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Guengerich FP. Roles of Individual Human Cytochrome P450 Enzymes in Drug Metabolism. Pharmacol Rev 2024; 76:1104-1132. [PMID: 39054072 DOI: 10.1124/pharmrev.124.001173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/28/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024] Open
Abstract
Our knowledge of the roles of individual cytochrome P450 (P450) enzymes in drug metabolism has developed considerably in the past 30 years, and this base has been of considerable use in avoiding serious issues with drug interactions and issues due to variations. Some newer approaches are being considered for "phenotyping" metabolism reactions with new drug candidates. Endogenous biomarkers are being used for noninvasive estimation of levels of individual P450 enzymes. There is also the matter of some remaining "orphan" P450s, which have yet to be assigned reactions. Practical problems that continue in drug development include predicting drug-drug interactions, predicting the effects of polymorphic and other P450 variations, and evaluating interspecies differences in drug metabolism, particularly in the context of "metabolism in safety testing" regulatory issues ["disproportionate (human) metabolites"]. SIGNIFICANCE STATEMENT: Cytochrome P450 enzymes are the major catalysts involved in drug metabolism. The characterization of their individual roles has major implications in drug development and clinical practice.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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2
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Guengerich FP. Ninety-eight semesters of cytochrome P450 enzymes and related topics-What have I taught and learned? J Biol Chem 2024; 300:105625. [PMID: 38185246 PMCID: PMC10847173 DOI: 10.1016/j.jbc.2024.105625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 01/09/2024] Open
Abstract
This Reflection article begins with my family background and traces my career through elementary and high school, followed by time at the University of Illinois, Vanderbilt University, the University of Michigan, and then for 98 semesters as a Vanderbilt University faculty member. My research career has dealt with aspects of cytochrome P450 enzymes, and the basic biochemistry has had applications in fields as diverse as drug metabolism, toxicology, medicinal chemistry, pharmacogenetics, biological engineering, and bioremediation. I am grateful for the opportunity to work with the Journal of Biological Chemistry not only as an author but also for 34 years as an Editorial Board Member, Associate Editor, Deputy Editor, and interim Editor-in-Chief. Thanks are extended to my family and my mentors, particularly Profs. Harry Broquist and Minor J. Coon, and the more than 170 people who have trained with me. I have never lost the enthusiasm for research that I learned in the summer of 1968 with Harry Broquist, and I have tried to instill this in the many trainees I have worked with. A sentence I use on closing slides is "It's not just a laboratory-it's a fraternity."
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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McCarty KD, Liu L, Tateishi Y, Wapshott-Stehli HL, Guengerich FP. The multistep oxidation of cholesterol to pregnenolone by human cytochrome P450 11A1 is highly processive. J Biol Chem 2024; 300:105495. [PMID: 38006947 PMCID: PMC10716780 DOI: 10.1016/j.jbc.2023.105495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
Cytochrome P450 (P450, CYP) 11A1 is the classical cholesterol side chain cleavage enzyme (P450scc) that removes six carbons of the side chain, the first and rate-limiting step in the synthesis of all mammalian steroids. The reaction is a 3-step, 6-electron oxidation that proceeds via formation of 22R-hydroxy (OH) and 20R,22R-(OH)2 cholesterol, yielding pregnenolone. We expressed human P450 11A1 in bacteria, purified the enzyme in the absence of nonionic detergents, and assayed pregnenolone formation by HPLC-mass spectrometry of the dansyl hydrazone. The reaction was inhibited by the nonionic detergent Tween 20, and several lipids did not enhance enzymatic activity. The 22R-OH and 20R,22R-(OH)2 cholesterol intermediates were bound to P450 11A1 relatively tightly, as judged by steady-state optical titrations and koff rates. The electron donor adrenodoxin had little effect on binding; the substrate cholesterol showed a ∼5-fold stimulatory effect on the binding of adrenodoxin to P450 11A1. Presteady-state single-turnover kinetic analysis was consistent with a highly processive reaction with rates of intermediate oxidation steps far exceeding dissociation rates for products and substrates. The presteady-state kinetic analysis revealed a second di-OH cholesterol product, separable by HPLC, in addition to 20R,22R-(OH)2 cholesterol, which we characterized as a rotamer that was also converted to pregnenolone at a similar rate. The first oxidation step (at C-22) is the slowest, limiting the overall rate of cleavage. d3-Cholesterol showed no kinetic deuterium isotope effect on C-22, indicating that C-H bond cleavage is not rate-limiting in the first hydroxylation step.
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Affiliation(s)
- Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lu Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yasuhiro Tateishi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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4
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Gerhards J, Volkov LI, Corbo JC, Malan D, Sasse P. Enzymatic vitamin A 2 production enables red-shifted optogenetics. Pflugers Arch 2023; 475:1409-1419. [PMID: 37987804 PMCID: PMC10730639 DOI: 10.1007/s00424-023-02880-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
Optogenetics is a technology using light-sensitive proteins to control signaling pathways and physiological processes in cells and organs and has been applied in neuroscience, cardiovascular sciences, and many other research fields. Most commonly used optogenetic actuators are sensitive to blue and green light, but red-light activation would allow better tissue penetration and less phototoxicity. Cyp27c1 is a recently deorphanized cytochrome P450 enzyme that converts vitamin A1 to vitamin A2, thereby red-shifting the spectral sensitivity of visual pigments and enabling near-infrared vision in some aquatic species.Here, we investigated the ability of Cyp27c1-generated vitamin A2 to induce a shift in spectral sensitivity of the light-gated ion channel Channelrhodopsin-2 (ChR2) and its red-shifted homolog ReaChR. We used patch clamp to measure photocurrents at specific wavelengths in HEK 293 cells expressing ChR2 or ReaChR. Vitamin A2 incubation red-shifted the wavelength for half-maximal currents (λ50%) by 6.8 nm for ChR2 and 12.4 nm for ReaChR. Overexpression of Cyp27c1 in HEK 293 cells showed mitochondrial localization, and HPLC analysis showed conversion of vitamin A1 to vitamin A2. Notably, the λ50% of ChR2 photocurrents was red-shifted by 10.5 nm, and normalized photocurrents at 550 nm were about twofold larger with Cyp27c1 expression. Similarly, Cyp27c1 shifted the λ50% of ReaChR photocurrents by 14.3 nm and increased normalized photocurrents at 650 nm almost threefold.Since vitamin A2 incubation is not a realistic option for in vivo applications and expression of Cyp27c1 leads to a greater red-shift in spectral sensitivity, we propose co-expression of this enzyme as a novel strategy for red-shifted optogenetics.
