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Vasilogianni AM, Alrubia S, El-Khateeb E, Al-Majdoub ZM, Couto N, Achour B, Rostami-Hodjegan A, Barber J. Complementarity of two proteomic data analysis tools in the identification of drug-metabolising enzymes and transporters in human liver. Mol Omics 2024; 20:115-127. [PMID: 37975521 DOI: 10.1039/d3mo00144j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Several software packages are available for the analysis of proteomic LC-MS/MS data, including commercial (e.g. Mascot/Progenesis LC-MS) and open access software (e.g. MaxQuant). In this study, Progenesis and MaxQuant were used to analyse the same data set from human liver microsomes (n = 23). Comparison focussed on the total number of peptides and proteins identified by the two packages. For the peptides exclusively identified by each software package, distribution of peptide length, hydrophobicity, molecular weight, isoelectric point and score were compared. Using standard cut-off peptide scores, we found an average of only 65% overlap in detected peptides, with surprisingly little consistency in the characteristics of peptides exclusively detected by each package. Generally, MaxQuant detected more peptides than Progenesis, and the additional peptides were longer and had relatively lower scores. Progenesis-specific peptides tended to be more hydrophilic and basic relative to peptides detected only by MaxQuant. At the protein level, we focussed on drug-metabolising enzymes (DMEs) and transporters, by comparing the number of unique peptides detected by the two packages for these specific proteins of interest, and their abundance. The abundance of DMEs and SLC transporters showed good correlation between the two software tools, but ABC showed less consistency. In conclusion, in order to maximise the use of MS datasets, we recommend processing with more than one software package. Together, Progenesis and MaxQuant provided excellent coverage, with a core of common peptides identified in a very robust way.
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Affiliation(s)
- Areti-Maria Vasilogianni
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
- DMPK, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Sarah Alrubia
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
- Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Eman El-Khateeb
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
- Clinical Pharmacy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
- Certara Inc (Simcyp Division), 1 Concourse Way, Sheffield, UK
| | - Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Narciso Couto
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
| | - Brahim Achour
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
- Certara Inc (Simcyp Division), 1 Concourse Way, Sheffield, UK
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
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Wankaew N, Chariyavilaskul P, Chamnanphon M, Assawapitaksakul A, Chetruengchai W, Pongpanich M, Shotelersuk V. Genotypic and phenotypic landscapes of 51 pharmacogenes derived from whole-genome sequencing in a Thai population. PLoS One 2022; 17:e0263621. [PMID: 35176049 PMCID: PMC8853512 DOI: 10.1371/journal.pone.0263621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/22/2022] [Indexed: 12/30/2022] Open
Abstract
Differences in drug responses in individuals are partly due to genetic variations in pharmacogenes, which differ among populations. Here, genome sequencing of 171 unrelated Thai individuals from all regions of Thailand was used to call star alleles of 51 pharmacogenes by Stargazer, determine allele and genotype frequencies, predict phenotype and compare high-impact variant frequencies between Thai and other populations. Three control genes, EGFR, VDR, and RYR1, were used, giving consistent results. Every individual had at least three genes with variant or altered phenotype. Forty of the 51 pharmacogenes had at least one individual with variant or altered phenotype. Moreover, thirteen genes had at least 25% of individuals with variant or altered phenotype including SLCO1B3 (97.08%), CYP3A5 (88.3%), CYP2C19 (60.82%), CYP2A6 (60.2%), SULT1A1 (56.14%), G6PD (54.39%), CYP4B1 (50.00%), CYP2D6 (48.65%), CYP2F1 (46.41%), NAT2 (40.35%), SLCO2B1 (28.95%), UGT1A1 (28.07%), and SLCO1B1 (26.79%). Allele frequencies of high impact variants from our samples were most similar to East Asian. Remarkably, we identified twenty predicted high impact variants which have not previously been reported. Our results provide information that contributes to the implementation of pharmacogenetic testing in Thailand and other Southeast Asian countries, bringing a step closer to personalized medicine.
