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García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. CELL GENOMICS 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
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Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
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Weh KM, Turgeon DK, Rubenstein JH, Clarke JL, Howell AB, Chang AC, Kresty LA. Proanthocyanidins mitigate bile acid-induced changes in GSTT2 levels in a panel of racially diverse patient-derived primary esophageal cell cultures. Mol Carcinog 2022; 61:281-287. [PMID: 34758158 PMCID: PMC8837669 DOI: 10.1002/mc.23369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 01/11/2023]
Abstract
Persistent and symptomatic reflux of gastric and duodenal contents, known as gastroesophageal reflux disease (GERD), is the strongest risk factor for esophageal adenocarcinoma (EAC). Despite similar rates of GERD and other risk factors across racial groups, EAC progression disproportionately impacts Caucasians. We recently reported that elevated tissue levels of the detoxification enzyme GSTT2 in the esophagi of Blacks compared to Caucasians may contribute protection. Herein, we extend our research to investigate whether cranberry proanthocyanidins (C-PAC) mitigate bile acid-induced damage and GSTT2 levels utilizing a racially diverse panel of patient-derived primary esophageal cultures. We have shown that C-PACs mitigate reflux-induced DNA damage through GSTT2 upregulation in a rat esophageal reflux model, but whether effects are recapitulated in humans or differentially based on race remains unknown. We isolated normal primary esophageal cells from Black and Caucasian patients and assessed GSTT2 protein levels and cellular viability following exposure to a bile acid cocktail with and without C-PAC treatment. Constitutive GSTT2 levels were significantly elevated in Black (2.9-fold) compared to Caucasian patients, as were GSTT2 levels in Black patients with GERD. C-PAC treatment induced GSTT2 levels 1.6-fold in primary normal esophageal cells. GSTT2 induction by C-PAC was greatest in cells with constitutively low GSTT2 expression. Overall, C-PAC mitigated bile-induced reductions of GSTT2 and subsequent loss of cell viability regardless of basal GSTT2 expression or race. These data support that C-PAC may be a safe efficacious agent to promote epithelial fitness through GSTT2 induction and in turn protect against bile acid-induced esophageal injury.
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Affiliation(s)
- Katherine M. Weh
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA,Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Danielle K. Turgeon
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Joel H. Rubenstein
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA,Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA,LTC Charles S Kettles Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
| | - Jennifer L. Clarke
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
| | - Amy B. Howell
- Marucci Center for Blueberry and Cranberry Research, Rutgers University, Chatsworth, New Jersey, USA
| | - Andrew C. Chang
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA,Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura A. Kresty
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, Michigan, USA,Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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Ayuso P, García-Martín E, Agúndez JAG. Variability of the Genes Involved in the Cellular Redox Status and Their Implication in Drug Hypersensitivity Reactions. Antioxidants (Basel) 2021; 10:antiox10020294. [PMID: 33672092 PMCID: PMC7919686 DOI: 10.3390/antiox10020294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022] Open
Abstract
Adverse drug reactions are a major cause of morbidity and mortality. Of the great diversity of drugs involved in hypersensitivity drug reactions, the most frequent are non-steroidal anti-inflammatory drugs followed by β-lactam antibiotics. The redox status regulates the level of reactive oxygen and nitrogen species (RONS). RONS interplay and modulate the action of diverse biomolecules, such as inflammatory mediators and drugs. In this review, we address the role of the redox status in the initiation, as well as in the resolution of inflammatory processes involved in drug hypersensitivity reactions. We summarize the association findings between drug hypersensitivity reactions and variants in the genes that encode the enzymes related to the redox system such as enzymes related to glutathione: Glutathione S-transferase (GSTM1, GSTP, GSTT1) and glutathione peroxidase (GPX1), thioredoxin reductase (TXNRD1 and TXNRD2), superoxide dismutase (SOD1, SOD2, and SOD3), catalase (CAT), aldo-keto reductase (AKR), and the peroxiredoxin system (PRDX1, PRDX2, PRDX3, PRDX4, PRDX5, PRDX6). Based on current evidence, the most relevant candidate redox genes related to hypersensitivity drug reactions are GSTM1, TXNRD1, SOD1, and SOD2. Increasing the understanding of pharmacogenetics in drug hypersensitivity reactions will contribute to the development of early diagnostic or prognosis tools, and will help to diminish the occurrence and/or the severity of these reactions.
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Affiliation(s)
- Pedro Ayuso
- Correspondence: ; Tel.: +34-927257000 (ext. 51038)
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Genome-wide human brain eQTLs: In-depth analysis and insights using the UKBEC dataset. Sci Rep 2019; 9:19201. [PMID: 31844111 PMCID: PMC6915738 DOI: 10.1038/s41598-019-55590-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/30/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding the complexity of the human brain transcriptome architecture is one of the most important human genetics study areas. Previous studies have applied expression quantitative trait loci (eQTL) analysis at the genome-wide level of the brain to understand the underlying mechanisms relating to neurodegenerative diseases, primarily at the transcript level. To increase the resolution of our understanding, the current study investigates multi/single-region, transcript/exon-level and cis versus trans-acting eQTL, across 10 regions of the human brain. Some of the key findings of this study are: (i) only a relatively small proportion of eQTLs will be detected, where the sensitivity is under 5%; (ii) when an eQTL is acting in multiple regions (MR-eQTL), it tends to have very similar effects on gene expression in each of these regions, as well as being cis-acting; (iii) trans-acting eQTLs tend to have larger effects on expression compared to cis-acting eQTLs and tend to be specific to a single region (SR-eQTL) of the brain; (iv) the cerebellum has a very large number of eQTLs that function exclusively in this region, compared with other regions of the brain; (v) importantly, an interactive visualisation tool (Shiny app) was developed to visualise the MR/SR-eQTL at transcript and exon levels.