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Affiliation(s)
- Johanna Gerhards
- Institute of Physiology I, Medical Faculty, University of Bonn, 53125, Bonn, Germany
| | - Leo I Volkov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Daniela Malan
- Institute of Physiology I, Medical Faculty, University of Bonn, 53125, Bonn, Germany.
| | - Philipp Sasse
- Institute of Physiology I, Medical Faculty, University of Bonn, 53125, Bonn, Germany.
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Petkova-Kirova P, Baas S, Wagenpfeil G, Hartz P, Unger MM, Bernhardt R. SNPs in cytochrome P450 genes decide on the fate of individuals with genetic predisposition to Parkinson's disease. Front Pharmacol 2023; 14:1244516. [PMID: 37601072 PMCID: PMC10436510 DOI: 10.3389/fphar.2023.1244516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Parkinson's disease (PD) is one of the most frequent neurological diseases affecting millions of people worldwide. While the majority of PD cases are of unknown origin (idiopathic), about 5%-10% are familial and linked to mutations in different known genes. However, there are also people with a genetic predisposition to PD who do not develop the disease. To elucidate factors leading to the manifestation of PD we compared the occurrence of single nucleotide polymorphisms (SNPs) in various cytochrome P450 (P450) genes in people with a genetic predisposition and suffering from PD (GPD) to that of people, who are genetically predisposed, but show no symptoms of the disease (GUN). We used the PPMI (Parkinson's Progression Markers Initiative) database and the gene sequences of all 57 P450s as well as their three redox partners. Corresponding odds ratios (OR) and confidence intervals (CI) were calculated to assess the incidence of the various SNPs in the two groups of individuals and consequently their relation to PD. We identified for the first time SNPs that are significantly (up to 10fold!) over- or under-represented in GPD patients compared to GUN. SNPs with OR > 5 were found in 10 P450s being involved in eicosanoid, vitamin A and D metabolism as well as cholesterol degradation pointing to an important role of endogenous factors for the manifestation of PD clinical symptoms. Moreover, 12 P450s belonging to all P450 substrate classes as well as POR have SNPs that are significantly under-represented (OR < 0.2) in GPD compared to GUN, indicating a protective role of those SNPs and the corresponding P450s regarding disease advancement. To the best of our knowledge our data for the first time demonstrate an association between known PD predisposition genes and SNPs in other genes, shown here for different P450 genes and for their redox partner POR, which promote the manifestation of the disease in familial PD. Our results thus shed light onto the pathogenesis of PD, especially the switch from GUN to GPD and might further help to advance novel strategies for preventing the development or progression of the disease.
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Affiliation(s)
- Polina Petkova-Kirova
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Gudrun Wagenpfeil
- Institut für Medizinische Biometrie, Epidemiologie und Medizinische Informatik, Universität des Saarlandes, Homburg, Germany
| | - Philip Hartz
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Rita Bernhardt
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
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Glass SM, Tateishi Y, Guengerich FP, Wang HJ. 3,4-Desaturation of retinoic acid by cytochrome P450 27C1 prevents P450-mediated catabolism. Arch Biochem Biophys 2023; 743:109669. [PMID: 37356607 PMCID: PMC11500474 DOI: 10.1016/j.abb.2023.109669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/28/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
Cytochrome P450 (P450, CYP) 27C1 is expressed in human skin and catalyzes the 3,4-desaturation of retinoids. The enzyme has a relatively high specificity constant (kcat/Km), and ∼¼ of the retinoids in human skin are in the desaturated form but their function is unknown. 3,4-Dehydroretinoic acid (also didehydroretinoic acid, ddRA) has similar affinity as all-trans retinoic acid (atRA) for retinoid X and retinoic acid receptors (RXRs/RAR). The metabolism of ddRA is unknown, and we considered the hypothesis that desaturation might be a protective mechanism in maintaining active retinoid levels in the body. There are limited theoretical products that can result from ddRA oxidation. We optimized conditions for oxidation of atRA by human liver microsomes-a slow loss of atRA was seen due to 4-oxidation but no loss of ddRA was observed under the same conditions. We evaluated the HPLC peaks that were observed in microsomal incubations with ddRA using UV spectroscopy, NaBH4 and NaBD4 reduction, and mass spectrometry. None were potential ddRA oxidation products, and none were increased in the presence of the P450 cofactor NADPH. Known P450 inhibitors had no effects on the levels of these compounds. We conclude that ddRA is not readily oxidized by P450s and that one role of desaturation may be the maintenance of levels of functional retinoids.
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Affiliation(s)
- Sarah M Glass
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Yasuhiro Tateishi
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - F Peter Guengerich
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Hong-Jaan Wang
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States; School of Pharmacy, National Defense Medical Center, Taipei, Taiwan, ROC.
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7
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Schulz V, Freibert SA, Boss L, Mühlenhoff U, Stehling O, Lill R. Mitochondrial [2Fe-2S] ferredoxins: new functions for old dogs. FEBS Lett 2023; 597:102-121. [PMID: 36443530 DOI: 10.1002/1873-3468.14546] [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] [Received: 10/20/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022]
Abstract
Ferredoxins (FDXs) comprise a large family of iron-sulfur proteins that shuttle electrons from NADPH and FDX reductases into diverse biological processes. This review focuses on the structure, function and specificity of mitochondrial [2Fe-2S] FDXs that are related to bacterial FDXs due to their endosymbiotic inheritance. Their classical function in cytochrome P450-dependent steroid transformations was identified around 1960, and is exemplified by mammalian FDX1 (aka adrenodoxin). Thirty years later the essential function in cellular Fe/S protein biogenesis was discovered for the yeast mitochondrial FDX Yah1 that is additionally crucial for the formation of haem a and ubiquinone CoQ6 . In mammals, Fe/S protein biogenesis is exclusively performed by the FDX1 paralog FDX2, despite the high structural similarity of both proteins. Recently, additional and specific roles of human FDX1 in haem a and lipoyl cofactor biosyntheses were described. For lipoyl synthesis, FDX1 transfers electrons to the radical S-adenosyl methionine-dependent lipoyl synthase to kickstart its radical chain reaction. The high target specificity of the two mammalian FDXs is contained within small conserved sequence motifs, that upon swapping change the target selection of these electron donors.