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Affiliation(s)
- Natnicha Wankaew
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monpat Chamnanphon
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pathology, Faculty of Medicine, Srinakharinwirot University, Nakornnayok, Thailand
| | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Age-related Inflammation and Degeneration Research Unit, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
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Enlo-Scott Z, Bäckström E, Mudway I, Forbes B. Drug metabolism in the lungs: opportunities for optimising inhaled medicines. Expert Opin Drug Metab Toxicol 2021; 17:611-625. [DOI: 10.1080/17425255.2021.1908262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zachary Enlo-Scott
- Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Erica Bäckström
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ian Mudway
- MRC Centre for Environment and Health, School of Population Health & Environmental Sciences, Imperial College London, London, United Kingdom; National Institute for Health Research, Health Protection Research Units in Chemical and Radiation Threats and Hazards and Environmental Exposures and Health, Imperial College London, London, UK
| | - Ben Forbes
- Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King’s College London, London, UK
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Mortezaei Z, Tavallaei M, Hosseini SM. Considering smoking status, coexpression network analysis of non-small cell lung cancer at different cancer stages, exhibits important genes and pathways. J Cell Biochem 2019; 120:19172-19185. [PMID: 31271232 DOI: 10.1002/jcb.29246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/23/2019] [Indexed: 02/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer among smokers, nonsmokers, women, and young individuals. Tobacco smoking and different stages of the NSCLC have important roles in cancer evolution and require different treatments. Existence of poorly effective therapeutic options for the NSCLC brings special attention to targeted therapies by considering genetic alterations. In this study, we used RNA-Seq data to compare expression levels of RefSeq genes and to find some genes with similar expression levels. We utilized the "Weighted Gene Co-expression Network Analysis" method for three different datasets to create coexpressed genetic modules having relations with the smoking status and different stages of the NSCLC. Our results indicate seven important genetic modules having important associations with the smoking status and cancer stages. Based on investigated genetic modules and their biological explanation, we then identified 13 newly candidate genes and 7 novel transcription factors in association with the NSCLC, the smoking status, and cancer stages. We then examined those results using other datasets and explained our results biologically to illustrate some important genes in relation with the smoking status and metastatic stage of the NSCLC that can bring some crucial information about cancer evolution. Our genetic findings also can be used as some therapeutic targets for different clinical conditions of the NSCLC.
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Affiliation(s)
- Zahra Mortezaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmood Tavallaei
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sayed Mostafa Hosseini
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Boei JJWA, Vermeulen S, Klein B, Hiemstra PS, Verhoosel RM, Jennen DGJ, Lahoz A, Gmuender H, Vrieling H. Xenobiotic metabolism in differentiated human bronchial epithelial cells. Arch Toxicol 2017; 91:2093-2105. [PMID: 27738743 PMCID: PMC5399058 DOI: 10.1007/s00204-016-1868-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/06/2016] [Indexed: 11/30/2022]
Abstract
Differentiated human bronchial epithelial cells in air liquid interface cultures (ALI-PBEC) represent a promising alternative for inhalation studies with rodents as these 3D airway epithelial tissue cultures recapitulate the human airway in multiple aspects, including morphology, cell type composition, gene expression and xenobiotic metabolism. We performed a detailed longitudinal gene expression analysis during the differentiation of submerged primary human bronchial epithelial cells into ALI-PBEC to assess the reproducibility and inter-individual variability of changes in transcriptional activity during this process. We generated ALI-PBEC cultures from four donors and focussed our analysis on the expression levels of 362 genes involved in biotransformation, which are of primary importance for toxicological studies. Expression of various of these genes (e.g., GSTA1, ADH1C, ALDH1A1, CYP2B6, CYP2F1, CYP4B1, CYP4X1 and CYP4Z1) was elevated following the mucociliary differentiation of airway epithelial cells into a pseudo-stratified epithelial layer. Although a substantial number of genes were differentially expressed between donors, the differences in fold changes were generally small. Metabolic activity measurements applying a variety of different cytochrome p450 substrates indicated that epithelial cultures at the early stages of differentiation are incapable of biotransformation. In contrast, mature ALI-PBEC cultures were proficient in the metabolic conversion of a variety of substrates albeit with considerable variation between donors. In summary, our data indicate a distinct increase in biotransformation capacity during differentiation of PBECs at the air-liquid interface and that the generation of biotransformation competent ALI-PBEC cultures is a reproducible process with little variability between cultures derived from four different donors.
