1
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Uno Y, Shimizu M, Yamazaki H. A variety of cytochrome P450 enzymes and flavin-containing monooxygenases in dogs and pigs commonly used as preclinical animal models. Biochem Pharmacol 2024:116124. [PMID: 38490520 DOI: 10.1016/j.bcp.2024.116124] [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: 01/16/2024] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Drug oxygenation is mainly mediated by cytochromes P450 (P450s, CYPs) and flavin-containing monooxygenases (FMOs). Polymorphic variants of P450s and FMOs are known to influence drug metabolism. Species differences exist in terms of drug metabolism and can be important when determining the contributions of individual enzymes. The success of research into drug-metabolizing enzymes and their impacts on drug discovery and development has been remarkable. Dogs and pigs are often used as preclinical animal models. This research update provides information on P450 and FMO enzymes in dogs and pigs and makes comparisons with their human enzymes. Newly identified dog CYP3A98, a testosterone 6β- and estradiol 16α-hydroxylase, is abundantly expressed in small intestine and is likely the major CYP3A enzyme in small intestine, whereas dog CYP3A12 is the major CYP3A enzyme in liver. The roles of recently identified dog CYP2J2 and pig CYP2J33/34/35 were investigated. FMOs have been characterized in humans and several other species including dogs and pigs. P450 and FMO family members have been characterized also in cynomolgus macaques and common marmosets. P450s have industrial applications and have been the focus of attention of many pharmaceutical companies. The techniques used to investigate the roles of P450/FMO enzymes in drug oxidation and clinical treatments have not yet reached maturity and require further development. The findings summarized here provide a foundation for understanding individual pharmacokinetic and toxicological results in dogs and pigs as preclinical models and will help to further support understanding of the molecular mechanisms of human P450/FMO functionality.
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Affiliation(s)
- Yasuhiro Uno
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-city, Kagoshima 890-0065, Japan
| | - Makiko Shimizu
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Hiroshi Yamazaki
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan.
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2
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Uno Y, Makiguchi M, Ushirozako G, Tsukiyama-Kohara K, Shimizu M, Yamazaki H. Molecular and functional characterization of flavin-containing monooxygenases (FMO1-6) in tree shrews. Comp Biochem Physiol C Toxicol Pharmacol 2024; 277:109835. [PMID: 38215804 DOI: 10.1016/j.cbpc.2024.109835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/08/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024]
Abstract
Flavin-containing monooxygenases (FMOs) are a family of important drug oxygenation enzymes that, in humans, consist of five functional enzymes (FMO1-5) and a pseudogene (FMO6P). The tree shrew is a non-rodent primate-like species that is used in various biomedical studies, but its usefulness in drug metabolism research has not yet been investigated. In this study, tree shrew FMO1-6 cDNAs were isolated and characterized by sequence analysis, tissue expression, and metabolic function. Compared with human FMOs, tree shrew FMOs showed sequence identities of 85-90 % and 81-89 %, respectively, for cDNA and amino acids. Phylogenetic analysis showed that each tree shrew and human FMO were closely clustered. The genomic and genetic structures of the FMO genes were conserved in tree shrews and humans. Among the five tissue types analyzed (lung, heart, kidney, small intestine, and liver), FMO3 and FMO1 mRNAs were most abundant in liver and kidney, respectively. Recombinant tree shrew FMO1-6 proteins expressed in bacterial membranes all mediated benzydamine and trimethylamine N-oxygenations and methyl p-tolyl sulfide S-oxygenation. The selective human FMO3 substrate trimethylamine was predominantly metabolized by tree shrew FMO3. Additionally, tree shrew FMO6 was active toward trimethylamine, as is cynomolgus macaque FMO6, in contrast with the absence of activity of the human FMO6P pseudogene product. Tree shrew FMO1-6, which are orthologous to human FMOs (FMO1-5 and FMO6P) were identified, and tree shrew FMO3 has functional and molecular features generally comparable to those of human FMO3 as the predominant FMO in liver.
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Affiliation(s)
- Yasuhiro Uno
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-city, Kagoshima 890-0065, Japan.
| | - Miaki Makiguchi
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Genki Ushirozako
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-city, Kagoshima 890-0065, Japan
| | - Kyoko Tsukiyama-Kohara
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima-city, Kagoshima 890-0065, Japan
| | - Makiko Shimizu
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan.
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3
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A resource for integrated genomic analysis of the human liver. Sci Rep 2022; 12:15151. [PMID: 36071064 PMCID: PMC9452507 DOI: 10.1038/s41598-022-18506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we generated whole-transcriptome RNA-Seq from n = 192 genotyped liver samples and used these data with existing data from the GTEx Project (RNA-Seq) and previous liver eQTL (microarray) studies to create an enhanced transcriptomic sequence resource in the human liver. Analyses of genotype-expression associations show pronounced enrichment of associations with genes of drug response. The associations are primarily consistent across the two RNA-Seq datasets, with some modest variation, indicating the importance of obtaining multiple datasets to produce a robust resource. We further used an empirical Bayesian model to compare eQTL patterns in liver and an additional 20 GTEx tissues, finding that MHC genes, and especially class II genes, are enriched for liver-specific eQTL patterns. To illustrate the utility of the resource to augment GWAS analysis with small sample sizes, we developed a novel meta-analysis technique to combine several liver eQTL data sources. We also illustrate its application using a transcriptome-enhanced re-analysis of a study of neutropenia in pancreatic cancer patients. The associations of genotype with liver expression, including splice variation and its genetic associations, are made available in a searchable genome browser.
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4
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Xu H, Zhen Q, Bai M, Fang L, Zhang Y, Li B, Ge H, Moon S, Chen W, Fu W, Xu Q, Zhou Y, Yu Y, Lin L, Yong L, Zhang T, Chen S, Liu S, Zhang H, Chen R, Cao L, Zhang Y, Zhang R, Yang H, Hu X, Akey JM, Jin X, Sun L. Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals. Genome Res 2021; 31:1150-1158. [PMID: 34155038 PMCID: PMC8256863 DOI: 10.1101/gr.267963.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 05/10/2021] [Indexed: 12/30/2022]
Abstract
Protein-truncating variants (PTVs) have important impacts on phenotype diversity and disease. However, their population genetics characteristics in more globally diverse populations are not well defined. Here, we describe patterns of PTVs in 1320 genes sequenced in 10,539 healthy controls and 9434 patients with psoriasis, all of Han Chinese ancestry. We identify 8720 PTVs, of which 77% are novel, and estimate 88% of all PTVs are deleterious and subject to purifying selection. Furthermore, we show that individuals with psoriasis have a significantly higher burden of PTVs compared to controls (P = 0.02). Finally, we identified 18 PTVs in 14 genes with unusually high levels of population differentiation, consistent with the action of local adaptation. Our study provides insights into patterns and consequences of PTVs.
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Affiliation(s)
- Huixin Xu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Qi Zhen
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Mingzhou Bai
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Lin Fang
- Guangdong Engineering Research Center of Life Sciences Bigdata, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Yong Zhang
- Guangdong Engineering Research Center of Life Sciences Bigdata, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Bao Li
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
| | - Huiyao Ge
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Sunjin Moon
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
| | - Weiwei Chen
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Wenqing Fu
- Microsoft Corporation, Redmond, Washington 98052, USA
| | - Qiongqiong Xu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Yuwen Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yafeng Yu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Long Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Yong
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Tao Zhang
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Shirui Chen
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 510006, Guangdong, China
| | - Hui Zhang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Ruoyan Chen
- The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Lu Cao
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Yuanwei Zhang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Ruixue Zhang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Huanjie Yang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Xia Hu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
| | - Joshua M Akey
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
| | - Xin Jin
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Liangdan Sun
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Anhui, Hefei 230032, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, China
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5
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Schlebusch CM, Sjödin P, Breton G, Günther T, Naidoo T, Hollfelder N, Sjöstrand AE, Xu J, Gattepaille LM, Vicente M, Scofield DG, Malmström H, de Jongh M, Lombard M, Soodyall H, Jakobsson M. Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens. Mol Biol Evol 2021; 37:2944-2954. [PMID: 32697301 PMCID: PMC7530619 DOI: 10.1093/molbev/msaa140] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.