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Affiliation(s)
- Vinzent Schulz
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Linda Boss
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Oliver Stehling
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
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8
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Coleman T, Doherty DZ, Zhang T, Podgorski MN, Qiao R, Lee JHZ, Bruning JB, De Voss JJ, Zhou W, Bell SG. Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation. Chem Asian J 2022; 17:e202200986. [PMID: 36268769 PMCID: PMC10100021 DOI: 10.1002/asia.202200986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/18/2022] [Indexed: 11/07/2022]
Abstract
The cytochrome P450 family of monooxygenase enzymes have essential biological roles involving the selective oxidation of carbon-hydrogen bonds. They can also catalyze other important metabolic reactions including desaturation to form alkenes. Currently the factors that control the partition between P450 hydroxylation and desaturation pathways are poorly defined. The CYP199A4 enzyme from the bacterium Rhodopseudomonas palustris HaA2 catalyzes the oxidation of 4-ethyl- and 4-isopropyl- benzoic acids with hydroxylation and desaturation occurring in significant quantities. Here we demonstrate that 4-cyclopropylbenzoic acid is regioselectively hydroxylated by CYP199A4 at the benzylic carbon. In contrast, the oxidation of 4-n-propylbenzoic acid by CYP199A4 results in three major metabolites: an alkene from desaturation and two hydroxylation products at the benzylic (Cα) and Cβ carbons in similar quantities. Extending the length of the alkyl substituent resulted in 4-n-butylbenzoic acid being oxidized at the benzylic position (45%) and desaturated (55%). In contrast, 4-isobutylbenzoic generated very little alkene (5%) but was hydroxylated at the benzylic position (54%) and at the tertiary Cβ position (41%). The oxidation of 4-n-propylbenzoic acid by the F298 V mutant of CYP199A4 occurred with no hydroxylation at Cβ and a significant increase in metabolites arising from desaturation (73%). The X-ray crystal structures of CYP199A4 with each substrate revealed that they bind in the active site with the alkyl substituent positioned over the heme. However, the longer alkylbenzoic acids were bound in a different conformation as was 4-n-propylbenzoic acid in the F298 V mutant. Overall, the changes in metabolite distribution could be ascribed to bond strength differences and the position of the alkyl group relative to the heme.
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Affiliation(s)
- Tom Coleman
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
| | - Daniel Z. Doherty
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
| | - Ting Zhang
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071P. R. China
| | | | - Ruihong Qiao
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071P. R. China
| | - Joel H. Z. Lee
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
| | - John B. Bruning
- School of Biological SciencesUniversity of AdelaideAdelaideSA, 5005Australia
| | - James J. De Voss
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQLD, 4072Australia
| | - Weihong Zhou
- College of Life Sciences and The State Key Laboratory of Medicinal Chemical BiologyNankai UniversityTianjin300071P. R. China
| | - Stephen G. Bell
- Department of ChemistryUniversity of AdelaideAdelaideSA, 5005Australia
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D MO, C TZ, R SP. Human orphan cytochromes P450: An update. Curr Drug Metab 2022; 23:CDM-EPUB-128186. [PMID: 36503398 DOI: 10.2174/1389200224666221209153032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022]
Abstract
Orphan cytochromes P450 (CYP) are enzymes whose biological functions and substrates are unknown. However, the use of new experimental strategies has allowed obtaining more information about their relevance in the metabolism of endogenous and exogenous compounds. Likewise, the modulation of their expression and activity has been associated with pathogenesis and prognosis in different diseases. In this work, we review the regulatory pathways and the possible role of orphan CYP to provide evidence that allow us to stop considering some of them as orphan enzymes and to propose them as possible therapeutic targets in the design of new strategies for the treatment of diseases associated with CYP-mediated metabolism.
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Affiliation(s)
- Molina-Ortiz D
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
| | - Torres-Zárate C
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
| | - Santes-Palacios R
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Coyoacán, Mexico City, México, 04530
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Lou L, Chen L, Wu Y, Zhang G, Qiu R, Su J, Zhao Z, Lu Z, Liao M, Deng X. Identification of hub genes and construction of prognostic nomogram for patients with Wilms tumors. Front Oncol 2022; 12:982110. [PMID: 36338682 PMCID: PMC9634477 DOI: 10.3389/fonc.2022.982110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/05/2022] [Indexed: 12/03/2022] Open
Abstract
Background In children, Wilms' tumors are the most common urological cancer with unsatisfactory prognosis, but few molecular prognostic markers have been discovered for it. With the rapid development of high-throughput quantitative proteomic and transcriptomic approaches, the molecular mechanisms of various cancers have been comprehensively explored. This study aimed to uncover the molecular mechanisms underlying Wilms tumor and build predictive models by use of microarray and RNA-seq data. Methods Gene expression datasets were downloaded from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) databases. Bioinformatics methods wereutilized to identified hub genes, and these hub genes were validated by experiment. Nomogram predicting OS was developed using genetic risk score model and clinicopathological variables. Results CDC20, BUB1 and CCNB2 were highly expressed in tumor tissues and able to affect cell proliferation and the cell cycle of SK-NEP-1 cells. This may reveal molecular biology features and a new therapeutic target of Wilms tumour.7 genes were selected as prognostic genes after univariate, Lasso, and multivariate Cox regression analyses and had good accuracy, a prognostic nomogram combined gene model with clinical factors was completed with high accuracy. Conclusions The current study discovered CDC20,BUB1 and CCNB2 as hub-genes associated with Wilms tumor, providing references to understand the pathogenesis and be considered a novel candidate to target therapy and construct novel nomogram, incorporating both clinical risk factors and gene model, could be appropriately applied in preoperative individualized prediction of malignancy in patients with Wilms tumor.