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Affiliation(s)
- Jan J. W. A. Boei
- Department of Human Genetics, Leiden University Medical Center, Postal Zone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Sylvia Vermeulen
- Department of Human Genetics, Leiden University Medical Center, Postal Zone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Binie Klein
- Department of Human Genetics, Leiden University Medical Center, Postal Zone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Renate M. Verhoosel
- Department of Pulmonology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Danyel G. J. Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Agustin Lahoz
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria-Fundación Hospital La Fe, 46009 Valencia, Spain
| | | | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Postal Zone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
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Annalora AJ, Marcus CB, Iversen PL. Alternative Splicing in the Cytochrome P450 Superfamily Expands Protein Diversity to Augment Gene Function and Redirect Human Drug Metabolism. Drug Metab Dispos 2017; 45:375-389. [DOI: 10.1124/dmd.116.073254] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
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Bailey LA, Nascarella MA, Kerper LE, Rhomberg LR. Hypothesis-based weight-of-evidence evaluation and risk assessment for naphthalene carcinogenesis. Crit Rev Toxicol 2015; 46:1-42. [PMID: 26202831 PMCID: PMC4732411 DOI: 10.3109/10408444.2015.1061477] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/09/2015] [Indexed: 11/13/2022]
Abstract
Inhalation of naphthalene causes olfactory epithelial nasal tumors in rats (but not in mice) and benign lung adenomas in mice (but not in rats). The limited available human data have not identified an association between naphthalene exposure and increased respiratory cancer risk. Assessing naphthalene's carcinogenicity in humans, therefore, depends entirely on experimental evidence from rodents. We evaluated the respiratory carcinogenicity of naphthalene in rodents, and its potential relevance to humans, using our Hypothesis-Based Weight-of-Evidence (HBWoE) approach. We systematically and comparatively reviewed data relevant to key elements in the hypothesized modes of action (MoA) to determine which is best supported by the available data, allowing all of the data from each realm of investigation to inform interpretation of one another. Our analysis supports a mechanism that involves initial metabolism of naphthalene to the epoxide, followed by GSH depletion, cytotoxicity, chronic inflammation, regenerative hyperplasia, and tumor formation, with possible weak genotoxicity from downstream metabolites occurring only at high cytotoxic doses, strongly supporting a non-mutagenic threshold MoA in the rat nose. We also conducted a dose-response analysis, based on the likely MoA, which suggests that the rat nasal MoA is not relevant in human respiratory tissues at typical environmental exposures. Our analysis illustrates how a thorough WoE evaluation can be used to support a MoA, even when a mechanism of action cannot be fully elucidated. A non-mutagenic threshold MoA for naphthalene-induced rat nasal tumors should be considered as a basis to determine human relevance and to guide regulatory and risk-management decisions.
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De Palma G, Manno M. Metabolic polymorphisms and biomarkers of effect in the biomonitoring of occupational exposure to low-levels of benzene: state of the art. Toxicol Lett 2014; 231:194-204. [PMID: 25447454 DOI: 10.1016/j.toxlet.2014.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/07/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022]
Abstract
Current levels of occupational exposure to benzene, a genotoxic human carcinogen, in Western countries are reduced by two-three orders of magnitude (from ppm to ppb) as compared to the past. However, as benzene toxicity is strongly dependent on biotransformation and recent evidence underlines a higher efficiency of bio-activation pathways at lower levels of exposure, toxic effects at low doses could be higher than expected, particularly in susceptible individuals. Currently, biological monitoring can allow accurate exposure assessment, relying on sensitive and specific enough biomarkers of internal dose. The availability of similarly reliable biomarkers of early effect or susceptibility could greatly improve the risk assessment process to such an extent that risk could even be assessed at the individual level. As to susceptibility biomarkers, functional genetic polymorphisms of relevant biotransformation enzymes may modulate the risk of adverse effects (NQO1) and the levels of biomarkers of internal dose, in particular S-phenylmercapturic acid (GSTM1, GSTT1, GSTA1). Among biomarkers of early effect, genotoxicity indicators, although sensitive in some cases, are too aspecific for routine use in occupational health surveillance programmes. Currently only the periodical blood cell count seems suitable enough to be applied in the longitudinal monitoring of effects from benzene exposure. Novel biomarkers of early effect are expected from higher collaboration among toxicologists and clinicians, also using advanced "omics" techniques.