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Affiliation(s)
- Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Stockholm and Uppsala, Sweden
| | - Per Sjödin
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Gwenna Breton
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Thijessen Naidoo
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Stockholm and Uppsala, Sweden
| | - Nina Hollfelder
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Agnes E Sjöstrand
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jingzi Xu
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Lucie M Gattepaille
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Douglas G Scofield
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Michael de Jongh
- Department of Anthropology and Archaeology, University of South Africa, Pretoria, South Africa
| | - Marlize Lombard
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.,Academy of Science of South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Stockholm and Uppsala, Sweden
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6
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Huang S, Howington MB, Dobry CJ, Evans CR, Leiser SF. Flavin-Containing Monooxygenases Are Conserved Regulators of Stress Resistance and Metabolism. Front Cell Dev Biol 2021; 9:630188. [PMID: 33644069 PMCID: PMC7907451 DOI: 10.3389/fcell.2021.630188] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/15/2021] [Indexed: 01/14/2023] Open
Abstract
Flavin-Containing Monooxygenases are conserved xenobiotic-detoxifying enzymes. Recent studies have revealed endogenous functions of FMOs in regulating longevity in Caenorhabditis elegans and in regulating aspects of metabolism in mice. To explore the cellular mechanisms of FMO's endogenous function, here we demonstrate that all five functional mammalian FMOs may play similar endogenous roles to improve resistance to a wide range of toxic stresses in both kidney and liver cells. We further find that stress-activated c-Jun N-terminal kinase activity is enhanced in FMO-overexpressing cells, which may lead to increased survival under stress. Furthermore, FMO expression modulates cellular metabolic activity as measured by mitochondrial respiration, glycolysis, and metabolomics analyses. FMO expression augments mitochondrial respiration and significantly changes central carbon metabolism, including amino acid and energy metabolism pathways. Together, our findings demonstrate an important endogenous role for the FMO family in regulation of cellular stress resistance and major cellular metabolic activities including central carbon metabolism.
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Affiliation(s)
- Shijiao Huang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Marshall B. Howington
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, United States
| | - Craig J. Dobry
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Charles R. Evans
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Scott F. Leiser
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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7
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Carvalho Henriques B, Yang EH, Lapetina D, Carr MS, Yavorskyy V, Hague J, Aitchison KJ. How Can Drug Metabolism and Transporter Genetics Inform Psychotropic Prescribing? Front Genet 2020; 11:491895. [PMID: 33363564 PMCID: PMC7753050 DOI: 10.3389/fgene.2020.491895] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/25/2020] [Indexed: 12/11/2022] Open
Abstract
Many genetic variants in drug metabolizing enzymes and transporters have been shown to be relevant for treating psychiatric disorders. Associations are strong enough to feature on drug labels and for prescribing guidelines based on such data. A range of commercial tests are available; however, there is variability in included genetic variants, methodology, and interpretation. We herein provide relevant background for understanding clinical associations with specific variants, other factors that are relevant to consider when interpreting such data (such as age, gender, drug-drug interactions), and summarize the data relevant to clinical utility of pharmacogenetic testing in psychiatry and the available prescribing guidelines. We also highlight areas for future research focus in this field.
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Affiliation(s)
| | - Esther H. Yang
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Diego Lapetina
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michael S. Carr
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Vasyl Yavorskyy
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Joshua Hague
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Katherine J. Aitchison
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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8
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Ingram CJE, Ekong R, Ansari-Pour N, Bradman N, Swallow DM. Group-based pharmacogenetic prediction: is it feasible and do current NHS England ethnic classifications provide appropriate data? THE PHARMACOGENOMICS JOURNAL 2020; 21:47-59. [PMID: 32683419 DOI: 10.1038/s41397-020-0175-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Inter-individual variation of drug metabolising enzymes (DMEs) leads to variable efficacy of many drugs and even adverse drug responses. Consequently, it would be desirable to test variants of many DMEs before drug treatment. Inter-ethnic differences in frequency mean that the choice of SNPs to test may vary across population groups. Here we examine the utility of testing representative groups as a way of assessing what variants might be tested. We show that publicly available population information is potentially useful for determining loci for pre-treatment genetic testing, and for determining the most prevalent risk haplotypes in defined groups. However, we also show that the NHS England classifications have limitations for grouping for these purposes, in particular for people of African descent. We conclude: (1) genotyping of hospital patients and people from the hospital catchment area confers no advantage over using samples from appropriate existing ethnic group collections or publicly available data, (2) given the current NHS England Black African grouping, a decision as to whether to test, would have to apply to all patients of recent Black African ancestry to cover reported risk alleles and (3) the current scarcity of available genome and drug effect data from Africans is a problem for both testing and treatment decisions.
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Affiliation(s)
- Catherine J E Ingram
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Rosemary Ekong
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK
| | - Neil Bradman
- Henry Stewart Group, 40-41 Museum Street, London, WC1A 1LT, UK
| | - Dallas M Swallow
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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9
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Masuyama Y, Nishikawa M, Yasuda K, Sakaki T, Ikushiro S. Whole-cell dependent biosynthesis of N- and S-oxides using human flavin containing monooxygenases expressing budding yeast. Drug Metab Pharmacokinet 2020; 35:274-280. [PMID: 32305264 DOI: 10.1016/j.dmpk.2020.01.007] [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: 10/24/2019] [Revised: 01/16/2020] [Accepted: 01/27/2020] [Indexed: 10/24/2022]
Abstract
Flavin containing monooxygenases (FMOs) represent one of the predominant types of phase I drug metabolizing enzymes (DMEs), and thus play an important role in the metabolism of xeno- and endobiotics for the generation of their corresponding oxides. These oxides often display biological activities, however they are difficult to study since their chemical or biological synthesis is generally challenging even though only small amounts are required to evaluate their efficacy and safety. Previously, we constructed a DME expression system for cytochrome P450, UDP-glucuronosyltransferase (UGT), and sulfotransferase (SULT) using yeast cells, and successfully produced xenobiotic metabolites in a whole-cell dependent manner. In this study, we developed a heterologous expression system for human FMOs, including FMO1-FMO5, in Saccharomyces cerevisiae and examined its N- and S-oxide productivity. The recombinant yeast cells expressed each of the FMO successfully, and the FMO4 transformant produced N- and S-oxide metabolites at several milligrams per liter within 24 h. This whole-cell dependent biosynthesis enabled the production of N- and S-oxides without the use of the expensive cofactor NADPH. Such novel yeast expression system could be a powerful tool for the production of oxide metabolites.
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Affiliation(s)
- Yuuka Masuyama
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Miyu Nishikawa
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
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10
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Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs. Nat Struct Mol Biol 2019; 27:14-24. [PMID: 31873300 DOI: 10.1038/s41594-019-0347-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/01/2019] [Indexed: 02/02/2023]
Abstract
Flavin-containing monooxygenases (FMOs) are ubiquitous in all domains of life and metabolize a myriad of xenobiotics, including toxins, pesticides and drugs. However, despite their pharmacological importance, structural information remains bereft. To further our understanding behind their biochemistry and diversity, we used ancestral-sequence reconstruction, kinetic and crystallographic techniques to scrutinize three ancient mammalian FMOs: AncFMO2, AncFMO3-6 and AncFMO5. Remarkably, all AncFMOs could be crystallized and were structurally resolved between 2.7- and 3.2-Å resolution. These crystal structures depict the unprecedented topology of mammalian FMOs. Each employs extensive membrane-binding features and intricate substrate-profiling tunnel networks through a conspicuous membrane-adhering insertion. Furthermore, a glutamate-histidine switch is speculated to induce the distinctive Baeyer-Villiger oxidation activity of FMO5. The AncFMOs exhibited catalysis akin to human FMOs and, with sequence identities between 82% and 92%, represent excellent models. Our study demonstrates the power of ancestral-sequence reconstruction as a strategy for the crystallization of proteins.