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Affiliation(s)
- Lei Lou
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Pediatric Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Luping Chen
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yaohao Wu
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Gang Zhang
- Department of Pediatric Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ronglin Qiu
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jianhang Su
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zhuangjie Zhao
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zijie Lu
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Minyi Liao
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaogeng Deng
- Department of Pediatric Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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11
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Mo HY, Wei QY, Zhong QH, Zhao XY, Guo D, Han J, Noracharttiyapot W, Visser L, van den Berg A, Xu YM, Lau ATY. Cytochrome P450 27C1 Level Dictates Lung Cancer Tumorigenicity and Sensitivity towards Multiple Anticancer Agents and Its Potential Interplay with the IGF-1R/Akt/p53 Signaling Pathway. Int J Mol Sci 2022; 23:7853. [PMID: 35887201 PMCID: PMC9324654 DOI: 10.3390/ijms23147853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023] Open
Abstract
Cytochrome P450 enzymes (CYP450s) exert mighty catalytic actions in cellular metabolism and detoxication, which play pivotal roles in cell fate determination. Preliminary data shows differential expression levels of CYP27C1, one of the "orphan P450s" in human lung cancer cell lines. Here, we study the functions of CYP27C1 in lung cancer progression and drug endurance, and explore its potential to be a diagnostic and therapeutic target for lung cancer management. Quantitative real-time PCR and immunoblot assays were conducted to estimate the transcription and protein expression level of CYP27C1 in human lung cancer cell lines, which was relatively higher in A549 and H1975 cells, but was lower in H460 cells. Stable CYP27C1-knockdown A549 and H1975 cell lines were established, in which these cells showed enhancement in cell proliferation, colony formation, and migration. In addition, aberrant IGF-1R/Akt/p53 signal transduction was also detected in stable CYP27C1-knockdown human lung cancer cells, which exhibited greater tolerance towards the treatments of anticancer agents (including vinorelbine, picropodophyllin, pacritinib, and SKLB610). This work, for the first time, reveals that CYP27C1 impacts lung cancer cell development by participating in the regulation of the IGF-1R/Akt/p53 signaling pathway, and the level of CYP27C1 plays indispensable roles in dictating the cellular sensitivity towards multiple anticancer agents.
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Affiliation(s)
- Hai-Ying Mo
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Qi-Yao Wei
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Qiu-Hua Zhong
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Xiao-Yun Zhao
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Dan Guo
- Department of Pathology, Shantou University Medical College, Shantou 515041, China
| | - Jin Han
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Wachiraporn Noracharttiyapot
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Lydia Visser
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
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12
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Kim HJ, Ishida K, Ishida‐Ito M, Hertweck C. Sequential Allylic Alcohol Formation by a Multifunctional Cytochrome P450 Monooxygenase with Rare Redox Partners. Angew Chem Int Ed Engl 2022; 61:e202203264. [PMID: 35416382 PMCID: PMC9322674 DOI: 10.1002/anie.202203264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/21/2022]
Abstract
Caryoynencin is a toxic and antifungal fatty acid derivative produced by a number of plant-pathogenic and insect-protective bacteria (Trinickia caryophylli and Burkholderia spp.). In addition to the reactive tetrayne unit, the presence of an allylic alcohol moiety is critical for antimicrobial activities. By a combination of mutational analyses, heterologous expression and in vitro reconstitution experiments we show that the cytochrome P450 monooxygenase CayG catalyzes the complex transformation of a saturated carbon backbone into an allylic alcohol. Unexpectedly, CayG employs a ferritin-like protein (CayK) or a rubredoxin (CayL) component for electron transport. A desaturation-hydroxylation sequence was deduced from a time-course study and in vitro biotransformations with pathway intermediates, substrate analogues, protegencin congeners from Pseudomonas protegens Pf-5, and synthetic derivatives. This unusual multifunctional oxygenase may inspire future biocatalytic applications.
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Affiliation(s)
- Hak Joong Kim
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Keishi Ishida
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Mie Ishida‐Ito
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Christian Hertweck
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute (HKI)Beutenbergstr. 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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13
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Kim HJ, Ishida K, Ishida-Ito M, Hertweck C. Sequential Allylic Alcohol Formation by a Multifunctional Cytochrome P450 Monooxygenase with Rare Redox Partners. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hak Joong Kim
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Mie Ishida-Ito
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll Institute: Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Department of Biomolecular Chemistry Beutenbergstr. 11a 07745 Jena GERMANY
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14
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O’Connor C, Varshosaz P, Moise AR. Mechanisms of Feedback Regulation of Vitamin A Metabolism. Nutrients 2022; 14:nu14061312. [PMID: 35334970 PMCID: PMC8950952 DOI: 10.3390/nu14061312] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
Vitamin A is an essential nutrient required throughout life. Through its various metabolites, vitamin A sustains fetal development, immunity, vision, and the maintenance, regulation, and repair of adult tissues. Abnormal tissue levels of the vitamin A metabolite, retinoic acid, can result in detrimental effects which can include congenital defects, immune deficiencies, proliferative defects, and toxicity. For this reason, intricate feedback mechanisms have evolved to allow tissues to generate appropriate levels of active retinoid metabolites despite variations in the level and format, or in the absorption and conversion efficiency of dietary vitamin A precursors. Here, we review basic mechanisms that govern vitamin A signaling and metabolism, and we focus on retinoic acid-controlled feedback mechanisms that contribute to vitamin A homeostasis. Several approaches to investigate mechanistic details of the vitamin A homeostatic regulation using genomic, gene editing, and chromatin capture technologies are also discussed.