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Affiliation(s)
- G De Palma
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Section of Public Health and Human Sciences, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy.
| | - M Manno
- Department of Public Health, Section of Occupational Medicine and Toxicology, University of Napoli Federico II, Via S. Pansini, 5, 80131 Napoli, Italy
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Korytina G, Kochetova O, Akhmadishina L, Viktorova E, Victorova T. Polymorphisms of cytochrome p450 genes in three ethnic groups from Russia. Balkan Med J 2012; 29:252-60. [PMID: 25207010 DOI: 10.5152/balkanmedj.2012.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 05/22/2012] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE To determine the prevalence of the most common allelic variants of CYP1A1, CYP1A2, CYP1B1, CYP2C9, CYP2E1, CYP2F1, CYP2J2 and CYP2S1 in a representative sample of the three ethnic groups (Russians, Tatars and Bashkirs) from Republic of Bashkortostan (Russia), and compare the results with existing data published for other populations. MATERIAL AND METHODS CYPs genotypes were determined in 742 DNA samples of healthy unrelated individuals representative of three ethnic groups. The CYPs gene polymorphisms were examined using the PCR-RLFP method. RESULTS Analysis of the CYP1A1 (rs1048943, rs4646903), CYP1A2 (rs762551), CYP2E1 (rs2031920) allele, genotype and haplotype frequencies revealed significant differences among healthy residents of the Republic of Bashkortostan of different ethnicities. Distribution of allele and genotype frequencies of CYP1A2 (rs35694136), CYP1B1 (rs1056836), CYP2C9 (rs1799853, rs1057910), CYP2F1 (rs11399890), CYP2J2 (rs890293), CYP2S1 (rs34971233, rs338583) genes were similar in Russians, Tatars, and Bashkirs. Analysis of the CYPs genes allele frequency distribution patterns among the ethnic groups from the Republic of Bashkortostan in comparison with the different populations worldwide was conducted. CONCLUSION The peculiarities of the allele frequency distribution of CYPs genes in the ethnic groups of the Republic of Bashkortostan should be taken into consideration in association and pharmacogenetic studies. The results of the present investigation will be of great help in elucidating the genetic background of drug response, susceptibility to cancer and complex diseases, as well as in determining the toxic potentials of environmental pollutants in our region.
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Affiliation(s)
- Gülnaz Korytina
- Institute of Biochemistry and Genetics, Genomics, Ufa, Russian Federation
| | - Olga Kochetova
- Institute of Biochemistry and Genetics, Genomics, Ufa, Russian Federation
| | | | - Elena Viktorova
- George-August University of Göttingen, Genomics, Göttingen, Germany
| | - Tatyana Victorova
- Institute of Biochemistry and Genetics, Genomics, Ufa, Russian Federation
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Predicting the effects of frameshifting indels. Genome Biol 2012; 13:R9. [PMID: 22322200 PMCID: PMC3334572 DOI: 10.1186/gb-2012-13-2-r9] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 11/18/2011] [Accepted: 02/09/2012] [Indexed: 02/02/2023] Open
Abstract
Each human has approximately 50 to 280 frameshifting indels, yet their implications are unknown. We created SIFT Indel, a prediction method for frameshifting indels that has 84% accuracy. The percentage of human frameshifting indels predicted to be gene-damaging is negatively correlated with allele frequency. We also show that although the first frameshifting indel in a gene causes loss of function, there is a tendency for the second frameshifting indel to compensate and restore protein function. SIFT Indel is available at http://sift-dna.org/www/SIFT_indels2.html
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Akhmadishina LZ, Korytina GF, Victorova TV. CYP1B1 (4326C > G), CYP2F1 (c.14_15insC), CYP2J2 (−76G > T), and CYP2S1 (13106C > T and 13255A > G) polymorphisms and genetic predisposition to chronic respiratory diseases induced by smoking and occupational factors. RUSS J GENET+ 2011. [DOI: 10.1134/s102279541109002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Leclerc J, Courcot-Ngoubo Ngangue E, Cauffiez C, Allorge D, Pottier N, Lafitte JJ, Debaert M, Jaillard S, Broly F, Lo-Guidice JM. Xenobiotic metabolism and disposition in human lung: transcript profiling in non-tumoral and tumoral tissues. Biochimie 2011; 93:1012-27. [PMID: 21376776 DOI: 10.1016/j.biochi.2011.02.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 02/22/2011] [Indexed: 11/30/2022]