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Abstract
Flavin-containing monooxygenases (FMOs) catalyze the oxygenation of numerous foreign chemicals. This review considers the roles of FMOs in the metabolism of endogenous substrates and in physiological processes, and focuses on FMOs of human and mouse. Tyramine, phenethylamine, trimethylamine, cysteamine, methionine, lipoic acid and lipoamide have been identified as endogenous or dietary-derived substrates of FMOs in vitro. However, with the exception of trimethylamine, the role of FMOs in the metabolism of these compounds in vivo is unclear. The use, as experimental models, of knockout-mouse lines deficient in various Fmo genes has revealed previously unsuspected roles for FMOs in endogenous metabolic processes. FMO1 has been identified as a novel regulator of energy balance that acts to promote metabolic efficiency, and also as being involved in the biosynthesis of taurine, by catalyzing the S-oxygenation of hypotaurine. FMO5 has been identified as a regulator of metabolic ageing and glucose homeostasis that apparently acts by sensing or responding to gut bacteria. Thus, FMOs do not function only as xenobiotic-metabolizing enzymes and there is a risk that exposure to drugs and environmental chemicals that are substrates or inducers of FMOs would perturb the endogenous functions of these enzymes.
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12
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Phillips IR, Shephard EA. Flavin-containing monooxygenase 3 (FMO3): genetic variants and their consequences for drug metabolism and disease. Xenobiotica 2019; 50:19-33. [DOI: 10.1080/00498254.2019.1643515] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ian R. Phillips
- Research Department of Structural and Molecular Biology, University College London, London, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Elizabeth A. Shephard
- Research Department of Structural and Molecular Biology, University College London, London, UK
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Perez-Paramo YX, Chen G, Ashmore JH, Watson CJW, Nasrin S, Adams-Haduch J, Wang R, Gao YT, Koh WP, Yuan JM, Lazarus P. Nicotine- N'-Oxidation by Flavin Monooxygenase Enzymes. Cancer Epidemiol Biomarkers Prev 2018; 28:311-320. [PMID: 30381441 DOI: 10.1158/1055-9965.epi-18-0669] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/22/2018] [Accepted: 10/04/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The major mode of metabolism of nicotine is by hydroxylation via cytochrome P450 (CYP) 2A6, but it can also undergo glucuronidation by UDP-glucuronosyltransferases and oxidation by flavin monooxygenases (FMO). The goal of this study was to examine the potential importance of FMOs in nicotine metabolism and assess the potential impact of missense polymorphisms in active FMOs on nicotine-N'-oxide (NOX) formation. METHODS Urine samples from 106 current Chinese smokers were analyzed for nicotine metabolites by mass spectrometry. Wild-type FMOs 1-5 and their most prevalent nonsynonymous variants were cloned and overexpressed in HEK293 cells, and were tested in oxidation reactions against nicotine. RESULTS A strong inverse correlation was observed between the ratio of urinary 3'-hydroxycotinine/cotinine, a measure of CYP2A6 activity, and the urinary levels of NOX alone (r = -0.383; P < 0.001) or NOX measured as a ratio of total nicotine metabolites (r = -0.414; P < 0.001) in smokers. In addition to FMO1 and FMO3, the functional FMO2427Q isoform was active against nicotine, whereas FMO4 and FMO5 exhibited low activity against nicotine (K m > 5.0 mmol/L). Significant (P < 0.05) decreases in N'-oxidation activity (V max/K m) were observed for the FMO1I303V, FMO3N61S, FMO3D132H, FMO3V257M, and FMO3E308G variants in vitro when compared with their respective wild-type isoforms; the truncated FMO2Q472stop isoform exhibited no enzyme activity. CONCLUSIONS These data indicate that increases in nicotine-N'-oxidation occur in subjects with deficient CYP2A6 activity, and that several FMO enzymes are active in nicotine-N'-oxidation. IMPACT Several common missense FMO variants are associated with altered enzyme activity against nicotine and may play an important role in nicotine metabolism in low-CYP2A6 activity subjects.
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Affiliation(s)
- Yadira X Perez-Paramo
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Gang Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Joseph H Ashmore
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Christy J W Watson
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Shamema Nasrin
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Jennifer Adams-Haduch
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Woon-Puay Koh
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington.
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Veeravalli S, Karu K, Scott F, Fennema D, Phillips IR, Shephard EA. Effect of Flavin-Containing Monooxygenase Genotype, Mouse Strain, and Gender on Trimethylamine N-oxide Production, Plasma Cholesterol Concentration, and an Index of Atherosclerosis. Drug Metab Dispos 2017; 46:20-25. [PMID: 29070510 PMCID: PMC5733448 DOI: 10.1124/dmd.117.077636] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/19/2017] [Indexed: 11/22/2022] Open
Abstract
The objectives of the study were to determine the contribution, in mice, of members of the flavin-containing monooxygenase (FMO) family to the production of trimethylamine (TMA) N-oxide (TMAO), a potential proatherogenic molecule, and whether under normal dietary conditions differences in TMAO production were associated with changes in plasma cholesterol concentration or with an index of atherosclerosis (Als). Concentrations of urinary TMA and TMAO and plasma cholesterol were measured in 10-week-old male and female C57BL/6J and CD-1 mice and in mouse lines deficient in various Fmo genes (Fmo1−/−, 2−/−, 4−/−, and Fmo5−/−). In female mice most TMA N-oxygenation was catalyzed by FMO3, but in both genders 11%–12% of TMA was converted to TMAO by FMO1. Gender-, Fmo genotype-, and strain-related differences in TMAO production were accompanied by opposite effects on plasma cholesterol concentration. Plasma cholesterol was negatively, but weakly, correlated with TMAO production and urinary TMAO concentration. Fmo genotype had no effect on Als. There was no correlation between Als and either TMAO production or urinary TMAO concentration. Our results indicate that under normal dietary conditions TMAO does not increase plasma cholesterol or act as a proatherogenic molecule.
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Affiliation(s)
- Sunil Veeravalli
- Institute of Structural and Molecular Biology (S.V., F.S., D.F., I.R.P., E.A.S.) and Mass Spectrometry Facility, Department of Chemistry (K.K.), University College London, London, United Kingdom; and School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom (I.R.P.)
| | - Kersti Karu
- Institute of Structural and Molecular Biology (S.V., F.S., D.F., I.R.P., E.A.S.) and Mass Spectrometry Facility, Department of Chemistry (K.K.), University College London, London, United Kingdom; and School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom (I.R.P.)
| | - Flora Scott
- Institute of Structural and Molecular Biology (S.V., F.S., D.F., I.R.P., E.A.S.) and Mass Spectrometry Facility, Department of Chemistry (K.K.), University College London, London, United Kingdom; and School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom (I.R.P.)
| | - Diede Fennema
- Institute of Structural and Molecular Biology (S.V., F.S., D.F., I.R.P., E.A.S.) and Mass Spectrometry Facility, Department of Chemistry (K.K.), University College London, London, United Kingdom; and School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom (I.R.P.)
| | - Ian R Phillips
- Institute of Structural and Molecular Biology (S.V., F.S., D.F., I.R.P., E.A.S.) and Mass Spectrometry Facility, Department of Chemistry (K.K.), University College London, London, United Kingdom; and School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom (I.R.P.)
| | - Elizabeth A Shephard
- Institute of Structural and Molecular Biology (S.V., F.S., D.F., I.R.P., E.A.S.) and Mass Spectrometry Facility, Department of Chemistry (K.K.), University College London, London, United Kingdom; and School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom (I.R.P.)