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Ramírez B, Niño-Orrego MJ, Cárdenas D, Ariza KE, Quintero K, Contreras Bravo NC, Tamayo-Agudelo C, González MA, Laissue P, Fonseca Mendoza DJ. Copy number variation profiling in pharmacogenetics CYP-450 and GST genes in Colombian population. BMC Med Genomics 2019; 12:110. [PMID: 31324178 PMCID: PMC6642477 DOI: 10.1186/s12920-019-0556-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/05/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Copy Number variation (CNVs) in genes related to drug absorption, distribution, metabolism and excretion (ADME) are relevant in the interindividual variability of drug response. Studies of the CNVs in ADME genes in Latin America population are lacking. The objective of the study was to identify the genetic variability of CNVs in CYP-450 and GST genes in a subgroup of individuals of Colombian origin. METHODS Genomic DNA was isolated from 123 healthy individuals from a Colombian population. Multiplex Ligation-Dependent Probe Amplification (MLPA) was performed for the identification of CNVs in 40 genomic regions of 11 CYP-450 and 3 GST genes. The genetic variability, allelic and genotypic frequencies were analyzed. RESULTS We found that 13 out of 14 genes had CNVs: 5 (35.7%) exhibited deletions and duplications, while 8 (57.1%) presented either deletions or duplications.. 33.3% of individuals carried deletions and duplications while 49.6% had a unique type of CNV (deletion or duplication). The allelic frequencies of the CYP and GST genes were 0 to 47.6% (allele null), 0 to 17.5% (duplicated alleles) and 37 to 100% (normal alleles). CONCLUSIONS Our results describe, for the first time, the genomic profile of CNVs in a subgroup of Colombian population in GST and CYP-450 genes. GST genes indicated greater genetic variability than CYP-450 genes. The data obtained contributes to the knowledge of genetic profiles in Latin American subgroups. Although the clinical relevance of CNVs has not been fully established, it is a valuable source of pharmacogenetic variability data with potential involvement in the response to medications.
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Affiliation(s)
- Brian Ramírez
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - María José Niño-Orrego
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Daniel Cárdenas
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Kevin Enrique Ariza
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Karol Quintero
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Nora Constanza Contreras Bravo
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Caroll Tamayo-Agudelo
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - María Alejandra González
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Paul Laissue
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Dora Janeth Fonseca Mendoza
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia.
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Abstract
Esophageal cancer (EC) is an extremely aggressive cancer with one of the highest mortality rates. The cancer is generally only diagnosed at the later stages and has a poor 5-year survival rate due to the limited treatment options. China and South Africa are two countries with a very high prevalence rate of EC. EC rates in South Africa have been on the increase, and esophageal squamous cell carcinoma is the predominant subtype and a primary cause of cancer-related deaths in the black and male mixed ancestry populations in South Africa. The incidence of EC is highest in the Eastern Cape Province, especially in the rural areas such as the Transkei, where the consumption of foods contaminated with Fusarium verticillioides is thought to play a major contributing role to the incidence of EC. China is responsible for almost half of all new cases of EC globally. In China, the prevalence of EC varies greatly. However, the two main areas of high prevalence are the southern Taihang Mountain area (Linxian, Henan Province) and the north Jiangsu area. In both countries, environmental toxins play a major role in increasing the chance that an individual will develop EC. These associative factors include tobacco use, alcohol consumption, nutritional deficiencies and exposure to environmental toxins. However, genetic polymorphisms also play a role in predisposing individuals to EC. These include single-nucleotide polymorphisms that can be found in both protein-coding genes and in non-coding sequences such as miRNAs. The aim of this review is to summarize the contribution of genetic polymorphisms to EC in South Africa and to compare and contrast this to the genetic polymorphisms observed in EC in the most comprehensively studied population group, the Chinese.