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Affiliation(s)
- Catherine O’Connor
- MD Program, Northern Ontario School of Medicine, 317-MSE Bldg., 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada;
| | - Parisa Varshosaz
- Biology and Biomolecular Sciences Ph.D. Program, Northern Ontario School of Medicine, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | - Alexander R. Moise
- Medical Sciences Division, Northern Ontario School of Medicine, 317-MSE Bldg., 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada
- Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
- Correspondence: ; Tel.: +1-705-662-7253
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15
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Coleman T, Kirk AM, Lee JHZ, Doherty DZ, Bruning JB, Krenske EH, De Voss JJ, Bell SG. Different Geometric Requirements for Cytochrome P450-Catalyzed Aliphatic Versus Aromatic Hydroxylation Results in Chemoselective Oxidation. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alicia M. Kirk
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joel H. Z. Lee
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Daniel Z. Doherty
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
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16
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Glass SM, Webb SN, Guengerich FP. Binding of cytochrome P450 27C1, a retinoid desaturase, to its accessory protein adrenodoxin. Arch Biochem Biophys 2021; 714:109076. [PMID: 34732331 DOI: 10.1016/j.abb.2021.109076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 01/11/2023]
Abstract
Of the 57 human cytochrome P450 (P450) enzymes, seven are mitochondrial: 11A1, 11B1, 11B2, 24A1, 27A1, 27B1, and 27C1. Mitochondrial P450s utilize an electron transport system with adrenodoxin (Adx) and NADPH-adrenodoxin reductase (AdR). AdR reduces Adx, which then transfers electrons to the P450. The interactions between proteins in the mitochondrial P450 system are largely driven by electrostatic interactions, though the specifics vary depending on the P450. Unlike other mitochondrial P450s, the interaction between P450 27C1, a retinoid 3,4-desaturase expressed in the skin, and Adx remains largely uncharacterized. In this work, we utilized an Alexa Fluor 488 C5 maleimide-labeled Adx to measure binding affinities between Adx and P450 27C1 or AdR. Both proteins bound Adx tightly, with Kd values < 100 nM, and binding affinities decreased with increasing ionic strength, supporting the role of electrostatic interactions in mediating these interactions. Cross-linking mass spectrometry and computational modeling were performed to identify interactions between P450 27C1 and Adx. While the residues of Adx identified in interactions were consistent with studies of other mitochondrial P450s, the binding interface of P450 27C1 was quite large and supported multiple Adx binding positions, including ones outside of the canonical Adx binding site. Additionally, Adx did not appear to be an allosteric effector of P450 27C1 substrate binding, in contrast to some other mitochondrial P450s. Overall, we conclude that P450-Adx interactions are P450-specific.
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Affiliation(s)
- Sarah M Glass
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Stephany N Webb
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States.
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17
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Cellular retinoid-binding proteins transfer retinoids to human cytochrome P450 27C1 for desaturation. J Biol Chem 2021; 297:101142. [PMID: 34480899 PMCID: PMC8511960 DOI: 10.1016/j.jbc.2021.101142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/23/2022] Open
Abstract
Cytochrome P450 27C1 (P450 27C1) is a retinoid desaturase expressed in the skin that catalyzes the formation of 3,4-dehydroretinoids from all-trans retinoids. Within the skin, retinoids are important regulators of proliferation and differentiation. In vivo, retinoids are bound to cellular retinol-binding proteins (CRBPs) and cellular retinoic acid–binding proteins (CRABPs). Interaction with these binding proteins is a defining characteristic of physiologically relevant enzymes in retinoid metabolism. Previous studies that characterized the catalytic activity of human P450 27C1 utilized a reconstituted in vitro system with free retinoids. However, it was unknown whether P450 27C1 could directly interact with holo-retinoid-binding proteins to receive all-trans retinoid substrates. To assess this, steady-state kinetic assays were conducted with free all-trans retinoids and holo-CRBP-1, holo-CRABP-1, and holo-CRABP-2. For holo-CRBP-1 and holo-CRABP-2, the kcat/Km values either decreased 5-fold or were equal to the respective free retinoid values. The kcat/Km value for holo-CRABP-1, however, decreased ∼65-fold in comparison with reactions with free all-trans retinoic acid. These results suggest that P450 27C1 directly accepts all-trans retinol and retinaldehyde from CRBP-1 and all-trans retinoic acid from CRABP-2, but not from CRABP-1. A difference in substrate channeling between CRABP-1 and CRABP-2 was also supported by isotope dilution experiments. Analysis of retinoid transfer from holo-CRABPs to P450 27C1 suggests that the decrease in kcat observed in steady-state kinetic assays is due to retinoid transfer becoming rate-limiting in the P450 27C1 catalytic cycle. Overall, these results illustrate that, like the CYP26 enzymes involved in retinoic acid metabolism, P450 27C1 interacts with cellular retinoid-binding proteins.
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18
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Corbo JC. Vitamin A 1/A 2 chromophore exchange: Its role in spectral tuning and visual plasticity. Dev Biol 2021; 475:145-155. [PMID: 33684435 DOI: 10.1016/j.ydbio.2021.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023]
Abstract
Vertebrate rod and cone photoreceptors detect light via a specialized organelle called the outer segment. This structure is packed with light-sensitive molecules known as visual pigments that consist of a G-protein-coupled, seven-transmembrane protein known as opsin, and a chromophore prosthetic group, either 11-cis retinal ('A1') or 11-cis 3,4-didehydroretinal ('A2'). The enzyme cyp27c1 converts A1 into A2 in the retinal pigment epithelium. Replacing A1 with A2 in a visual pigment red-shifts its spectral sensitivity and broadens its bandwidth of absorption at the expense of decreased photosensitivity and increased thermal noise. The use of vitamin A2-based visual pigments is strongly associated with the occupation of aquatic habitats in which the ambient light is red-shifted. By modulating the A1/A2 ratio in the retina, an organism can dynamically tune the spectral sensitivity of the visual system to better match the predominant wavelengths of light in its environment. As many as a quarter of all vertebrate species utilize A2, at least during a part of their life cycle or under certain environmental conditions. A2 utilization therefore represents an important and widespread mechanism of sensory plasticity. This review provides an up-to-date account of the A1/A2 chromophore exchange system.
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Affiliation(s)
- Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, United States.
