of Primary IndustriesOrange Agricultural InstituteOrangeNew South WalesAustralia
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRCOil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Yu Qiu
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Anyu Zhu
- Diversity Arrays Technology P/LUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Andrzej Kilian
- Diversity Arrays Technology P/LUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Brian Cullis
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research AustraliaUniversity of WollongongWollongongNew South WalesAustralia
| | - Graham D. Farquhar
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Hilary Stuart‐Williams
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - David Tabah
- Advanta Seeds Pty LtdToowoombaQueenslandAustralia
| | | | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRCOil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanHubeiChina
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7
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QPRT Acts as an Independent Prognostic Factor in Invasive Breast Cancer. JOURNAL OF ONCOLOGY 2022; 2022:6548644. [PMID: 35251175 PMCID: PMC8894024 DOI: 10.1155/2022/6548644] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/22/2021] [Indexed: 11/18/2022]
Abstract
Background. Quinolinic acid phosphoribosyltransferase (QPRT) is a rate-limiting enzyme that encodes the uronic acid pathway, which is involved in cell cycle progression and cancer cell metabolism. Some studies have demonstrated the progrowth effect of QPRT on breast cancer (BRCA) tumour cells, but its mechanism of action requires further exploration. Methods. We investigated the expression of QPRT and the prognosis of patients with different tumours by performing a pan-cancer analysis of QPRT. Prognostic values for overall survival (OS) were determined using uni- and multivariate Cox proportional hazard analyses. The prognostic survival of patients with a different pathological staging of BRCA and with QPRT high and low expression was also analysed. We also explored the relevant pathways by which QPRT affected BRCA tumorigenesis by gene set enrichment analysis (GSEA) and western blotting. The impact of QPRT on the PI3K/Akt pathway was also evaluated. Results. Pan-cancer analysis revealed significant QPRT expression in pan-cancer and correlated with prognosis in most tumour patients. QPRT was also highly expressed in BRCA when patients had poor prognoses, and its expression was associated with different pathological BRCA subtypes. GSEA revealed an association between BRCA progression and the cell cycle and the phosphatidylinositol 3-kinase (PI3K)/Akt signalling pathway, and this association was confirmed by western blotting. Conclusion. QPRT is highly expressed in breast cancer and particularly in HER2 breast cancer. Upregulated QPRT expression is an independent predictor of breast cancer prognosis and promotes breast cancer progression by activating the PI3K/Akt signalling pathway.
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8
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Tannous C, Booz GW, Altara R, Muhieddine DH, Mericskay M, Refaat MM, Zouein FA. Nicotinamide adenine dinucleotide: Biosynthesis, consumption and therapeutic role in cardiac diseases. Acta Physiol (Oxf) 2021; 231:e13551. [PMID: 32853469 DOI: 10.1111/apha.13551] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an abundant cofactor that plays crucial roles in several cellular processes. NAD can be synthesized de novo starting with tryptophan, or from salvage pathways starting with NAD precursors like nicotinic acid (NA), nicotinamide (NAM) or nicotinamide riboside (NR), referred to as niacin/B3 vitamins, arising from dietary supply or from cellular NAD catabolism. Given the interconversion between its oxidized (NAD+ ) and reduced form (NADH), NAD participates in a wide range of reactions: regulation of cellular redox status, energy metabolism and mitochondrial biogenesis. Plus, NAD acts as a signalling molecule, being a cosubstrate for several enzymes such as sirtuins, poly-ADP-ribose-polymerases (PARPs) and some ectoenzymes like CD38, regulating critical biological processes like gene expression, DNA repair, calcium signalling and circadian rhythms. Given the large number of mitochondria present in cardiac tissue, the heart has the highest NAD levels and is one of the most metabolically demanding organs. In several models of heart failure, myocardial NAD levels are depressed and this depression is caused by mitochondrial dysfunction, metabolic remodelling and inflammation. Emerging evidence suggests that regulating NAD homeostasis by NAD precursor supplementation has therapeutic efficiency in improving myocardial bioenergetics and function. This review provides an overview of the latest understanding of the different NAD biosynthesis pathways, as well as its role as a signalling molecule particularly in cardiac tissue. We highlight the significance of preserving NAD equilibrium in various models of heart diseases and shed light on the potential pharmacological interventions aiming to use NAD boosters as therapeutic agents.