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Affiliation(s)
- Mohammed Alaouna
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rodney Hull
- Research, Innovation & Engagements Portfolio, Mangosuthu University of Technology, Durban, South Africa,
| | - Clement Penny
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zodwa Dlamini
- Research, Innovation & Engagements Portfolio, Mangosuthu University of Technology, Durban, South Africa,
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Ferrer-Torres D, Nancarrow DJ, Steinberg H, Wang Z, Kuick R, Weh KM, Mills RE, Ray D, Ray P, Lin J, Chang AC, Reddy RM, Orringer MB, Canto MI, Shaheen NJ, Kresty LA, Chak A, Wang TD, Rubenstein JH, Beer DG. Constitutively Higher Level of GSTT2 in Esophageal Tissues From African Americans Protects Cells Against DNA Damage. Gastroenterology 2019; 156:1404-1415. [PMID: 30578782 PMCID: PMC6441633 DOI: 10.1053/j.gastro.2018.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND & AIMS African American and European American individuals have a similar prevalence of gastroesophageal reflux disease (GERD), yet esophageal adenocarcinoma (EAC) disproportionately affects European American individuals. We investigated whether the esophageal squamous mucosa of African American individuals has features that protect against GERD-induced damage, compared with European American individuals. METHODS We performed transcriptional profile analysis of esophageal squamous mucosa tissues from 20 African American and 20 European American individuals (24 with no disease and 16 with Barrett's esophagus and/or EAC). We confirmed our findings in a cohort of 56 patients and analyzed DNA samples from patients to identify associated variants. Observations were validated using matched genomic sequence and expression data from lymphoblasts from the 1000 Genomes Project. A panel of esophageal samples from African American and European American subjects was used to confirm allele-related differences in protein levels. The esophageal squamous-derived cell line Het-1A and a rat esophagogastroduodenal anastomosis model for reflux-generated esophageal damage were used to investigate the effects of the DNA-damaging agent cumene-hydroperoxide (cum-OOH) and a chemopreventive cranberry proanthocyanidin (C-PAC) extract, respectively, on levels of protein and messenger RNA (mRNA). RESULTS We found significantly higher levels of glutathione S-transferase theta 2 (GSTT2) mRNA in squamous mucosa from African American compared with European American individuals and associated these with variants within the GSTT2 locus in African American individuals. We confirmed that 2 previously identified genomic variants at the GSTT2 locus, a 37-kb deletion and a 17-bp promoter duplication, reduce expression of GSTT2 in tissues from European American individuals. The nonduplicated 17-bp promoter was more common in tissue samples from populations of African descendant. GSTT2 protected Het-1A esophageal squamous cells from cum-OOH-induced DNA damage. Addition of C-PAC increased GSTT2 expression in Het-1A cells incubated with cum-OOH and in rats with reflux-induced esophageal damage. C-PAC also reduced levels of DNA damage in reflux-exposed rat esophagi, as observed by reduced levels of phospho-H2A histone family member X. CONCLUSIONS We found GSTT2 to protect esophageal squamous cells against DNA damage from genotoxic stress and that GSTT2 expression can be induced by C-PAC. Increased levels of GSTT2 in esophageal tissues of African American individuals might protect them from GERD-induced damage and contribute to the low incidence of EAC in this population.
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Affiliation(s)
- Daysha Ferrer-Torres
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Derek J. Nancarrow
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Hannah Steinberg
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Zhuwen Wang
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Rork Kuick
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109
| | - Katherine M. Weh
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Ryan E. Mills
- Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109
| | - Paramita Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109
| | - Jules Lin
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Andrew C. Chang
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Rishindra M. Reddy
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Mark B. Orringer
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Marcia I. Canto
- Department of Medicine, Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, MD 21287
| | - Nicholas J. Shaheen
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina, Chapel Hill NC 27599
| | - Laura A. Kresty
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Amitabh Chak
- Department of Medicine, Gastroenterology, Case Western Reserve University, Cleveland, OH 44106
| | - Thomas D. Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI 48109
| | - Joel H. Rubenstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor MI 48109
| | - David G. Beer
- Department of Surgery, Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI 48109
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High-performance liquid chromatography-based assay for glutathione transferase theta 2 activity: Application to characterize interindividual variability in human liver fractions. J Pharm Biomed Anal 2018; 156:181-188. [DOI: 10.1016/j.jpba.2018.04.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/13/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023]
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Drinking Water Disinfection By-products, Genetic Polymorphisms, and Birth Outcomes in a European Mother-Child Cohort Study. Epidemiology 2018; 27:903-11. [PMID: 27468006 DOI: 10.1097/ede.0000000000000544] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND We examined the association between exposure during pregnancy to trihalomethanes, the most common water disinfection by-products, and birth outcomes in a European cohort study (Health Impacts of Long-Term Exposure to Disinfection By-Products in Drinking Water). We took into account exposure through different water uses, measures of water toxicity, and genetic susceptibility. METHODS We enrolled 14,005 mothers (2002-2010) and their children from France, Greece, Lithuania, Spain, and the UK. Information on lifestyle- and water-related activities was recorded. We ascertained residential concentrations of trihalomethanes through regulatory records and ad hoc sampling campaigns and estimated route-specific trihalomethane uptake by trimester and for whole pregnancy. We examined single nucleotide polymorphisms and copy number variants in disinfection by-product metabolizing genes in nested case-control studies. RESULTS Average levels of trihalomethanes ranged from around 10 μg/L to above the regulatory limits in the EU of 100 μg/L between centers. There was no association between birth weight and total trihalomethane exposure during pregnancy (β = 2.2 g in birth weight per 10 μg/L of trihalomethane, 95% confidence interval = 3.3, 7.6). Birth weight was not associated with exposure through different routes or with specific trihalomethane species. Exposure to trihalomethanes was not associated with low birth weight (odds ratio [OR] per 10 μg/L = 1.02, 95% confidence interval = 0.95, 1.10), small-for-gestational age (OR = 0.99, 0.94, 1.03) and preterm births (OR = 0.98, 0.9, 1.05). We found no gene-environment interactions for mother or child polymorphisms in relation to preterm birth or small-for-gestational age. CONCLUSIONS In this large European study, we found no association between birth outcomes and trihalomethane exposures during pregnancy in the total population or in potentially genetically susceptible subgroups. (See video abstract at http://links.lww.com/EDE/B104.).