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19
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Everts HB, Akuailou EN. Retinoids in Cutaneous Squamous Cell Carcinoma. Nutrients 2021; 13:E153. [PMID: 33466372 PMCID: PMC7824907 DOI: 10.3390/nu13010153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Animal studies as early as the 1920s suggested that vitamin A deficiency leads to squamous cell metaplasia in numerous epithelial tissues including the skin. However, humans usually die from vitamin A deficiency before cancers have time to develop. A recent long-term cohort study found that high dietary vitamin A reduced the risk of cutaneous squamous cell carcinoma (cSCC). cSCC is a form of nonmelanoma skin cancer that primarily occurs from excess exposure to ultraviolet light B (UVB). These cancers are expensive to treat and can lead to metastasis and death. Oral synthetic retinoids prevent the reoccurrence of cSCC, but side effects limit their use in chemoprevention. Several proteins involved in vitamin A metabolism and signaling are altered in cSCC, which may lead to retinoid resistance. The expression of vitamin A metabolism proteins may also have prognostic value. This article reviews what is known about natural and synthetic retinoids and their metabolism in cSCC.
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Affiliation(s)
- Helen B Everts
- Department of Nutrition and Food Sciences, Texas Woman's University, Denton, TX 76209, USA
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20
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Child SA, Reddish MJ, Glass SM, Goldfarb MH, Barckhausen IR, Guengerich FP. Functional interactions of adrenodoxin with several human mitochondrial cytochrome P450 enzymes. Arch Biochem Biophys 2020; 694:108596. [PMID: 32980349 DOI: 10.1016/j.abb.2020.108596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 12/11/2022]
Abstract
Seven of the 57 human cytochrome P450 (P450) enzymes are mitochondrial and carry out important reactions with steroids and vitamins A and D. These seven P450s utilize an electron transport chain that includes NADPH, NADPH-adrenodoxin reductase (AdR), and adrenodoxin (Adx) instead of the diflavin NADPH-P450 reductase (POR) used by the other P450s in the endoplasmic reticulum. Although numerous studies have been published involving mitochondrial P450 systems, the experimental conditions vary considerably. We compared human Adx and bovine Adx, a commonly used component, and found very similar catalytic activities in reactions catalyzed by human P450s 11B2, 27A1, and 27C1. Binding constants of 6-200 nM were estimated for Adx binding to these P450s using microscale thermophoresis. All P450 catalytic reactions were saturated at 10 μM Adx, and higher concentrations were not inhibitory up to at least 50 μM. Collectively these studies demonstrate the tight binding of Adx (both human and bovine) to AdR and to several mitochondrial P450s and provide guidance for optimization of Adx-dependent P450 reactions.
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Affiliation(s)
- Stella A Child
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Michael J Reddish
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Sarah M Glass
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Margo H Goldfarb
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - Ian R Barckhausen
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States
| | - F Peter Guengerich
- The Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232-0146, United States.
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21
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Yuan YH, Zhou J, Zhang Y, Xu MD, Wu J, Li W, Wu MY, Li DM. Identification of key genes and pathways downstream of the β-catenin-TCF7L1 complex in pancreatic cancer cells using bioinformatics analysis. Oncol Lett 2019; 18:1117-1132. [PMID: 31423172 PMCID: PMC6607041 DOI: 10.3892/ol.2019.10444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 04/15/2019] [Indexed: 12/16/2022] Open
Abstract
As a key component of the Wnt signaling pathway, the β-catenin-transcription factor 7 like 1 (TCF7L1) complex activates transcription and regulates downstream target genes that serve important roles in the pathology of pancreatic cancer. To identify associated key genes and pathways downstream of the β-catenin-TCF7L1 complex in pancreatic cancer cells, the current study used the gene expression profiles GSE57728 and GSE90926 downloaded from the Gene Expression Omnibus. GSE57728 is an array containing information regarding β-catenin knockdown and GSE90926 was developed by high throughput sequencing to provide information regarding TCF7L1 knockdown. Subsequently, differentially expressed genes (DEGs) were sorted separately and the shared 88 DEGs, including 37 upregulated and 51 downregulated genes, were screened. Clustering analysis of these DEGs was performed by heatmap analysis. Functional and pathway enrichment analyses were then performed using FunRich software and Database for Annotation, Visualization and Integrated Discovery, which revealed that the DEGs were predominantly enriched in terms associated with transport, transcription factor activity, and cytokine and chemokine mediated signaling pathway process. A DEG-associated protein-protein interaction (PPI) network, consisting of 58 nodes and 171 edges, was then constructed using Cytoscape software and the 15 genes with top node degrees were selected as the hub genes. Overall survival (OS) analysis of the 88 DEGs was performed and the relevant gene expression datasets were downloaded from The Cancer Genome Atlas. Consequently, three upregulated and seven downregulated genes were identified to be associated with prognosis. Furthermore, high expression levels of five downregulated genes, including CXCL5, CYP27C1, FUBP1, CDK14 and TRIM24, were associated with worse OS. In addition, CDK14 and TRIM24 were revealed as hub genes in the PPI network and both were confirmed to be involved in the Wnt/β-catenin pathway and phosphoinositide 3-kinase/Akt signaling pathway. Promoter analysis was also applied to the five downregulated DEGs associated with prognosis, which revealed that TCF7L1 may serve as a transcription factor of the DEGs. In conclusion, the genes and pathways identified in the current study may provide potential targets for the diagnosis and treatment of pancreatic cancer.