Abstract
The lung is directly exposed to a wide variety of inhaled toxicants and carcinogens. In order to improve our knowledge of the cellular processing of these compounds in the respiratory tract, we investigated the mRNA expression level of 380 genes encoding xenobiotic-metabolizing enzymes (XME), transporters, nuclear receptors and transcription factors, in pulmonary parenchyma (PP), bronchial mucosa (BM) and tumoral lung tissues from 12 patients with non-small cell lung cancer (NSCLC). Using a high throughput quantitative real-time RT-PCR method, we found that ADH1B, CYP4B1, CES1 and GSTP1 are the major XME genes expressed both in BM and PP. Our results also documented the predominant role played by the xenosensor AhR in human lung. The gene expression profiles were different for BM and PP, with a tendency toward increased mRNA levels of phase I and phase II XME genes in BM, suggesting major differences in the initial stages of xenobiotic metabolism. Some of the significantly overexpressed genes in BM (i.e. CYP2F1, CYP2A13, CYP2W1, NQO1…) encode proteins involved in the bioactivation of procarcinogens, pointing out distinct susceptibility to xenobiotics and their toxic effects between these two tissue types. Additionally, interindividual differences in transcript levels observed for some genes may be of genetic origin and may contribute to the variability in response to environmental exposure and, consequently, in the risk of developing lung diseases. A global decrease in gene expression was observed in tumoral specimens. Some of the proteins are involved in the metabolism or transport of anti-cancer drugs and their influence in the response of tumors to chemotherapy should be considered. In conclusion, the present study provides an overview of the cellular response to toxicants and drugs in healthy and cancerous human lung tissues, and thus improves our understanding of the mechanisms of chemical carcinogenesis as well as cellular resistance to chemotherapy.
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Affiliation(s)
- Julie Leclerc
- Equipe d'accueil EA4483, Faculté de Médecine Pôle Recherche, Université Lille Nord de France, 1 Place de Verdun, 59045 Lille, France.
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13
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Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family. J Mol Evol 2010; 72:56-71. [DOI: 10.1007/s00239-010-9402-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 10/25/2010] [Indexed: 01/23/2023]
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Saghir SA, Zhang F, Rick DL, Kan L, Bus JS, Bartels MJ. Authors response to Huff et al., “Clarifying carcinogenicity of ethylbenzene”. Regul Toxicol Pharmacol 2010. [DOI: 10.1016/j.yrtph.2010.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Devos A, Lino Cardenas CL, Glowacki F, Engels A, Lo-Guidice JM, Chevalier D, Allorge D, Broly F, Cauffiez C. Genetic polymorphism of CYP2U1, a cytochrome P450 involved in fatty acids hydroxylation. Prostaglandins Leukot Essent Fatty Acids 2010; 83:105-10. [PMID: 20630735 DOI: 10.1016/j.plefa.2010.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Revised: 06/16/2010] [Accepted: 06/24/2010] [Indexed: 11/25/2022]
Abstract
The human cytochrome P450 2U1 (CYP2U1) has been described as a novel extrahepatic P450. CYP2U1 is a highly conserved gene mainly expressed in brain and thymus, but also at lower levels in kidney, lung or heart. This selective tissue distribution suggests important endogenous functions, in particular in the conversion of arachidonic acid into two bioactive compounds, the 19- and 20-HETE. To investigate the extent of CYP2U1 genetic polymorphism in 70 French individuals, a screening for sequence variations in the 5'-flanking and protein encoding regions was performed using PCR-SSCP and sequencing strategies. Four polymorphisms were identified and correspond to -204C>A and -241T>C in the 5'-flanking region, -37G>A in the 5'-untranslated region, and IVS2-17T>C in the intron 2. The most frequent mutations, -241T>C (59.7%) and IVS2-17T>C (66.0%), did not seem to alter CYP2U1 lung expression. These results suggest that CYP2U1 exhibits few genetic variations and support a probable role in endogenous processes.