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Khrunin AV, Filippova IN, Aliev AM, Tupitsina TV, Slominsky PA, Limborska SA. GSTM1 copy number variation in the context of single nucleotide polymorphisms in the human GSTM cluster. Mol Cytogenet 2016; 9:30. [PMID: 27099630 PMCID: PMC4837583 DOI: 10.1186/s13039-016-0241-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023] Open
Abstract
Background GSTM1 gene deletion is one of the most known copy number polymorphisms in human genome. It is most likely caused by homologous recombination between the repeats flanking the gene. However, taking into account that the deletion has no crucial effects on human well-being, and the ability of other GSTMs to compensate for the lack of GSTM1, a role for additional factors affecting GSTM1 deletion can be proposed. Our goal was to explore the relationships between GSTM1 deletion polymorphism and single nucleotide polymorphisms (SNPs) in the region of the GSTM cluster that includes GSTM2, GSTM3, GSTM4, and GSTM5 in addition to GSTM1. Results Real-time polymerase chain reaction was used to quantify the number of GSTM1 copies. Fourteen SNPs from the region were tested and their allelic patterns were compared in groups of Russian individuals subdivided according to their GSTM1 deletion genotypes. Linkage disequilibrium-based haplotype analysis showed substantial differences of haplotype frequencies between the groups, especially between individuals with homozygous GSTM1 −/− and +/+ genotypes. Exploration of the results of phasing of GSTM1 and SNP genotypes revealed unequal segregation of GSTM1 + and − alleles at different haplotypes. Conclusions The observed differences in haplotype patterns suggest the potential role of genetic context in GSTM1 deletion frequency (appearance) and in the determination of the deletion-related effects.
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Affiliation(s)
- Andrey V Khrunin
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Irina N Filippova
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Aydar M Aliev
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Tat'yana V Tupitsina
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Petr A Slominsky
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
| | - Svetlana A Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 Russia
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11
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Lu L, Pandey AK, Houseal MT, Mulligan MK. The Genetic Architecture of Murine Glutathione Transferases. PLoS One 2016; 11:e0148230. [PMID: 26829228 PMCID: PMC4734686 DOI: 10.1371/journal.pone.0148230] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 01/14/2016] [Indexed: 12/17/2022] Open
Abstract
Glutathione S-transferase (GST) genes play a protective role against oxidative stress and may influence disease risk and drug pharmacokinetics. In this study, massive multiscalar trait profiling across a large population of mice derived from a cross between C57BL/6J (B6) and DBA2/J (D2)—the BXD family—was combined with linkage and bioinformatic analyses to characterize mechanisms controlling GST expression and to identify downstream consequences of this variation. Similar to humans, mice show a wide range in expression of GST family members. Variation in the expression of Gsta4, Gstt2, Gstz1, Gsto1, and Mgst3 is modulated by local expression QTLs (eQTLs) in several tissues. Higher expression of Gsto1 in brain and liver of BXD strains is strongly associated (P < 0.01) with inheritance of the B6 parental allele whereas higher expression of Gsta4 and Mgst3 in brain and liver, and Gstt2 and Gstz1 in brain is strongly associated with inheritance of the D2 parental allele. Allele-specific assays confirmed that expression of Gsto1, Gsta4, and Mgst3 are modulated by sequence variants within or near each gene locus. We exploited this endogenous variation to identify coexpression networks and downstream targets in mouse and human. Through a combined systems genetics approach, we provide new insight into the biological role of naturally occurring variants in GST genes.
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Affiliation(s)
- Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38106, United States of America
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, 226001, China
| | - Ashutosh K. Pandey
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38106, United States of America
| | - M. Trevor Houseal
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38106, United States of America
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38106, United States of America
- * E-mail:
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Jaffe AE, Hyde T, Kleinman J, Weinbergern DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C. Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. BMC Bioinformatics 2015; 16:372. [PMID: 26545828 PMCID: PMC4636836 DOI: 10.1186/s12859-015-0808-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/30/2015] [Indexed: 12/26/2022] Open
Abstract
Background Genomic data production is at its highest level and continues to increase, making available novel primary data and existing public data to researchers for exploration. Here we explore the consequences of “batch” correction for biological discovery in two publicly available expression datasets. We consider this to include the estimation of and adjustment for wide-spread systematic heterogeneity in genomic measurements that is unrelated to the effects under study, whether it be technical or biological in nature. Methods We present three illustrative data analyses using surrogate variable analysis (SVA) and describe how to perform artifact discovery in light of natural heterogeneity within biological groups, secondary biological questions of interest, and non-linear treatment effects in a dataset profiling differentiating pluripotent cells (GSE32923) and another from human brain tissue (GSE30272). Results Careful specification of biological effects of interest is very important to factor-based approaches like SVA. We demonstrate greatly sharpened global and gene-specific differential expression across treatment groups in stem cell systems. Similarly, we demonstrate how to preserve major non-linear effects of age across the lifespan in the brain dataset. However, the gains in precisely defining known effects of interest come at the cost of much other information in the “cleaned” data, including sex, common copy number effects and sample or cell line-specific molecular behavior. Conclusions Our analyses indicate that data “cleaning” can be an important component of high-throughput genomic data analysis when interrogating explicitly defined effects in the context of data affected by robust technical artifacts. However, caution should be exercised to avoid removing biological signal of interest. It is also important to note that open data exploration is not possible after such supervised “cleaning”, because effects beyond those stipulated by the researcher may have been removed. With the goal of making these statistical algorithms more powerful and transparent to researchers in the biological sciences, we provide exploratory plots and accompanying R code for identifying and guiding “cleaning” process (https://github.com/andrewejaffe/StemCellSVA). The impact of these methods is significant enough that we have made newly processed data available for the brain data set at http://braincloud.jhmi.edu/plots/ and GSE30272. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0808-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew E Jaffe
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA. .,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD, 21205, USA.