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Affiliation(s)
- Yi-Hang Yuan
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jian Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Yan Zhang
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Meng-Dan Xu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jing Wu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China.,PREMED Key Laboratory for Precision Medicine, Soochow University, Suzhou, Jiangsu 215021, P.R. China.,Comprehensive Cancer Center, Suzhou Xiangcheng People's Hospital, Suzhou, Jiangsu 215000, P.R. China
| | - Meng-Yao Wu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Dao-Ming Li
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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22
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Guengerich FP, Wilkey CJ, Phan TTN. Human cytochrome P450 enzymes bind drugs and other substrates mainly through conformational-selection modes. J Biol Chem 2019; 294:10928-10941. [PMID: 31147443 DOI: 10.1074/jbc.ra119.009305] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/29/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) enzymes are major catalysts involved in the oxidations of most drugs, steroids, carcinogens, fat-soluble vitamins, and natural products. The binding of substrates to some of the 57 human P450s and other mammalian P450s is more complex than a two-state system and has been proposed to involve mechanisms such as multiple ligand occupancy, induced-fit, and conformational-selection. Here, we used kinetic analysis of binding with multiple concentrations of substrates and computational modeling of these data to discern possible binding modes of several human P450s. We observed that P450 2D6 binds its ligand rolapitant in a mechanism involving conformational-selection. P450 4A11 bound the substrate lauric acid via conformational-selection, as did P450 2C8 with palmitic acid. Binding of the steroid progesterone to P450 21A2 was also best described by a conformational-selection model. Hexyl isonicotinate binding to P450 2E1 could be described by either a conformational-selection or an induced-fit model. Simulation of the binding of the ligands midazolam, bromocriptine, testosterone, and ketoconazole to P450 3A4 was consistent with an induced-fit or a conformational-selection model, but the concentration dependence of binding rates for varying both P450 3A4 and midazolam concentrations revealed discordance in the parameters, indicative of conformational-selection. Binding of the P450s 2C8, 2D6, 3A4, 4A11, and 21A2 was best described by conformational-selection, and P450 2E1 appeared to fit either mode. These findings highlight the complexity of human P450-substrate interactions and that conformational-selection is a dominant feature of many of these interactions.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
| | - Clayton J Wilkey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Thanh T N Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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23
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Rendic SP, Peter Guengerich F. Human cytochrome P450 enzymes 5-51 as targets of drugs and natural and environmental compounds: mechanisms, induction, and inhibition - toxic effects and benefits. Drug Metab Rev 2019; 50:256-342. [PMID: 30717606 DOI: 10.1080/03602532.2018.1483401] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytochrome P450 (P450, CYP) enzymes have long been of interest due to their roles in the metabolism of drugs, pesticides, pro-carcinogens, and other xenobiotic chemicals. They have also been of interest due to their very critical roles in the biosynthesis and metabolism of steroids, vitamins, and certain eicosanoids. This review covers the 22 (of the total of 57) human P450s in Families 5-51 and their substrate selectivity. Furthermore, included is information and references regarding inducibility, inhibition, and (in some cases) stimulation by chemicals. We update and discuss important aspects of each of these 22 P450s and questions that remain open.
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Affiliation(s)
| | - F Peter Guengerich
- b Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
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24
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Guengerich FP, Wilkey CJ, Glass SM, Reddish MJ. Conformational selection dominates binding of steroids to human cytochrome P450 17A1. J Biol Chem 2019; 294:10028-10041. [PMID: 31072872 DOI: 10.1074/jbc.ra119.008860] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/06/2019] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 (P450, CYP) enzymes are the major catalysts involved in the oxidation of steroids as well as many other compounds. Their versatility has been explained in part by flexibility of the proteins and complexity of the binding mechanisms. However, whether these proteins bind their substrates via induced fit or conformational selection is not understood. P450 17A1 has a major role in steroidogenesis, catalyzing the two-step oxidations of progesterone and pregnenolone to androstenedione and dehydroepiandrosterone, respectively, via 17α-hydroxy (OH) intermediates. We examined the interaction of P450 17A1 with its steroid substrates by analyzing progress curves (UV-visible spectroscopy), revealing that the rates of binding of any of these substrates decreased with increasing substrate concentration, a hallmark of conformational selection. Further, when the concentration of 17α-OH pregnenolone was held constant and the P450 concentration increased, the binding rate increased, and such opposite patterns are also diagnostic of conformational selection. Kinetic simulation modeling was also more consistent with conformational selection than with an induced-fit mechanism. Cytochrome b 5 partially enhances P450 17A1 lyase activity by altering the P450 17A1 conformation but did not measurably alter the binding of 17α-OH pregnenolone or 17α-OH progesterone, as judged by the apparent Kd and binding kinetics. The P450 17A1 inhibitor abiraterone also bound to P450 17A1 in a multistep manner, and modeling indicated that the selective inhibition of the two P450 17A1 steps by the drug orteronel can be rationalized only by a multiple-conformation model. In conclusion, P450 17A1 binds its steroid substrates via conformational selection.
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Affiliation(s)
- F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Clayton J Wilkey
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Sarah M Glass
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Michael J Reddish
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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25
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Abstract
In honor of the 100th birthday of Dr. Herbert Tabor, JBC's Editor-in-Chief for 40 years, I will review here JBC's extensive coverage of the field of cytochrome P450 (P450) research. Research on the reactions catalyzed by these enzymes was published in JBC before it was even realized that they were P450s, i.e. they have a "pigment" with an absorption maximum at 450 nm. After the P450 pigment discovery, reported in JBC in 1962, the journal proceeded to publish the methods for measuring P450 activities and many seminal findings. Since then, the P450 field has grown extensively, with significant progress in characterizing these enzymes, including structural features, catalytic mechanisms, regulation, and many other aspects of P450 biochemistry. JBC has been the most influential journal in the P450 field. As with many other research areas, Dr. Tabor deserves a great deal of the credit for significantly advancing this burgeoning and important topic of research.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
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26
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Abstract
Enzymes are complex biological catalysts and are critical to life. Most oxidations of chemicals are catalyzed by cytochrome P450 (P450, CYP) enzymes, which generally utilize mixed-function oxidase stoichiometry, utilizing pyridine nucleotides as electron donors: NAD(P)H + O2 + R → NAD(P)+ + RO + H2O (where R is a carbon substrate and RO is an oxidized product). The catalysis of oxidations is largely understood in the context of the heme iron-oxygen complex generally referred to as Compound I, formally FeO3+, whose basis was in peroxidase chemistry. Many X-ray crystal structures of P450s are now available (≥ 822 structures from ≥146 different P450s) and have helped in understanding catalytic specificity. In addition to hydroxylations, P450s catalyze more complex oxidations, including C-C bond formation and cleavage. Enzymes derived from P450s by directed evolution can even catalyze more unusual reactions, e.g. cyclopropanation. Current P450 questions under investigation include the potential role of the intermediate Compound 0 (formally FeIII-O2 -) in catalysis of some reactions, the roles of high- and low-spin forms of Compound I, the mechanism of desaturation, the roles of open and closed structures of P450s in catalysis, the extent of processivity in multi-step oxidations, and the role of the accessory protein cytochrome b 5. More global questions include exactly how structure drives function, prediction of catalysis, and roles of multiple protein conformations.