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Mekonnen E, Bekele E. An ancestral human genetic variant linked to an ancient disease: A novel association of FMO2 polymorphisms with tuberculosis (TB) in Ethiopian populations provides new insight into the differential ethno-geographic distribution of FMO2*1. PLoS One 2017; 12:e0184931. [PMID: 28981537 PMCID: PMC5628799 DOI: 10.1371/journal.pone.0184931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 09/01/2017] [Indexed: 11/19/2022] Open
Abstract
The human FMO2 (flavin-containing monooxygenase 2) gene has been shown to be involved in innate immunity against microbial infections, including tuberculosis (TB), via the modulation of oxidative stress levels. It has also been found to possess a curious loss-of-function mutation (FMO2*1/FMO2*2) that demonstrates a distinctive differentiation in expression, function and ethno-geographic distribution. However, despite evidences of ethnic-specific genetic associations in the inflammatory profile of TB, no studies were done to investigate whether these patterns of variations correlate with evidences for the involvement of FMO2 in antimicrobial immune responses and ethnic differences in the distribution of FMO2 polymorphisms except for some pharmacogenetic data that suggest a potentially deleterious role for the functional variant (FMO2*1). This genetic epidemiological study was designed to investigate whether there is an association between FMO2 polymorphisms and TB, an ancient malady that remains a modern global health concern, in a sub-Saharan Africa setting where there is not only a relatively high co-prevalence of the disease and the ancestral FMO2*1 variant but also where both Mycobcaterium and Homo sapiens are considered to have originated and co-evolved. Blood samples and TB related clinical data were collected from ascertained TB cases and unrelated household controls (n = 292) from 3 different ethnic groups in Ethiopia. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of FMO2.We identified for the first time an association between FMO2 and TB both at the SNP and haplotype level. Two novel SNPs achieved a study-wide significance [chr1:171181877(A), p = 3.15E-07, OR = 4.644 and chr1:171165749(T), p = 3.32E-06, OR = 6.825] while multiple SNPs (22) showed nominal signals. The pattern of association suggested a protective effect of FMO2 against both active and latent TB with distinct genetic variants underlying the TB-progression pathway. The results were robust for population stratification. Haplotype-based tests confirmed the SNP-based results with a single haplotype bearing the ancestral-and-functional FMO2*1 "C" allele ("AGCTCTACAATCCCCTCGTTGCGC") explaining the overall association (haplotype-specific-p = 0.000103). Strikingly, not only was FMO2*1 nominally associated with reduced risk to "Active TB" (p = 0.0118, OR = 0.496) but it also does not co-segregate with the 5'-3' flanking top high-TB-risk alleles. The study provides an evidence for the existence of an evolutionary adaptation to an ancient disease based on an ancestral genetic variant acting in a haplotypic framework in Ethiopian populations.
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Affiliation(s)
- Ephrem Mekonnen
- Department of Microbial, Cellular, Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Health Biotechnology, Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Endashaw Bekele
- Department of Microbial, Cellular, Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
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Phillips IR, Shephard EA. Drug metabolism by flavin-containing monooxygenases of human and mouse. Expert Opin Drug Metab Toxicol 2016; 13:167-181. [PMID: 27678284 DOI: 10.1080/17425255.2017.1239718] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Flavin-containing monooxygenases (FMOs) play an important role in drug metabolism. Areas covered: We focus on the role of FMOs in the metabolism of drugs in human and mouse. We describe FMO genes and proteins of human and mouse; the catalytic mechanism of FMOs and their significance for drug metabolism; differences between FMOs and CYPs; factors contributing to potential underestimation of the contribution of FMOs to drug metabolism; the developmental and tissue-specific expression of FMO genes and differences between human and mouse; and factors that induce or inhibit FMOs. We discuss the contribution of FMOs of human and mouse to the metabolism of drugs and how genetic variation of FMOs affects drug metabolism. Finally, we discuss the utility of animal models for FMO-mediated drug metabolism in humans. Expert opinion: The contribution of FMOs to drug metabolism may be underestimated. As FMOs are not readily induced or inhibited and their reactions are generally detoxifications, the design of drugs that are metabolized predominantly by FMOs offers clinical advantages. Fmo1(-/-),Fmo2(-/-),Fmo4(-/-) mice provide a good animal model for FMO-mediated drug metabolism in humans. Identification of roles for FMO1 and FMO5 in endogenous metabolism has implications for drug therapy and initiates an exciting area of research.
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Affiliation(s)
- Ian R Phillips
- a Institute of Structural and Molecular Biology , University College London , London , UK.,b School of Biological and Chemical Sciences , Queen Mary University of London , London , UK
| | - Elizabeth A Shephard
- a Institute of Structural and Molecular Biology , University College London , London , UK
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17
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Liu T, Lin K. The distribution pattern of genetic variation in the transcript isoforms of the alternatively spliced protein-coding genes in the human genome. MOLECULAR BIOSYSTEMS 2016; 11:1378-88. [PMID: 25820936 DOI: 10.1039/c5mb00132c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
By enabling the transcription of multiple isoforms from the same gene locus, alternative-splicing mechanisms greatly expand the diversity of the human transcriptome and proteome. Currently, the alternatively spliced transcripts from each protein-coding gene locus in the human genome can be classified as either principal or non-principal isoforms, providing that they differ with respect to cross-species conservation or biological features. By mapping the variants from the 1000 Genomes Project onto the coding region of each isoform, an interesting pattern of the genetic variation distributions of the coding regions for these two types of transcript isoforms was revealed on a whole-genome scale: compared with the principal isoform-specific coding regions, the non-principal isoform-specific coding regions are significantly enriched in amino acid-changing variants, particularly those that have a strong impact on protein function and have higher derived allele frequencies, suggesting that non-principal isoform-specific substitutions are less likely to be related to phenotype changes or disease. The results herein can help us better understand the potential consequences of alternatively spliced products from a population perspective.
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Affiliation(s)
- Ting Liu
- College of Life Sciences, Beijing Normal University, No. 19, Xinjiekouwai Street, Haidian District, Beijing, 100875, P. R. China.
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18
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Geier M, Bachler T, Hanlon SP, Eggimann FK, Kittelmann M, Weber H, Lütz S, Wirz B, Winkler M. Human FMO2-based microbial whole-cell catalysts for drug metabolite synthesis. Microb Cell Fact 2015; 14:82. [PMID: 26062974 PMCID: PMC4464233 DOI: 10.1186/s12934-015-0262-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Getting access to authentic human drug metabolites is an important issue during the drug discovery and development process. Employing recombinant microorganisms as whole-cell biocatalysts constitutes an elegant alternative to organic synthesis to produce these compounds. The present work aimed for the generation of an efficient whole-cell catalyst based on the flavin monooxygenase isoform 2 (FMO2), which is part of the human phase I metabolism. RESULTS We show for the first time the functional expression of human FMO2 in E. coli. Truncations of the C-terminal membrane anchor region did not result in soluble FMO2 protein, but had a significant effect on levels of recombinant protein. The FMO2 biocatalysts were employed for substrate screening purposes, revealing trifluoperazine and propranolol as FMO2 substrates. Biomass cultivation on the 100 L scale afforded active catalyst for biotransformations on preparative scale. The whole-cell conversion of trifluoperazine resulted in perfectly selective oxidation to 48 mg (46% yield) of the corresponding N (1)-oxide with a purity >98%. CONCLUSIONS The generated FMO2 whole-cell catalysts are not only useful as screening tool for human metabolites of drug molecules but more importantly also for their chemo- and regioselective preparation on the multi-milligram scale.
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Affiliation(s)
- Martina Geier
- acib GmbH c/o Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
| | - Thorsten Bachler
- acib GmbH c/o Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
| | | | | | | | - Hansjörg Weber
- Institute of Organic Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010, Graz, Austria.
| | | | - Beat Wirz
- F. Hoffmann-La Roche Ltd., 4070, Basel, Switzerland.
| | - Margit Winkler
- acib GmbH c/o Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
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Gonzalez Malagon SG, Melidoni AN, Hernandez D, Omar BA, Houseman L, Veeravalli S, Scott F, Varshavi D, Everett J, Tsuchiya Y, Timms JF, Phillips IR, Shephard EA. The phenotype of a knockout mouse identifies flavin-containing monooxygenase 5 (FMO5) as a regulator of metabolic ageing. Biochem Pharmacol 2015; 96:267-77. [PMID: 26049045 PMCID: PMC4509511 DOI: 10.1016/j.bcp.2015.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/27/2015] [Indexed: 01/15/2023]
Abstract
We report the production and metabolic phenotype of a mouse line in which the Fmo5 gene is disrupted. In comparison with wild-type (WT) mice, Fmo5(-/-) mice exhibit a lean phenotype, which is age-related, becoming apparent after 20 weeks of age. Despite greater food intake, Fmo5(-/-) mice weigh less, store less fat in white adipose tissue (WAT), have lower plasma glucose and cholesterol concentrations and enhanced whole-body energy expenditure, due mostly to increased resting energy expenditure, with no increase in physical activity. An increase in respiratory exchange ratio during the dark phase, the period in which the mice are active, indicates a switch from fat to carbohydrate oxidation. In comparison with WT mice, the rate of fatty acid oxidation in Fmo5(-/-) mice is higher in WAT, which would contribute to depletion of lipid stores in this tissue, and lower in skeletal muscle. Five proteins were down regulated in the liver of Fmo5(-/-) mice: aldolase B, ketohexokinase and cytosolic glycerol 3-phosphate dehydrogenase (GPD1) are involved in glucose or fructose metabolism and GPD1 also in production of glycerol 3-phosphate, a precursor of triglyceride biosynthesis; HMG-CoA synthase 1 is involved in cholesterol biosynthesis; and malic enzyme 1 catalyzes the oxidative decarboxylation of malate to pyruvate, in the process producing NADPH for use in lipid and cholesterol biosynthesis. Down regulation of these proteins provides a potential explanation for the reduced fat deposits and lower plasma cholesterol characteristic of Fmo5(-/-) mice. Our results indicate that disruption of the Fmo5 gene slows metabolic ageing via pleiotropic effects.