| | - Thomas Hyde
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,Department of Psychiatry, Johns Hopkins School of Medicine, Baltimor, MD, 21205, USA.
| | - Joel Kleinman
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| | - Daniel R Weinbergern
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,Department of Psychiatry, Johns Hopkins School of Medicine, Baltimor, MD, 21205, USA. .,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205, USA.
| | - Joshua G Chenoweth
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA.
| | - Ronald D McKay
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA.
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD, 21205, USA.
| | - Carlo Colantuoni
- Lieber Institute for Brain Development, 855 N Wolfe St, Ste 300, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205, USA.
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Abstract
Esophageal cancer (EC) is one of the most common malignancies in low- and medium-income countries and represents a disease of public health importance because of its poor prognosis and high mortality rate in these regions. The striking variation in the prevalence of EC among different ethnic groups suggests a significant contribution of population-specific environmental and dietary factors to susceptibility to the disease. Although individuals within a demarcated geographical area are exposed to the same environment and share similar dietary habits, not all of them will develop the disease; thus genetic susceptibility to environmental risk factors may play a key role in the development of EC. A wide range of xenobiotic-metabolizing enzymes are responsible for the metabolism of carcinogens introduced via the diet or inhaled from the environment. Such dietary or environmental carcinogens can bind to DNA, resulting in mutations that may lead to carcinogenesis. Genes involved in the biosynthesis of these enzymes are all subject to genetic polymorphisms that can lead to altered expression or activity of the encoded proteins. Genetic polymorphisms may, therefore, act as molecular biomarkers that can provide important predictive information about carcinogenesis. The aim of this review is to discuss our current knowledge on the genetic risk factors associated with the development of EC in different populations; it addresses mainly the topics of genetic polymorphisms, gene-environment interactions, and carcinogenesis. We have reviewed the published data on genetic polymorphisms of enzymes involved in the metabolism of xenobiotics and discuss some of the potential gene-environment interactions underlying esophageal carcinogenesis. The main enzymes discussed in this review are the glutathione S-transferases (GSTs), N-acetyltransferases (NATs), cytochrome P450s (CYPs), sulfotransferases (SULTs), UDP-glucuronosyltransferases (UGTs), and epoxide hydrolases (EHs), all of which have key roles in the detoxification of environmental and dietary carcinogens. Finally, we discuss recent advances in the study of genetic polymorphisms associated with EC risk, specifically with regard to genome-wide association studies, and examine possible challenges of case-control studies that need to be addressed to better understand the interaction between genetic and environmental factors in esophageal carcinogenesis.
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Affiliation(s)
- Marco Matejcic
- a International Centre for Genetic Engineering and Biotechnology, Cape Town Component , Observatory , Cape Town , South Africa , and
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Iorio A, Polimanti R, Calandro M, Graziano ME, Piacentini S, Bucossi S, Squitti R, Lazzarin N, Scano G, Limbruno GM, Manfellotto D, Fuciarelli M. Explorative genetic association study of GSTT2B copy number variant in complex disease risks. Ann Hum Biol 2015. [PMID: 26207597 DOI: 10.3109/03014460.2015.1049206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Glutathione S-transferases (GSTs) are the main phase II enzymes involved in cellular detoxification. Through phase I and phase II detoxification reactions, the cell is able to detoxify endogenous and exogenous toxic compounds. AIMS This study focused attention on the GSTT2B copy number variant (CNV) in order to explore its involvement in the genetic pre-disposition to asthma, Alzheimer's disease (AD), allergic rhinitis (AR), essential hypertension (EH), hypothyroidism and recurrent miscarriage (RM). METHODS The study population consists of 1225 individuals divided into six case-control groups. The genotyping of the GSTT2B CNV was performed by using a duplex-PCR. Odds Ratios (ORs) were calculated, adjusting for the confounding variables, to estimate the association between GSTT2B CNV and the disease status. RESULTS The χ(2)-test and ORs did not show any association between this genetic marker and pathological phenotypes. CONCLUSION The data highlights that GSTT2B CNV is not associated with the investigated complex diseases in Italian patients. However, further investigations are necessary to replicate these findings in larger sample sizes and to explore other health-related phenotypes.