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Affiliation(s)
- Cynthia Tannous
- Department of Pharmacology and Toxicology Faculty of Medicine American University of Beirut Medical Center Beirut Lebanon
| | - George W. Booz
- Department of Pharmacology and Toxicology University of Mississippi Medical Center Jackson MS USA
| | - Raffaele Altara
- Department of Pathology School of Medicine University of Mississippi Medical Center Jackson MS USA
- Institute for Experimental Medical Research Oslo University Hospital and University of Oslo Oslo Norway
- KG Jebsen Center for Cardiac Research University of Oslo Oslo Norway
| | - Dina H. Muhieddine
- Department of Pharmacology and Toxicology Faculty of Medicine American University of Beirut Medical Center Beirut Lebanon
| | - Mathias Mericskay
- INSERM Department of Signalling and Cardiovascular Pathophysiology UMR‐S 1180 Université Paris‐Saclay Châtenay‐Malabry France
| | - Marwan M. Refaat
- Department of Internal Medicine Faculty of Medicine American University of Beirut Medical Center Beirut Lebanon
- Department of Biochemistry and Molecular Genetics Faculty of Medicine American University of Beirut Medical Center Beirut Lebanon
| | - Fouad A. Zouein
- Department of Pharmacology and Toxicology Faculty of Medicine American University of Beirut Medical Center Beirut Lebanon
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9
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Xie N, Zhang L, Gao W, Huang C, Huber PE, Zhou X, Li C, Shen G, Zou B. NAD + metabolism: pathophysiologic mechanisms and therapeutic potential. Signal Transduct Target Ther 2020; 5:227. [PMID: 33028824 PMCID: PMC7539288 DOI: 10.1038/s41392-020-00311-7] [Citation(s) in RCA: 392] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) and its metabolites function as critical regulators to maintain physiologic processes, enabling the plastic cells to adapt to environmental changes including nutrient perturbation, genotoxic factors, circadian disorder, infection, inflammation and xenobiotics. These effects are mainly achieved by the driving effect of NAD+ on metabolic pathways as enzyme cofactors transferring hydrogen in oxidation-reduction reactions. Besides, multiple NAD+-dependent enzymes are involved in physiology either by post-synthesis chemical modification of DNA, RNA and proteins, or releasing second messenger cyclic ADP-ribose (cADPR) and NAADP+. Prolonged disequilibrium of NAD+ metabolism disturbs the physiological functions, resulting in diseases including metabolic diseases, cancer, aging and neurodegeneration disorder. In this review, we summarize recent advances in our understanding of the molecular mechanisms of NAD+-regulated physiological responses to stresses, the contribution of NAD+ deficiency to various diseases via manipulating cellular communication networks and the potential new avenues for therapeutic intervention.
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Affiliation(s)
- Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Lu Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Wei Gao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Peter Ernst Huber
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobo Zhou
- First Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guobo Shen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| | - Bingwen Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
- CCU Molecular and Radiation Oncology, German Cancer Research Center; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- Department of Thoracic Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
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10
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Yue Z, Shusheng J, Hongtao S, Shu Z, Lan H, Qingyuan Z, Shaoqiang C, Yuanxi H. Silencing DSCAM-AS1 suppresses the growth and invasion of ER-positive breast cancer cells by downregulating both DCTPP1 and QPRT. Aging (Albany NY) 2020; 12:14754-14774. [PMID: 32716908 PMCID: PMC7425442 DOI: 10.18632/aging.103538] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/20/2020] [Indexed: 01/06/2023]
Abstract
Breast cancer (BC) remains a significant threat to the health of women; however, the mechanism underlying the initiation and progression of BC is poorly understood. We analyzed data from the Gene Expression Omnibus database and The Cancer Genome Atlas datasets to identify differentially expressed genes between BC and normal tissues. The roles of dCTP pyrophosphatase 1 (DCTPP1) and quinolinate phosphoribosyltransferase (QPRT) in BC cells were investigated after knocking down or overexpressing the genes. The regulatory effects of Down syndrome cell adhesion molecule antisense RNA 1 (DSCAM-AS1) on DCTPP1 and QPRT expression were determined using luciferase reporter, RNA immunoprecipitation, RNA pull-down, chromatin immunoprecipitation, and fluorescence in situ hybridization assays. DCTPP1 and QPRT were overexpressed in BC compared to normal tissues. Overexpression of DCTPP1 and QPRT was associated with poor BC progression and promoted growth, migration, and invasion of MCF7 and T47D cells but inhibited apoptosis. DSCAM-AS1 increased QPRT expression via competitively binding miRNA-150-5p and miRNA-2467-3p. DSCAM-AS1 promoted DCTPP1 gene transcription by affecting H3K27 acetylation and enhanced DCTPP1 mRNA stability by binding to the 3′ untranslated region, which collectively resulted in DCTPP1 overexpression. Overall, DSCAM-AS1 knockdown decreased both DCTPP1 and QPRT expression, inhibiting the growth, migration, and invasion of estrogen receptor-positive BC.