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Affiliation(s)
| | - Anna N Melidoni
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Diana Hernandez
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Bilal A Omar
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Lyndsey Houseman
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Sunil Veeravalli
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Flora Scott
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Jeremy Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Yugo Tsuchiya
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - John F Timms
- Women's Cancer, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Ian R Phillips
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Elizabeth A Shephard
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
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Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet 2014; 23:5866-78. [PMID: 24939910 PMCID: PMC4204768 DOI: 10.1093/hmg/ddu309] [Citation(s) in RCA: 320] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. Most of the genes for which we detected peptides were highly conserved. We found peptides for >96% of genes that evolved before bilateria. At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. We identified peptides for just 3% of these genes. We show that many of these genes behave more like non-coding genes than protein-coding genes and suggest that most are unlikely to code for proteins under normal circumstances. We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort.
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Affiliation(s)
| | - David Juan
- Structural Biology and Bioinformatics Programme and
| | - Jose Manuel Rodriguez
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK and
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK and
| | - Jesus Vazquez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and Bioinformatics Programme and, National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain,
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Petersen KE, Prows CA, Martin LJ, Maglo KN. Personalized medicine, availability, and group disparity: an inquiry into how physicians perceive and rate the elements and barriers of personalized medicine. Public Health Genomics 2014; 17:209-20. [PMID: 24852571 DOI: 10.1159/000362359] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/20/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The success of personalized medicine depends on factors influencing the availability and implementation of its new tools to individualize clinical care. However, little is known about physicians' views of the availability of personalized medicine across racial/ethnic groups and the relationship between perceived availability and clinical implementation. This study examines physicians' perceptions of key elements/tools and potential barriers to personalized medicine in connection with their perceptions of the availability of the latter across subpopulations. METHODS Study subjects consisted of physicians recruited from Cincinnati Children's Hospital Medical Center and UC Health. An electronic survey conducted from September 2012 to November 2012 recruited 104 physicians. Wilcoxon rank sum analysis compared groups. RESULTS Physicians were divided about whether personalized medicine contributes to health equality, as 37.4% of them believe that personalized medicine is currently available only for some subpopulations. They also rated the importance of racial/ethnic background almost as high as the importance of genetic information in the delivery of personalized medicine. Actual elements of personalized medicine rated highest include family history, drug-drug interaction alerts in medical records, and biomarker measurements to guide therapy. Costs of gene-based therapies and genetic testing were rated the most significant barriers. The ratings of several elements and barriers were associated with perceived availability of personalized medicine across subpopulations. CONCLUSION While physicians hold differing views about the availability and implementation of personalized medicine, they likewise establish complex relationships between race/ethnicity and personalized medicine that may carry serious implications for its clinical success.
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Affiliation(s)
- Katelin E Petersen
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
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The contribution of common UGT2B10 and CYP2A6 alleles to variation in nicotine glucuronidation among European Americans. Pharmacogenet Genomics 2014; 23:706-16. [PMID: 24192532 DOI: 10.1097/fpc.0000000000000011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND To develop a predictive genetic model of nicotine metabolism. UDP-glucuronosyltransferase-2B10 (UGT2B10) is the primary catalyst of nicotine glucuronidation. MATERIALS AND METHODS The conversion of deuterated (D2)-nicotine to D2-nicotine-glucuronide, D2-cotinine, D2-cotinine-glucuronide, and D2-trans-3'-hydroxycotinine were quantified in 188 European Americans, and the contribution of UGT2B10 genotype to variability in first-pass nicotine glucuronidation assessed, following a procedure previously applied to nicotine C-oxidation. The proportion of total nicotine converted to nicotine-glucuronide [D2-nicotine-glucuronide/(D2-nicotine+D2-nicotine-glucuronide+D2-cotinine+D2-cotinine-glucuronide+D2-trans-3'-hydroxycotinine)] was the primary phenotype. RESULTS The variant, rs61750900T (D67Y) (minor allele frequency=10%), is confirmed to abolish nicotine glucuronidation activity. Another variant, rs112561475G (N397D) (minor allele frequency=2%), is significantly associated with enhanced glucuronidation. rs112561475G is the ancestral allele of a well-conserved amino acid, indicating that the majority of human UGT2B10 alleles are derived hypomorphic alleles. CONCLUSION CYP2A6 and UGT2B10 genotype explain 53% of the variance in oral nicotine glucuronidation in this sample. CYP2A6 and UGT2B10 genetic variants are also significantly associated with undeuterated (D0) nicotine glucuronidation in individuals smoking ad libitum. We find no evidence for further common variation markedly influencing hepatic UGT2B10 expression in European Americans.
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Veeravalli S, Omar BA, Houseman L, Hancock M, Gonzalez Malagon SG, Scott F, Janmohamed A, Phillips IR, Shephard EA. The phenotype of a flavin-containing monooyxgenase knockout mouse implicates the drug-metabolizing enzyme FMO1 as a novel regulator of energy balance. Biochem Pharmacol 2014; 90:88-95. [PMID: 24792439 DOI: 10.1016/j.bcp.2014.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 11/28/2022]
Abstract
Flavin-containing monooxygenases (FMOs) of mammals are thought to be involved exclusively in the metabolism of foreign chemicals. Here, we report the unexpected finding that mice lacking Fmos 1, 2 and 4 exhibit a lean phenotype and, despite similar food intake, weigh less and store less triglyceride in white adipose tissue (WAT) than wild-type mice. This is a consequence of enhanced whole-body energy expenditure, due mostly to increased resting energy expenditure (REE). This is fuelled, in part, by increased fatty acid β-oxidation in skeletal muscle, which would contribute to depletion of lipid stores in WAT. The enhanced energy expenditure is attributed, in part, to an increased capacity for exercise. There is no evidence that the enhanced REE is due to increased adaptive thermogenesis; instead, our results are consistent with the operation in WAT of a futile energy cycle. In contrast to FMO2 and FMO4, FMO1 is highly expressed in metabolic tissues, including liver, kidney, WAT and BAT. This and other evidence implicates FMO1 as underlying the phenotype. The identification of a novel, previously unsuspected, role for FMO1 as a regulator of energy homeostasis establishes, for the first time, a role for a mammalian FMO in endogenous metabolism. Thus, FMO1 can no longer be considered to function exclusively as a xenobiotic-metabolizing enzyme. Consequently, chronic administration of drugs that are substrates for FMO1 would be expected to affect energy homeostasis, via competition for endogenous substrates, and, thus, have important implications for the general health of patients and their response to drug therapy.