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Affiliation(s)
- Andrea Iorio
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Renato Polimanti
- b Department of Psychiatry , Yale University School of Medicine , West Haven , CT , USA
| | - Melania Calandro
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | | | - Sara Piacentini
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Serena Bucossi
- c Department of Clinical Neuroscience , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Isola Tiberina , Rome , Italy .,d Department of Neurology , 'Campus Bio-Medico' University , Rome , Italy
| | - Rosanna Squitti
- c Department of Clinical Neuroscience , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Isola Tiberina , Rome , Italy .,e Laboratorio Neurodegenerazione , IRCCS San Raffaele Pisana , Rome , Italy
| | | | - Giuseppina Scano
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | - Giancarlo Maria Limbruno
- g Clinical Pathology Department , AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital , Rome , Italy
| | | | - Maria Fuciarelli
- a Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
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Zhang X, Gierman HJ, Levy D, Plump A, Dobrin R, Goring HHH, Curran JE, Johnson MP, Blangero J, Kim SK, O’Donnell CJ, Emilsson V, Johnson AD. Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics 2014; 15:532. [PMID: 24973796 PMCID: PMC4102726 DOI: 10.1186/1471-2164-15-532] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 06/18/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs. RESULTS We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5' or 3' positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for genes involved in xenobiotic metabolism and mitochondrial function, suggesting these eQTLs may have adaptive origins. Several strong eQTLs (CDK5RAP2, NBPFs) coincide with regions of reported human lineage selection. The intersection of new kidney and plaque eQTLs with related GWAS suggest possible gene prioritization. For example, butyrophilins are now linked to arterial pathogenesis via multiple genetic and expression studies. Expression QTL and GWAS results are made available as a community resource through the NHLBI GRASP database [http://apps.nhlbi.nih.gov/grasp/]. CONCLUSIONS Expression QTLs inform the interpretation of human trait variability, and may account for a greater fraction of phenotypic variability than protein-coding variants. The synthesis of available tissue eQTL data highlights many strong cis-eQTLs that may have important biologic roles and could serve as positive controls in future studies. Our results indicate some strong tissue-ubiquitous eQTLs may have adaptive origins in humans. Efforts to expand the genetic, splicing and tissue coverage of known eQTLs will provide further insights into human gene regulation.
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Affiliation(s)
- Xiaoling Zhang
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
| | - Hinco J Gierman
- />Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Daniel Levy
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
| | - Andrew Plump
- />Sanofi Aventis Pharmaceuticals, Bridgewater, NJ 08807 USA
| | - Radu Dobrin
- />Johnson & Johnson Pharmaceutical Research and Development, Radnor, PA 19477 USA
| | - Harald HH Goring
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Joanne E Curran
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Matthew P Johnson
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - John Blangero
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Stuart K Kim
- />Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Christopher J O’Donnell
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
- />Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Andrew D Johnson
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
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Yang H, Volfovsky N, Rattray A, Chen X, Tanaka H, Strathern J. GAP-Seq: a method for identification of DNA palindromes. BMC Genomics 2014; 15:394. [PMID: 24885769 PMCID: PMC4057610 DOI: 10.1186/1471-2164-15-394] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 04/26/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Closely spaced long inverted repeats, also known as DNA palindromes, can undergo intrastrand annealing to form DNA hairpins. The ability to form these hairpins results in genome instability, difficulties in maintaining clones in Escherichia coli and major problems for most DNA sequencing approaches. Because of their role in genomic instability and gene amplification in some human cancers, it is important to develop systematic approaches to detect and characterize DNA palindromes. RESULTS We developed a new protocol to identify palindromes that couples the S1 nuclease treated Cot0 DNA (GAPF) with high-throughput sequencing (GAP-Seq). Unlike earlier protocols, it does not involve restriction enzymatic digestion prior to DNA snap-back thereby preserving longer DNA sequences. It also indicates the location of the novel junction, which can then be recovered. Using MCF-7 breast cancer cell line as the proof-of-principle analysis, we have identified 35 palindrome candidates and physically characterized the top 5 candidates and their junctions. Because this protocol eliminates many of the false positives that plague earlier techniques, we have improved palindrome identification. CONCLUSIONS The GAP-Seq approach underscores the importance of developing new tools for identifying and characterizing palindromes, and provides a new strategy to systematically assess palindromes in genomes. It will be useful for studying human cancers and other diseases associated with palindromes.
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Affiliation(s)
- Hui Yang
- />Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Cancer Research and Development Center, Frederick, MD 21702 USA
| | - Natalia Volfovsky
- />ABCC/ ISP, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Alison Rattray
- />Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Cancer Research and Development Center, Frederick, MD 21702 USA
| | - Xiongfong Chen
- />ABCC/ ISP, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Hisashi Tanaka
- />Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195 USA
| | - Jeffrey Strathern
- />Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Cancer Research and Development Center, Frederick, MD 21702 USA
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Coskunpinar E, Canbay E, Oltulu YM, Tiryakioglu NO, Bugra D. GSTT1 is deregulated in left colon tumors. Asian Pac J Cancer Prev 2014; 15:2319-21. [PMID: 24716977 DOI: 10.7314/apjcp.2014.15.5.2319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Our aim was to determine GSTT1 expression levels in left colon tumors and paired normal tissue in order to identify specific alterations in GSTT1 mRNA levels. Alterations in GSTT1 expression in twenty-four left- sided colon tumors and paired cancer free tissue were determined by qRT-PCR. Significant fold changes were determined with t-test. When compared with cancer free tissue, left colon cancers showed a significant decrease in GSTT1 expression. However, GSTT1 mRNA levels among different grades increased gradually in correlation with tumor grade. Our results suggest that downregulation of GSTT1 in left-sided colon cancers is an early event and is reversed with cancer progression, probably due to cellular defense mechanisms as a response to changes in the microenvironment.