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Affiliation(s)
- Aurore Devos
- EA2679, Faculté de Médecine, Pôle Recherche, Université Lille Nord de France, France
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Korytina GF, Akhmadishina LZ, Victorova TV. Frequencies of CYP1B1 and CYP2F1 polymorphic variants in three ethnic groups of Bashkortostan and in patients with chronic obstructive pulmonary disease. Mol Biol 2010; 44:28-32. [DOI: 10.1134/s002689331001005x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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D'Agostino J, Zhuo X, Shadid M, Morgan DG, Zhang X, Humphreys WG, Shu YZ, Yost GS, Ding X. The pneumotoxin 3-methylindole is a substrate and a mechanism-based inactivator of CYP2A13, a human cytochrome P450 enzyme preferentially expressed in the respiratory tract. Drug Metab Dispos 2009; 37:2018-27. [PMID: 19608696 DOI: 10.1124/dmd.109.027300] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
3-Methylindole (3MI), a respiratory tract toxicant, can be metabolized by a number of cytochromes P450 (P450), primarily through either dehydrogenation or epoxidation of the indole. In the present study, we assessed the bioactivation of 3MI by recombinant CYP2A13, a human P450 predominantly expressed in the respiratory tract. Four metabolites were detected, and the two principal ones were identified as indole-3-carbinol (I-3-C) and 3-methyloxindole (MOI). Bioactivation of 3MI by CYP2A13 was verified by the observation of three glutathione (GSH) adducts designated as GS-A1 (glutathione adduct 1), GS-A2 (glutathione adduct 2), and GS-A3 (glutathione adduct 3) in a NADPH- and GSH-fortified reaction system. GS-A1 and GS-A2 gave the same molecular ion at m/z 437, an increase of 305 Da over 3MI. Their structures are assigned to be 3-glutathionyl-S-methylindole and 3-methyl-2-glutathionyl-S-indole, respectively, on the basis of the mass fragmentation data obtained by high-resolution mass spectrometry. Kinetic parameters were determined for the formation of I-3-C (V(max) = 1.5 nmol/min/nmol of P450; K(m) = 14 muM), MOI (V(max) = 1.9 nmol/min/nmol of P450; K(m) = 15 muM) and 3-glutathionyl-S-methylindole (V(max) = 0.7 nmol/min/nmol of P450; K(m) = 13 muM). The structure of GS-A3, a minor adduct with a protonated molecular ion at m/z 453, is proposed to be 3-glutathionyl-S-3-methyloxindole. We also discovered that 3MI is a mechanism-based inactivator of CYP2A13, given that it produced a time-, cofactor-, and 3MI concentration-dependent loss of activity toward 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, with a relatively low K(I) value of approximately 10 muM and a k(inact) of 0.046 min(-1). Thus, CYP2A13 metabolizes 3MI through multiple bioactivation pathways, and the process can lead to a suicide inactivation of CYP2A13.
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Affiliation(s)
- Jaime D'Agostino
- New York State Department of Health, Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA
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Tournel G, Cauffiez C, Leclerc J, Billaut-Laden I, Allorge D, Chevalier D, Migot-Nabias F, Kenani A, Broly F, Lo-Guidice JM. CYP2F1 genetic polymorphism: identification of interethnic variations. Xenobiotica 2008; 37:1433-8. [PMID: 17943660 DOI: 10.1080/00498250701644403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Since human cytochrome P450 2F1 (CYP2F1) is predominantly expressed in lung tissue and is involved in the metabolism of various pneumotoxicants with potential carcinogenic effects, variations in the nucleotidic sequence of its gene may contribute to interindividual and interethnic differences in the susceptibility to lung tumorigenesis. The aim of the current study was to compare the frequency of a previously reported frameshift mutation, namely c.14_15insC, responsible for the synthesis of a severely truncated protein, between several populations of different ethnic origins. The frequencies of this polymorphism were 26.1, 51.6, 42.7 and 22.9% in French, Gabonese, Senegalese, and Tunisian population samples, respectively, thereby representing a substantial inter ethnic variation in the CYP2F1 gene. These findings provide data for further studies that investigate the potential association of CYP2F1 haplotypes with an incidence of lung cancer genesis in respect of ethnicity.
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Affiliation(s)
- G Tournel
- Equipe d'accueil 2679, Faculté de Médecine de Lille, Lille, France.
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