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Affiliation(s)
- Sunil Veeravalli
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Bilal A Omar
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Lyndsey Houseman
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Matthew Hancock
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | | | - Flora Scott
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Azara Janmohamed
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Ian R Phillips
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Elizabeth A Shephard
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
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Henderson MC, Siddens LK, Krueger SK, Stevens JF, Kedzie K, Fang WK, Heidelbaugh T, Nguyen P, Chow K, Garst M, Gil D, Williams DE. Flavin-containing monooxygenase S-oxygenation of a series of thioureas and thiones. Toxicol Appl Pharmacol 2014; 278:91-9. [PMID: 24727368 DOI: 10.1016/j.taap.2014.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
Mammalian flavin-containing monooxygenase (FMO) is active towards many drugs with a heteroatom having the properties of a soft nucleophile. Thiocarbamides and thiones are S-oxygenated to the sulfenic acid which can either react with glutathione and initiate a redox-cycle or be oxygenated a second time to the unstable sulfinic acid. In this study, we utilized LC-MS/MS to demonstrate that the oxygenation by hFMO of the thioureas under test terminated at the sulfenic acid. With thiones, hFMO catalyzed the second reaction and the sulfinic acid rapidly lost sulfite to form the corresponding imidazole. Thioureas are often pulmonary toxicants in mammals and, as previously reported by our laboratory, are excellent substrates for hFMO2. This isoform is expressed at high levels in the lung of most mammals, including non-human primates. Genotyping to date indicates that individuals of African (up to 49%) or Hispanic (2-7%) ancestry have at least one allele for functional hFMO2 in lung, but not Caucasians nor Asians. In this study the major metabolite formed by hFMO2 with thioureas from Allergan, Inc. was the sulfenic acid that reacted with glutathione. The majority of thiones were poor substrates for hFMO3, the major form in adult human liver. However, hFMO1, the major isoform expressed in infant and neonatal liver and adult kidney and intestine, readily S-oxygenated thiones under test, with Kms ranging from 7 to 160 μM and turnover numbers of 30-40 min(-1). The product formed was identified by LC-MS/MS as the imidazole. The activities of the mouse and human FMO1 and FMO3 orthologs were in good agreement with the exception of some thiones for which activity was much greater with hFMO1 than mFMO1.
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Affiliation(s)
- Marilyn C Henderson
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331-7301, USA
| | - Lisbeth K Siddens
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331-7301, USA
| | - Sharon K Krueger
- The Linus Pauling Institute, Oregon State University, Corvallis, OR 97331-7301, USA
| | - J Fred Stevens
- The Linus Pauling Institute, Oregon State University, Corvallis, OR 97331-7301, USA; College of Pharmacy, Oregon State University, Corvallis, OR 97331-7301, USA; Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331-7301, USA
| | - Karen Kedzie
- Department of Biological Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - Wenkui K Fang
- Department of Chemical Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - Todd Heidelbaugh
- Department of Chemical Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - Phong Nguyen
- Department of Chemical Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - Ken Chow
- Department of Chemical Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - Michael Garst
- Department of Chemical Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - Daniel Gil
- Department of Biological Sciences, Allergan, Inc., Irvine, CA 92623-9534, USA
| | - David E Williams
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331-7301, USA; The Linus Pauling Institute, Oregon State University, Corvallis, OR 97331-7301, USA; Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331-7301, USA.
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25
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Siddens LK, Krueger SK, Henderson MC, Williams DE. Mammalian flavin-containing monooxygenase (FMO) as a source of hydrogen peroxide. Biochem Pharmacol 2014; 89:141-7. [PMID: 24561181 DOI: 10.1016/j.bcp.2014.02.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/27/2022]
Abstract
Flavin-containing monooxygenase (FMO) oxygenates drugs/xenobiotics containing a soft nucleophile through a C4a hydroperoxy-FAD intermediate. Human FMOs 1, 2 and 3, expressed in Sf9 insect microsomes, released 30-50% of O₂ consumed as H₂O₂ upon addition of NADPH. Addition of substrate had little effect on H₂O₂ production. Two common FMO2 (the major isoform in the lung) genetic polymorphisms, S195L and N413K, were examined for generation of H₂O₂. FMO2 S195L exhibited higher "leakage", producing much greater amounts of H₂O₂, than ancestral FMO2 (FMO2.1) or the N413K variant. S195L was distinct in that H₂O₂ generation was much higher in the absence of substrate. Addition of superoxide dismutase did not impact H₂O₂ release. Catalase did not reduce levels of H₂O₂ with either FMO2.1 or FMO3 but inhibited H₂O₂ generated by FMO2 allelic variants N413K and S195L. These data are consistent with FMO molecular models. S195L resides in the GxGxSG/A NADP(+) binding motif, in which serine is highly conserved (76/89 known FMOs). We hypothesize that FMO, especially allelic variants such as FMO2 S195L, may enhance the toxicity of xenobiotics such as thioureas/thiocarbamides both by generation of sulfenic and sulfinic acid metabolites and enhanced release of reactive oxygen species (ROS) in the form of H₂O₂.
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Affiliation(s)
| | - Sharon K Krueger
- The Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA.
| | | | - David E Williams
- Department of Environmental and Molecular Toxicology, USA; The Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA.
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Bains RK, Kovacevic M, Plaster CA, Tarekegn A, Bekele E, Bradman NN, Thomas MG. Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa. BMC Genet 2013; 14:34. [PMID: 23641907 PMCID: PMC3655848 DOI: 10.1186/1471-2156-14-34] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/25/2013] [Indexed: 12/16/2022] Open
Abstract
Background Cytochrome P450 3A5 (CYP3A5) is an enzyme involved in the metabolism of many therapeutic drugs. CYP3A5 expression levels vary between individuals and populations, and this contributes to adverse clinical outcomes. Variable expression is largely attributed to four alleles, CYP3A5*1 (expresser allele); CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343) (low/non-expresser alleles). Little is known about CYP3A5 variability in Africa, a region with considerable genetic diversity. Here we used a multi-disciplinary approach to characterize CYP3A5 variation in geographically and ethnically diverse populations from in and around Africa, and infer the evolutionary processes that have shaped patterns of diversity in this gene. We genotyped 2538 individuals from 36 diverse populations in and around Africa for common low/non-expresser CYP3A5 alleles, and re-sequenced the CYP3A5 gene in five Ethiopian ethnic groups. We estimated the ages of low/non-expresser CYP3A5 alleles using a linked microsatellite and assuming a step-wise mutation model of evolution. Finally, we examined a hypothesis that CYP3A5 is important in salt retention adaptation by performing correlations with ecological data relating to aridity for the present day, 10,000 and 50,000 years ago. Results We estimate that ~43% of individuals within our African dataset express CYP3A5, which is lower than previous independent estimates for the region. We found significant intra-African variability in CYP3A5 expression phenotypes. Within Africa the highest frequencies of high-activity alleles were observed in equatorial and Niger-Congo speaking populations. Ethiopian allele frequencies were intermediate between those of other sub-Saharan African and non-African groups. Re-sequencing of CYP3A5 identified few additional variants likely to affect CYP3A5 expression. We estimate the ages of CYP3A5*3 as ~76,400 years and CYP3A5*6 as ~218,400 years. Finally we report that global CYP3A5 expression levels correlated significantly with aridity measures for 10,000 [Spearmann’s Rho= −0.465, p=0.004] and 50,000 years ago [Spearmann’s Rho= −0.379, p=0.02]. Conclusions Significant intra-African diversity at the CYP3A5 gene is likely to contribute to multiple pharmacogenetic profiles across the continent. Significant correlations between CYP3A5 expression phenotypes and aridity data are consistent with a hypothesis that the enzyme is important in salt-retention adaptation.
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Affiliation(s)
- Ripudaman K Bains
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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27
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Palmer AL, Leykam VL, Larkin A, Krueger SK, Phillips IR, Shephard EA, Williams DE. Metabolism and pharmacokinetics of the anti-tuberculosis drug ethionamide in a flavin-containing monooxygenase null mouse. Pharmaceuticals (Basel) 2012; 5:1147-59. [PMID: 23580869 PMCID: PMC3621790 DOI: 10.3390/ph5111147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/08/2012] [Accepted: 10/16/2012] [Indexed: 11/16/2022] Open
Abstract
Multiple drug resistance (MDR) in Mycobacterium tuberculosis (mTB), the causative agent for tuberculosis (TB), has led to increased use of second-line drugs, including ethionamide (ETA). ETA is a prodrug bioactivated by mycobacterial and mammalian flavin-containing monooxygenases (FMOs). FMO2 is the major isoform in the lungs of most mammals, including primates. In humans a polymorphism exists in the expression of FMO2. FMO2.2 (truncated, inactive) protein is produced by the common allele, while the ancestral allele, encoding active FMO2.1, has been documented only in individuals of African and Hispanic origin, at an incidence of up to 50% and 7%, respectively. We hypothesized that FMO2 variability in TB-infected individuals would yield differences in concentrations and ratios of ETA prodrug and metabolites. In this study we assessed the impact of the FMO2 genetic polymorphism on the pharmacokinetics of ETA after administration of a single oral dose of ETA (125 mg/kg) to wild type and triple Fmo1/2/4-null mice, measuring levels of prodrug vs. metabolites in plasma collected from 0 to 3.5 h post-gavage. All mice metabolized ETA to ETA S-oxide (ETASO) and 2-ethyl-4-amidopyridine (ETAA). Wild type mice had higher plasma concentrations of metabolites than of parent compound (p = 0.001). In contrast, Fmo1/2/4-null mice had higher plasma concentrations of parent compound than of metabolites (p = 0.0001). Thus, the human FMO2 genotype could impact the therapeutic efficacy and/or toxicity of ETA.