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Affiliation(s)
- Ender Coskunpinar
- Department of Molecular Medicine, Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey E-mail :
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Polimanti R, Piacentini S, Iorio A, De Angelis F, Kozlov A, Novelletto A, Fuciarelli M. Haplotype differences for copy number variants in the 22q11.23 region among human populations: a pigmentation-based model for selective pressure. Eur J Hum Genet 2014; 23:116-23. [PMID: 24667780 DOI: 10.1038/ejhg.2014.47] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 12/17/2022] Open
Abstract
Two gene clusters are tightly linked in a narrow region of chromosome 22q11.23: the macrophage migration inhibitory factor (MIF) gene family and the glutathione S-transferase theta class. Within 120 kb in this region, two 30-kb deletions reach high frequencies in human populations. This gives rise to four haplotypic arrangements, which modulate the number of genes in both families. The variable patterns of linkage disequilibrium (LD) between these copy number variants (CNVs) in diverse human populations remain poorly understood. We analyzed 2469 individuals belonging to 27 human populations with different ethnic origins. Then we correlated the genetic variability of 22q11.23 CNVs with environmental variables. We confirmed an increasing strength of LD from Africa to Asia and to Europe. Further, we highlighted strongly significant correlations between the frequency of one of the haplotypes and pigmentation-related variables: skin color (R(2)=0.675, P<0.001), distance from the equator (R(2)=0.454, P<0.001), UVA radiation (R(2)=0.439, P<0.001), and UVB radiation (R(2)=0.313, P=0.002). The fact that all MIF-related genes are retained on this haplotype and the evidences gleaned from experimental systems seem to agree with the role of MIF-related genes in melanogenesis. As such, we propose a model that explains the geographic and ethnic distribution of 22q11.23 CNVs among human populations, assuming that MIF-related gene dosage could be associated with adaptation to low UV radiation.
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Affiliation(s)
- Renato Polimanti
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Sara Piacentini
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Andrea Iorio
- Clinical Pathophysiology Center, AFaR - 'San Giovanni Calibita' Fatebenefratelli Hospital, Rome, Italy
| | - Flavio De Angelis
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Andrey Kozlov
- Institute and Museum of Anthropology, M. Lomonosov State University, Moscow, Russia
| | - Andrea Novelletto
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Maria Fuciarelli
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
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Board PG, Menon D. Glutathione transferases, regulators of cellular metabolism and physiology. Biochim Biophys Acta Gen Subj 2012. [PMID: 23201197 DOI: 10.1016/j.bbagen.2012.11.019] [Citation(s) in RCA: 259] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND The cytosolic glutathione transferases (GSTs) comprise a super family of proteins that can be categorized into multiple classes with a mixture of highly specific and overlapping functions. SCOPE OF REVIEW The review covers the genetics, structure and function of the human cytosolic GSTs with particular attention to their emerging roles in cellular metabolism. MAJOR CONCLUSIONS All the catalytically active GSTs contribute to the glutathione conjugation or glutathione dependant-biotransformation of xenobiotics and many catalyze glutathione peroxidase or thiol transferase reactions. GSTs also catalyze glutathione dependent isomerization reactions required for the synthesis of several prostaglandins and steroid hormones and the catabolism of tyrosine. An increasing body of work has implicated several GSTs in the regulation of cell signaling pathways mediated by stress-activated kinases like Jun N-terminal kinase. In addition, some members of the cytosolic GST family have been shown to form ion channels in intracellular membranes and to modulate ryanodine receptor Ca(2+) channels in skeletal and cardiac muscle. GENERAL SIGNIFICANCE In addition to their well established roles in the conjugation and biotransformation of xenobiotics, GSTs have emerged as significant regulators of pathways determining cell proliferation and survival and as regulators of ryanodine receptors that are essential for muscle function. This article is part of a Special Issue entitled Cellular functions of glutathione.
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Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Marotta M, Chen X, Inoshita A, Stephens R, Budd GT, Crowe JP, Lyons J, Kondratova A, Tubbs R, Tanaka H. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications. Breast Cancer Res 2012. [PMID: 23181561 PMCID: PMC4053137 DOI: 10.1186/bcr3362] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction Segmental duplications (low-copy repeats) are the recently duplicated genomic segments in the human genome that display nearly identical (> 90%) sequences and account for about 5% of euchromatic regions. In germline, duplicated segments mediate nonallelic homologous recombination and thus cause both non-disease-causing copy-number variants and genomic disorders. To what extent duplicated segments play a role in somatic DNA rearrangements in cancer remains elusive. Duplicated segments often cluster and form genomic blocks enriched with both direct and inverted repeats (complex genomic regions). Such complex regions could be fragile and play a mechanistic role in the amplification of the ERBB2 gene in breast tumors, because repeated sequences are known to initiate gene amplification in model systems. Methods We conducted polymerase chain reaction (PCR)-based assays for primary breast tumors and analyzed publically available array-comparative genomic hybridization data to map a common copy-number breakpoint in ERBB2-amplified primary breast tumors. We further used molecular, bioinformatics, and population-genetics approaches to define duplication contents, structural variants, and haplotypes within the common breakpoint. Results We found a large (> 300-kb) block of duplicated segments that was colocalized with a common-copy number breakpoint for ERBB2 amplification. The breakpoint that potentially initiated ERBB2 amplification localized in a region 1.5 megabases (Mb) on the telomeric side of ERBB2. The region is very complex, with extensive duplications of KRTAP genes, structural variants, and, as a result, a paucity of single-nucleotide polymorphism (SNP) markers. Duplicated segments are varied in size and degree of sequence homology, indicating that duplications have occurred recurrently during genome evolution. Conclusions Amplification of the ERBB2 gene in breast tumors is potentially initiated by a complex region that has unusual genomic features and thus requires rigorous, labor-intensive investigation. The haplotypes we provide could be useful to identify the potential association between the complex region and ERBB2 amplification.