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Affiliation(s)
- Zhang Yue
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jia Shusheng
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Song Hongtao
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zhao Shu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Huang Lan
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zhang Qingyuan
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Cheng Shaoqiang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Huang Yuanxi
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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Abstract
IMPACT STATEMENT NAD is a central metabolite connecting energy balance and organismal growth with genomic integrity and function. It is involved in the development of malignancy and has a regulatory role in the aging process. These processes are mediated by a diverse series of enzymes whose common focus is either NAD's biosynthesis or its utilization as a redox cofactor or enzyme substrate. These enzymes include dehydrogenases, cyclic ADP-ribose hydrolases, mono(ADP-ribosyl)transferases, poly(ADP-ribose) polymerases, and sirtuin deacetylases. This article describes the manifold pathways that comprise NAD metabolism and promotes an increased awareness of how perturbations in these systems may be important in disease prevention and/or progression.
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Affiliation(s)
- John Wr Kincaid
- Department of Nutrition, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,151230Case Comprehensive Cancer Center, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nathan A Berger
- 151230Case Comprehensive Cancer Center, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biochemistry, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Medicine, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Center for Science, Health and Society, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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12
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Jane EP, Premkumar DR, Thambireddy S, Golbourn B, Agnihotri S, Bertrand KC, Mack SC, Myers MI, Chattopadhyay A, Taylor DL, Schurdak ME, Stern AM, Pollack IF. Targeting NAD + Biosynthesis Overcomes Panobinostat and Bortezomib-Induced Malignant Glioma Resistance. Mol Cancer Res 2020; 18:1004-1017. [PMID: 32238439 DOI: 10.1158/1541-7786.mcr-19-0669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 12/17/2019] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
To improve therapeutic responses in patients with glioma, new combination therapies that exploit a mechanistic understanding of the inevitable emergence of drug resistance are needed. Intratumoral heterogeneity enables a low barrier to resistance in individual patients with glioma. We reasoned that targeting two or more fundamental processes that gliomas are particularly dependent upon could result in pleiotropic effects that would reduce the diversity of resistant subpopulations allowing convergence to a more robust therapeutic strategy. In contrast to the cytostatic responses observed with each drug alone, the combination of the histone deacetylase inhibitor panobinostat and the proteasome inhibitor bortezomib synergistically induced apoptosis of adult and pediatric glioma cell lines at clinically achievable doses. Resistance that developed was examined using RNA-sequencing and pharmacologic screening of resistant versus drug-naïve cells. Quinolinic acid phosphoribosyltransferase (QPRT), the rate-determining enzyme for de novo synthesis of NAD+ from tryptophan, exhibited particularly high differential gene expression in resistant U87 cells and protein expression in all resistant lines tested. Reducing QPRT expression reversed resistance, suggesting that QPRT is a selective and targetable dependency for the panobinostat-bortezomib resistance phenotype. Pharmacologic inhibition of either NAD+ biosynthesis or processes such as DNA repair that consume NAD+ or their simultaneous inhibition with drug combinations, specifically enhanced apoptosis in treatment-resistant cells. Concomitantly, de novo vulnerabilities to known drugs were observed. IMPLICATIONS: These data provide new insights into mechanisms of treatment resistance in gliomas, hold promise for targeting recurrent disease, and provide a potential strategy for further exploration of next-generation inhibitors.