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Affiliation(s)
- Amy L. Palmer
- Department of Environmental and Molecular Toxicology, Oregon State University, 1007 ALS Corvallis, OR 97331, USA; (A.L.P.); (V.L.L.); (A.L.)
| | - Virginia L. Leykam
- Department of Environmental and Molecular Toxicology, Oregon State University, 1007 ALS Corvallis, OR 97331, USA; (A.L.P.); (V.L.L.); (A.L.)
| | - Andrew Larkin
- Department of Environmental and Molecular Toxicology, Oregon State University, 1007 ALS Corvallis, OR 97331, USA; (A.L.P.); (V.L.L.); (A.L.)
| | - Sharon K. Krueger
- Linus Pauling Institute, Oregon State University, 307 Linus Pauling Institute Corvallis, OR 97331, USA;
| | - Ian R. Phillips
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK;
| | - Elizabeth A. Shephard
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK;
| | - David E. Williams
- Department of Environmental and Molecular Toxicology, Oregon State University, 1007 ALS Corvallis, OR 97331, USA; (A.L.P.); (V.L.L.); (A.L.)
- Linus Pauling Institute, Oregon State University, 307 Linus Pauling Institute Corvallis, OR 97331, USA;
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Prediction of sites under adaptive evolution in flavin-containing monooxygenases: Selection pattern revisited. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4380-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Horsfall LJ, Zeitlyn D, Tarekegn A, Bekele E, Thomas MG, Bradman N, Swallow DM. Prevalence of clinically relevant UGT1A alleles and haplotypes in African populations. Ann Hum Genet 2011; 75:236-46. [PMID: 21309756 DOI: 10.1111/j.1469-1809.2010.00638.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Variation of a short (TA)(n) repeat sequence (rs8175347) covering the TATA box of UGT1A1 (UDP-glucuronosyltransferase1A1) is associated with hyperbilirubinaemia (Gilbert's syndrome) and adverse drug reactions, and is used for dosage advice for irinotecan. Several reports indicate that the low-activity (risk) alleles ((TA)(7) and (TA)(8) )) are very frequent in Africans but the patterns of association with other variants in the UGT1A gene complex that may modulate these responses are not well known. rs8175347 and two other clinically relevant UGT1A variants (rs11692021 and rs10929302) were assayed in 2616 people from Europe and Africa. Low-activity (TA)(n) alleles frequencies were highest in equatorial Africa, (TA)(7,) being the most common in Cameroon, Ghana, southern Sudan, and in Ethiopian Anuak. Haplotypic diversity was also greatest in equatorial Africa, but in Ethiopia was very variable across ethnic groups. Resequencing of the promoter of a sample subset revealed no novel variations, but rs34547608 and rs887829 were typed and shown to be tightly associated with (TA)(n) . Our results illustrate the need for investigation of the effect of UGT1A variants other than (TA)(n) on the risk of irinotecan toxicity, as well as hyperbilirubinaemia due to hemolytic anaemia or human immunodeficiency virus protease inhibitors, so that appropriate pharmacogenetic advice can be given.
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Affiliation(s)
- Laura J Horsfall
- Department of Genetics, Evolution and Environment, University College London, Wolfson House, UK
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30
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CYP1A2 is more variable than previously thought: a genomic biography of the gene behind the human drug-metabolizing enzyme. Pharmacogenet Genomics 2010; 20:647-64. [DOI: 10.1097/fpc.0b013e32833e90eb] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Shephard EA, Phillips IR. The potential of knockout mouse lines in defining the role of flavin-containing monooxygenases in drug metabolism. Expert Opin Drug Metab Toxicol 2010; 6:1083-94. [DOI: 10.1517/17425255.2010.503705] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Novick RM, Vezina CM, Elfarra AA. Isoform distinct time-, dose-, and castration-dependent alterations in flavin-containing monooxygenase expression in mouse liver after 2,3,7,8-tetrachlorodibenzo-p-dioxin treatment. Biochem Pharmacol 2009; 79:1345-51. [PMID: 20036217 DOI: 10.1016/j.bcp.2009.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 01/07/2023]
Abstract
Flavin-containing monooxygenase (FMO) expression in male mouse liver is altered after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure or castration. Because TCDD is slowly eliminated from the body, we examined hepatic Fmo mRNA alterations for up to 32 days following 10 or 64 microg/kg TCDD exposure by oral gavage in male C57BL/6J mice. Fmo2 mRNA was significantly induced at 1, 4, and 8 days whereas Fmo3 mRNA was also induced at 32 days relative to controls. Fmo3 mRNA levels exhibited a dose-dependent increase at 4, 8, and 32 days after exposure; Fmo1, Fmo4, and Fmo5 mRNA did not exhibit clear trends. Because castration alone also increased Fmo2, Fmo3, and Fmo4 mRNA we examined the combined effects of castration and TCDD treatment on FMO expression. A greater than additive effect was observed with Fmo2 and Fmo3 mRNA expression. Fmo2 mRNA exhibited a 3-5-fold increase after castration or 10 microg/kg TCDD exposure by oral gavage, whereas an approximately 20-fold increase was observed between the sham-castrated control and castrated TCDD-treated mice. Similarly, treatment with 10 microg/kg TCDD alone increased Fmo3 mRNA 130- and 180-fold in the sham-castrated and castrated mice compared to their controls respectively, whereas, Fmo3 mRNA increased approximately 1900-fold between the sham control and castrated TCDD-treated mice. An increase in hepatic Fmo3 protein in TCDD-treated mice was observed by immunoblotting and assaying methionine S-oxidase activity. Collectively, these results provide evidence for isoform distinct time-, dose-, and castration-dependent effects of TCDD on FMO expression and suggest cross-talk between TCDD and testosterone signal transduction pathways.
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Affiliation(s)
- Rachel M Novick
- Department of Comparative Biosciences and Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI 53706, USA
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Hao DC, Chen SL, Mu J, Xiao PG. Molecular phylogeny, long-term evolution, and functional divergence of flavin-containing monooxygenases. Genetica 2009; 137:173-87. [PMID: 19579011 DOI: 10.1007/s10709-009-9382-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 06/23/2009] [Indexed: 01/21/2023]
Abstract
Flavin-containing monooxygenases (FMOs) metabolize xenobiotic compounds, many of which are clinically important, as well as endogenous substrates as part of a discrete physiological process. The FMO gene family is conserved and ancient with representatives present in all phyla so far examined. However, there is a lack of information regarding the long-term evolution and functional divergence of these proteins. This study represents the first attempt to characterize the long-term evolution followed by the members of this family. Our analysis shows that there is extensive silent divergence at the nucleotide level suggesting that this family has been subject to strong purifying selection at the protein level. Invertebrate FMOs have a polyphyletic origin. The functional divergence of FMOs 1-5 started before the split between amphibians and mammals. The vertebrate FMO5 is more ancestral than other four FMOs. Moreover, the existence of higher levels of codon bias was detected at the N-terminal ends, which can be ascribed to the critical role played by the FAD binding motif in this region. Finally, critical amino acid residues for FMO functional divergence (type I & II) after gene duplication were detected and characterized.
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Affiliation(s)
- Da Cheng Hao
- Laboratory of Biotechnology, Dalian Jiaotong University, 116028 Dalian, China.