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Affiliation(s)
- F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
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27
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Sausville LN, Gangadhariah MH, Chiusa M, Mei S, Wei S, Zent R, Luther JM, Shuey MM, Capdevila JH, Falck JR, Guengerich FP, Williams SM, Pozzi A. The Cytochrome P450 Slow Metabolizers CYP2C9*2 and CYP2C9*3 Directly Regulate Tumorigenesis via Reduced Epoxyeicosatrienoic Acid Production. Cancer Res 2018; 78:4865-4877. [PMID: 30012669 PMCID: PMC6125168 DOI: 10.1158/0008-5472.can-17-3977] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/31/2018] [Accepted: 07/11/2018] [Indexed: 01/02/2023]
Abstract
Increased expression of cytochrome P450 CYP2C9, together with elevated levels of its products epoxyeicosatrienoic acids (EET), is associated with aggressiveness in cancer. Cytochrome P450 variants CYP2C9*2 and CYP2C9*3 encode proteins with reduced enzymatic activity, and individuals carrying these variants metabolize drugs more slowly than individuals with wild-type CYP2C9*1, potentially affecting their response to drugs and altering their risk of disease. Although genetic differences in CYP2C9-dependent oxidation of arachidonic acid (AA) have been reported, the roles of CYP2C9*2 and CYP2C9*3 in EET biosynthesis and their relevance to disease are unknown. Here, we report that CYP2C9*2 and CYP2C9*3 metabolize AA less efficiently than CYP2C9*1 and that they play a role in the progression of non-small cell lung cancer (NSCLC) via impaired EET biosynthesis. When injected into mice, NSCLC cells expressing CYP2C9*2 and CYP2C9*3 produced lower levels of EETs and developed fewer, smaller, and less vascularized tumors than cells expressing CYP2C9*1. Moreover, endothelial cells expressing these two variants proliferated and migrated less than cells expressing CYP2C*1. Purified CYP2C9*2 and CYP2C9*3 exhibited attenuated catalytic efficiency in producing EETs, primarily due to impaired reduction of these two variants by NADPH-P450 reductase. Loss-of-function SNPs within CYP2C9*2 and CYP2C9*3 were associated with improved survival in female cases of NSCLC. Thus, decreased EET biosynthesis represents a novel mechanism whereby CYPC29*2 and CYP2C9*3 exert a direct protective role in NSCLC development.Significance: These findings report single nucleotide polymorphisms in the human CYP2C9 genes, CYP2C9*2 and CYP2C9*3, exert a direct protective role in tumorigenesis by impairing EET biosynthesis. Cancer Res; 78(17); 4865-77. ©2018 AACR.
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Affiliation(s)
- Lindsay N Sausville
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Mahesha H Gangadhariah
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathobiology, Cleveland Clinic, Cleveland, Ohio
| | - Manuel Chiusa
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shaojun Mei
- Diabetes Research and Training Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shouzuo Wei
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Roy Zent
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Veterans Affairs Hospital, Nashville, Tennessee
| | - James M Luther
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Megan M Shuey
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jorge H Capdevila
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John R Falck
- Division of Chemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ambra Pozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
- Veterans Affairs Hospital, Nashville, Tennessee
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28
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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29
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Kakimoto K, Murayama N, Takenaka S, Nagayoshi H, Lim YR, Kim V, Kim D, Yamazaki H, Komori M, Guengerich FP, Shimada T. Cytochrome P450 2A6 and other human P450 enzymes in the oxidation of flavone and flavanone. Xenobiotica 2018; 49:131-142. [PMID: 29310511 DOI: 10.1080/00498254.2018.1426133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
1. We previously reported that flavone and flavanone interact spectrally with cytochrome P450 (P450 or CYP) 2A6 and 2A13 and other human P450s and inhibit catalytic activities of these P450 enzymes. In this study, we studied abilities of CYP1A1, 1A2, 1B1, 2A6, 2A13, 2C9 and 3A4 to oxidize flavone and flavanone. 2. Human P450s oxidized flavone to 6- and 5-hydroxylated flavones, seven uncharacterized mono-hydroxylated flavones, and five di-hydroxylated flavones. CYP2A6 was most active in forming 6-hydroxy- and 5-hydroxyflavones and several mono- and di-hydroxylated products. 3. CYP2A6 was also very active in catalyzing flavanone to form 2'- and 6-hydroxyflavanones, the major products, at turnover rates of 4.8 min-1 and 1.3 min-1, respectively. Other flavanone metabolites were 4'-, 3'- and 7-hydroxyflavanone, three uncharacterized mono-hydroxylated flavanones and five mono-hydroxylated flavones, including 6-hydroxyflavone. CYP2A6 catalyzed flavanone to produce flavone at a turnover rate of 0.72 min-1 that was ∼3-fold higher than that catalyzed by CYP2A13 (0.29 min-1). 4. These results indicate that CYP2A6 and other human P450s have important roles in metabolizing flavone and flavanone, two unsubstituted flavonoids, present in dietary foods. Chemical mechanisms of P450-catalyzed desaturation of flavanone to form flavone are discussed.
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Affiliation(s)
- Kensaku Kakimoto
- a Osaka Institute of Public Health , Higashinari-ku , Osaka , Japan
| | - Norie Murayama
- b Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University , Machida , Tokyo , Japan
| | - Shigeo Takenaka
- c Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University , Habikino , Osaka , Japan
| | - Haruna Nagayoshi
- a Osaka Institute of Public Health , Higashinari-ku , Osaka , Japan
| | - Young-Ran Lim
- d Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Vitchan Kim
- d Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Donghak Kim
- d Department of Biological Sciences , Konkuk University , Seoul , Korea
| | - Hiroshi Yamazaki
- b Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University , Machida , Tokyo , Japan
| | - Masayuki Komori
- e Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan , and
| | - F Peter Guengerich
- f Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
| | - Tsutomu Shimada
- e Laboratory of Cellular and Molecular Biology, Veterinary Sciences, Osaka Prefecture University , Izumisano , Osaka , Japan , and
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