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Affiliation(s)
- Esther P Jane
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Daniel R Premkumar
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania. .,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute Brain Tumor Center, Pittsburgh, Pennsylvania
| | - Swetha Thambireddy
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brian Golbourn
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sameer Agnihotri
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute Brain Tumor Center, Pittsburgh, Pennsylvania
| | - Kelsey C Bertrand
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Stephen C Mack
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Max I Myers
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ansuman Chattopadhyay
- Molecular Biology Information Service, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - D Lansing Taylor
- Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Mark E Schurdak
- Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Andrew M Stern
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ian F Pollack
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania. .,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute Brain Tumor Center, Pittsburgh, Pennsylvania
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13
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Moraes JGN, Behura SK, Bishop JV, Hansen TR, Geary TW, Spencer TE. Analysis of the uterine lumen in fertility-classified heifers: II. Proteins and metabolites†. Biol Reprod 2020; 102:571-587. [PMID: 31616912 PMCID: PMC7331878 DOI: 10.1093/biolre/ioz197] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023] Open
Abstract
Survival and growth of the bovine conceptus is dependent on endometrial secretions or histotroph. Previously, serial blastocyst transfer was used to classify heifers as high fertile (HF), subfertile (SF), or infertile (IF). Here, we investigated specific histotroph components (proteins and metabolites) in the uterine lumen of day 17 fertility-classified heifers. Interferon tau (IFNT) was more abundant in uterine lumenal fluid (ULF) of pregnant HF than SF animals as the conceptus was longer in HF heifers. However, no differences in endometrial expression of selected classical and nonclassical interferon-stimulated genes (ISGs) were observed, suggesting that IFNT signaling in the endometrium of pregnant HF and SF heifers was similar. Pregnancy significantly increased the abundance of several proteins in ULF. Based on functional annotation, the abundance of a number of proteins involved in energy metabolism, oxidative stress, amino acid metabolism, and cell proliferation and differentiation were greater in the ULF of pregnant HF than SF heifers. Metabolomics analysis found that pregnancy only changed the metabolome composition of ULF from HF heifers. The majority of the metabolites that increased in the ULF of pregnant HF as compared to SF heifers were associated with energy and amino acid metabolism. The observed differences in ULF proteome and metabolome are hypothesized to influence uterine receptivity with consequences on conceptus development and survival in fertility-classified heifers.
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Affiliation(s)
- Joao G N Moraes
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jeanette V Bishop
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA and
| | - Thomas R Hansen
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA and
| | - Thomas W Geary
- USDA-ARS, Fort Keogh Livestock and Range Research Laboratory, Miles City, Montana, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
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14
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Minhas PS, Liu L, Moon PK, Joshi AU, Dove C, Mhatre S, Contrepois K, Wang Q, Lee BA, Coronado M, Bernstein D, Snyder MP, Migaud M, Majeti R, Mochly-Rosen D, Rabinowitz JD, Andreasson KI. Macrophage de novo NAD + synthesis specifies immune function in aging and inflammation. Nat Immunol 2018; 20:50-63. [PMID: 30478397 DOI: 10.1038/s41590-018-0255-3] [Citation(s) in RCA: 307] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/10/2018] [Indexed: 11/09/2022]
Abstract
Recent advances highlight a pivotal role for cellular metabolism in programming immune responses. Here, we demonstrate that cell-autonomous generation of nicotinamide adenine dinucleotide (NAD+) via the kynurenine pathway (KP) regulates macrophage immune function in aging and inflammation. Isotope tracer studies revealed that macrophage NAD+ derives substantially from KP metabolism of tryptophan. Genetic or pharmacological blockade of de novo NAD+ synthesis depleted NAD+, suppressed mitochondrial NAD+-dependent signaling and respiration, and impaired phagocytosis and resolution of inflammation. Innate immune challenge triggered upstream KP activation but paradoxically suppressed cell-autonomous NAD+ synthesis by limiting the conversion of downstream quinolinate to NAD+, a profile recapitulated in aging macrophages. Increasing de novo NAD+ generation in immune-challenged or aged macrophages restored oxidative phosphorylation and homeostatic immune responses. Thus, KP-derived NAD+ operates as a metabolic switch to specify macrophage effector responses. Breakdown of de novo NAD+ synthesis may underlie declining NAD+ levels and rising innate immune dysfunction in aging and age-associated diseases.