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Krueger SK, Henderson MC, Siddens LK, VanDyke JE, Benninghoff AD, Karplus PA, Furnes B, Schlenk D, Williams DE. Characterization of sulfoxygenation and structural implications of human flavin-containing monooxygenase isoform 2 (FMO2.1) variants S195L and N413K. Drug Metab Dispos 2009; 37:1785-91. [PMID: 19420133 DOI: 10.1124/dmd.109.027201] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Catalytically active human flavin-containing monooxygenase isoform 2 (FMO2.1) is encoded by an allele detected only in individuals of African or Hispanic origin. Genotyping and haplotyping studies indicate that S195L and N413K occasionally occur secondary to the functional FMO2*1 allele encoding reference protein Gln472. Sulfoxygenation under a range of conditions reveals the role these alterations may play in individuals expressing active FMO2 and provides insight into FMO structure. Expressed S195L lost rather than gained activity as pH was increased or when cholate was present. The activity of S195L was mostly eliminated after heating at 45 degrees C for 5 min in the absence of NADPH, but activity was preserved if NADPH was present. By contrast, Gln472 was less sensitive to heat, a response not affected by NADPH. A major consequence of the S195L mutation was a mean 12-fold increase in K(m) for NADPH compared with Gln472. Modeling an S213L substitution, the equivalent site, in the structural model of FMO from the Methylophaga bacterium leads to disruption of interactions with NADP(+). N413K had the same pattern of activity as Gln472 in response to pH, cholate, and magnesium, but product formation was always elevated by comparison. N413K also lost more activity when heated than Gln472; however, NADPH attenuated this loss. The major effects of N413K were increases in velocity and k(cat) compared with Gln472. Although these allelic variants are expected to occur infrequently as mutations to the FMO2*1 allele, they contribute to our overall understanding of mammalian FMO structure and function.
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Affiliation(s)
- Sharon K Krueger
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA.
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35
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Deletion of the mouse Fmo1 gene results in enhanced pharmacological behavioural responses to imipramine. Pharmacogenet Genomics 2009; 19:289-99. [DOI: 10.1097/fpc.0b013e328328d507] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Yngvadottir B, Xue Y, Searle S, Hunt S, Delgado M, Morrison J, Whittaker P, Deloukas P, Tyler-Smith C. A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs. Am J Hum Genet 2009; 84:224-34. [PMID: 19200524 DOI: 10.1016/j.ajhg.2009.01.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 01/10/2009] [Accepted: 01/14/2009] [Indexed: 12/17/2022] Open
Abstract
Nonsense SNPs introduce premature termination codons into genes and can result in the absence of a gene product or in a truncated and potentially harmful protein, so they are often considered disadvantageous and are associated with disease susceptibility. As such, we might expect the disrupted allele to be rare and, in healthy people, observed only in a heterozygous state. However, some, like those in the CASP12 and ACTN3 genes, are known to be present at high frequencies and to occur often in a homozygous state and seem to have been advantageous in recent human evolution. To evaluate the selective forces acting on nonsense SNPs as a class, we have carried out a large-scale experimental survey of nonsense SNPs in the human genome by genotyping 805 of them (plus control synonymous SNPs) in 1,151 individuals from 56 worldwide populations. We identified 169 genes containing nonsense SNPs that were variable in our samples, of which 99 were found with both copies inactivated in at least one individual. We found that the sampled humans differ on average by 24 genes (out of about 20,000) because of these nonsense SNPs alone. As might be expected, nonsense SNPs as a class were found to be slightly disadvantageous over evolutionary timescales, but a few nevertheless showed signs of being possibly advantageous, as indicated by unusually high levels of population differentiation, long haplotypes, and/or high frequencies of derived alleles. This study underlines the extent of variation in gene content within humans and emphasizes the importance of understanding this type of variation.
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Murphy EL, Murtagh FEM, Carey I, Sheerin NS. Understanding symptoms in patients with advanced chronic kidney disease managed without dialysis: use of a short patient-completed assessment tool. Nephron Clin Pract 2008; 111:c74-80. [PMID: 19088482 DOI: 10.1159/000183177] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 09/12/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND It is often believed that patients with advanced chronic kidney disease (CKD) stage 4-5 have few symptoms, and that dying with renal disease is relatively symptom-free. But the symptom burden of patients managed conservatively (without dialysis), with potentially high levels of comorbidity and poor functional status, is unknown. This clinical audit evaluated the prevalence and severity of symptoms in conservatively managed CKD stage 4-5 patients. METHODS Symptom data was collected from all conservatively managed patients from 2 renal units referred to a new renal palliative care service over a 10-month period between April 2005 and January 2006. Data on symptom prevalence and severity was collected as part of their routine clinical care, using a modified version of the Patient Outcome Scale--symptom module (POSs). This patient-completed instrument identifies the presence and severity of 17 symptoms. Demographic data was also collected, including estimated glomerular filtration rate (eGFR) using the MDRD formula, primary renal diagnosis and comorbidity. RESULTS Symptoms were evaluated in 55 patients, with a mean age of 82 years (SD 5.5, range 66-96). eGFR ranged from 3 to 30 ml/min (median 11, mean 12.75). In patients with CKD stage 4-5, managed without dialysis, the symptom burden is high. The most prevalent symptoms reported were weakness (75%), poor mobility (75%), poor appetite (58%), pain (56%), pruritus (56%) and dyspnoea (49%). The total number of symptoms each individual patient experienced ranged from 1 to 14 (median 7, mean 6.8). Symptoms were frequently reported as moderate, severe, or overwhelming; in 54% of patients with poor mobility, 48% with weakness, 30% with itching, 31% with anorexia and 27% with pain. No significant association was demonstrated between the number of symptoms experienced and either severity of renal disease or comorbidity score. CONCLUSIONS This structured clinical evaluation demonstrates the extent and severity of symptom burden in conservatively managed patients with CKD stage 4-5, and demonstrates the use of an appropriate clinical tool that can be used to assess the efficacy of treatment.
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Affiliation(s)
- Emma L Murphy
- Florence Nightingale School of Nursing and Midwifery, King's College London, London, UK.
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Francois AA, Nishida CR, de Montellano PRO, Phillips IR, Shephard EA. Human flavin-containing monooxygenase 2.1 catalyzes oxygenation of the antitubercular drugs thiacetazone and ethionamide. Drug Metab Dispos 2008; 37:178-86. [PMID: 18948378 DOI: 10.1124/dmd.108.024158] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The second-line antitubercular drugs thiacetazone (TAZ) and ethionamide (ETA) are bioactivated by the mycobacterial enzyme EtaA. We report here that human flavin-containing monooxygenase 2.1 (FMO2.1), which is expressed predominantly in the lung, catalyzes oxygenation of TAZ. The metabolites generated, the sulfenic acid, sulfinic acid, and carbodiimide derivatives, are the same as those produced by EtaA and human FMO1 and FMO3. Two of the metabolites, the sulfenic acid and carbodiimide, are known to be harmful to mammalian cells. FMO2.1 also catalyzes oxygenation of ETA, producing the S-oxide. We have developed a novel spectrophotometric assay for TAZ oxygenation. The assay was used to determine kinetic parameters for TAZ oxygenation catalyzed by human FMO1, FMO2.1, and FMO3 and by EtaA. Although the K(M) values for the four enzyme-catalyzed reactions are similar, k(cat) and, consequently, k(cat)/K(M) (the specificity constant) for FMO2.1-catalyzed TAZ oxygenation are much higher than those of FMO1, FMO3, or EtaA. This indicates that FMO2.1 is more effective in catalyzing TAZ oxygenation than are the other three enzymes and thus is likely to contribute substantially to the metabolism of TAZ, decreasing the availability of the prodrug to mycobacteria and producing toxic metabolites. Because of a genetic polymorphism, Europeans and Asians lack FMO2.1. However, in sub-Saharan Africa, a region in which tuberculosis is a major health problem, a substantial proportion of individuals express FMO2.1. Thus, our results may explain some of the observed interindividual differences in response to TAZ and ETA and have implications for the treatment of tuberculosis in sub-Saharan Africa.
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Affiliation(s)
- Asvi A Francois
- Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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