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Affiliation(s)
- Paras S Minhas
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA.,Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Ling Liu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Peter K Moon
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Amit U Joshi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Christopher Dove
- Department of Hematology, Stanford School of Medicine, Stanford, CA, USA
| | - Siddhita Mhatre
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Kevin Contrepois
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Qian Wang
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Brittany A Lee
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael Coronado
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Marie Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Ravindra Majeti
- Department of Hematology, Stanford School of Medicine, Stanford, CA, USA
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Katrin I Andreasson
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA. .,Stanford Neuroscience Institute, Stanford University, Stanford, CA, USA. .,Stanford Immunology Program, Stanford University, Stanford, CA, USA.
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15
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Jacobs KR, Castellano-Gonzalez G, Guillemin GJ, Lovejoy DB. Major Developments in the Design of Inhibitors along the Kynurenine Pathway. Curr Med Chem 2017; 24:2471-2495. [PMID: 28464785 PMCID: PMC5748880 DOI: 10.2174/0929867324666170502123114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/13/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Abstract
Disrupted kynurenine pathway (KP) metabolism has been implicated in the progression of neurodegenerative disease, psychiatric disorders and cancer. Modulation of enzyme activity along this pathway may therefore offer potential new therapeutic strategies for these conditions. Considering their prominent positions in the KP, the enzymes indoleamine 2,3-dioxygenase, kynurenine 3-monooxygenase and kynurenine aminotransferase, appear the most attractive targets. Already, increasing interest in this pathway has led to the identification of a number of potent and selective enzyme inhibitors with promising pre-clinical data and the elucidation of several enzyme crystal structures provides scope to rationalize the molecular mechanisms of inhibitor activity. The field seems poised to yield one or more inhibitors that should find clinical utility.
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Affiliation(s)
- Kelly R Jacobs
- Neuroinflammation Group, Department of Biomedical Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney. Australia
| | - Gloria Castellano-Gonzalez
- Neuroinflammation Group, Department of Biomedical Research, Faculty of Medicine and Health Sciences, Macquarie University, Sydney. Australia
| | - Gilles J Guillemin
- Department of Biomedical Research, Faculty of Medicine and Health Science, Macquarie University, 2 Technology Place, Sydney. Australia
| | - David B Lovejoy
- Department of Biomedical Research, Faculty of Medicine and Health Science, Macquarie University, 2 Technology Place, Sydney. Australia
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16
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Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys Acta Rev Cancer 2017; 1868:258-272. [PMID: 28549623 DOI: 10.1016/j.bbcan.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.
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Affiliation(s)
- James P Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK
| | - Susan Richman
- Department of Pathology and Tumour Biology, St James University Hospital, Leeds, UK
| | - Tim Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK.
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17
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Shirota M, Kinoshita K. Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw124. [PMID: 27589963 PMCID: PMC5009343 DOI: 10.1093/database/baw124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/04/2016] [Indexed: 01/24/2023]
Abstract
The protein coding sequences of the human reference genome GRCh38, RefSeq mRNA and UniProt protein databases are sometimes inconsistent with each other, due to polymorphisms in the human population, but the overall landscape of the discordant sequences has not been clarified. In this study, we comprehensively listed the discordant bases and regions between the GRCh38, RefSeq and UniProt reference sequences, based on the genomic coordinates of GRCh38. We observed that the RefSeq sequences are more likely to represent the major alleles than GRCh38 and UniProt, by assigning the alternative allele frequencies of the discordant bases. Since some reference sequences have minor alleles, functional and structural annotations may be performed based on rare alleles in the human population, thereby biasing these analyses. Some of the differences between the RefSeq and GRCh38 account for biological differences due to known RNA-editing sites. The definitions of the coding regions are frequently complicated by possible micro-exons within introns and by SNVs with large alternative allele frequencies near exon–intron boundaries. The mRNA or protein regions missing from GRCh38 were mainly due to small deletions, and these sequences need to be identified. Taken together, our results clarify overall consistency and remaining inconsistency between the reference sequences.
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Affiliation(s)
- Matsuyuki Shirota
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 9808575, Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 9808575, Japan Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 9808579, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 9808575, Japan Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 9808579, Japan Institute for Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 9808575, Japan
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