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Fischer K, Da Costa LA, García-Bailo B, Borchers CH, El-Sohemy A. Glutathione S-Transferase (GST) M1, but Not GSTT1, Genotype Influences Plasma Proteomic Profiles in Caucasian and East Asian Young Adults. J Proteome Res 2012; 11:5022-33. [DOI: 10.1021/pr3005887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Karina Fischer
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Institute of Food, Nutrition
and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Laura A. Da Costa
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3E2, Canada
| | - Bibiana García-Bailo
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3E2, Canada
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia
Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3E2, Canada
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Krepischi ACV, Pearson PL, Rosenberg C. Germline copy number variations and cancer predisposition. Future Oncol 2012; 8:441-50. [PMID: 22515447 DOI: 10.2217/fon.12.34] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We present an overview of the role of germline copy number variations (CNVs) in cancer predisposition. CNVs represent a significant source of genetic diversity, although the mechanisms by which they influence cancer susceptibility still remain largely unknown. Approximately 100 highly penetrant germline mutant genes are now known to cause cancer predisposition inherited in a Mendelian fashion; in this review, we show that nearly half of these genes have also been observed as rare CNVs associated with cancer. However, these highly penetrant alleles seem to account for less than 5% of all familial cancers. We surmise that most of the genetic risk of cancer in the general population must largely involve genes of low or moderate penetrance. In the last 5 years, studies have demonstrated that although common low penetrant CNVs are modest contributors to cancer individually, their combined impact on cancer predisposition must be taken into account in estimating cancer risk.
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Marotta M, Piontkivska H, Tanaka H. Molecular trajectories leading to the alternative fates of duplicate genes. PLoS One 2012; 7:e38958. [PMID: 22720000 PMCID: PMC3375281 DOI: 10.1371/journal.pone.0038958] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/14/2012] [Indexed: 11/21/2022] Open
Abstract
Gene duplication generates extra gene copies in which mutations can accumulate without risking the function of pre-existing genes. Such mutations modify duplicates and contribute to evolutionary novelties. However, the vast majority of duplicates appear to be short-lived and experience duplicate silencing within a few million years. Little is known about the molecular mechanisms leading to these alternative fates. Here we delineate differing molecular trajectories of a relatively recent duplication event between humans and chimpanzees by investigating molecular properties of a single duplicate: DNA sequences, gene expression and promoter activities. The inverted duplication of the Glutathione S-transferase Theta 2 (GSTT2) gene had occurred at least 7 million years ago in the common ancestor of African great apes and is preserved in chimpanzees (Pan troglodytes), whereas a deletion polymorphism is prevalent in humans. The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion. In contrast, selective constraint preserved duplicate divergence in chimpanzees. The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones. Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.
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Affiliation(s)
- Michael Marotta
- Department of Molecular Genetics, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America
| | - Hisashi Tanaka
- Department of Molecular Genetics, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
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Bustamante M, Danileviciute A, Espinosa A, Gonzalez JR, Subirana I, Cordier S, Chevrier C, Chatzi L, Grazuleviciene R, Sunyer J, Ibarluzea J, Ballester F, Villanueva CM, Nieuwenhuijsen M, Estivill X, Kogevinas M. Influence of fetal glutathione S-transferase copy number variants on adverse reproductive outcomes. BJOG 2012; 119:1141-6. [PMID: 22676722 DOI: 10.1111/j.1471-0528.2012.03400.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A nested case-control association study was designed to investigate the influence of maternal and fetal copy number variants (CNVs) on reproductive outcomes. Genotypes of ten CNVs encompassing GST and CYP genes were assessed. Significant associations were only found for child CNV genotypes. In particular, the child GSTM1 insertion allele was associated with prematurity protection (odds ratio, 95% CI: 0.67, 0.51-0.89; P < 0.01), whereas the child GSTT2B insertion allele was associated with an increased risk of being small for gestational age (odds ratio, 95% CI: 1.33, 1.07-1.67; P = 0.01). The study highlights the role of the fetal genome in prenatal development and also the need to analyse CNVs in a systematic manner.
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Affiliation(s)
- M Bustamante
- Centre for Research in Environmental Epidemiology, Barcelona, Spain.
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26
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Rudolph A, Hein R, Hoffmeister M, Försti A, Hemminki K, Risch A, Brenner H, Chang-Claude J. Copy number variations of GSTT1 and GSTM1, colorectal cancer risk and possible effect modification of cigarette smoking and menopausal hormone therapy. Int J Cancer 2012; 131:E841-8. [DOI: 10.1002/ijc.27428] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/30/2011] [Indexed: 12/23/2022]
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Matejcic M, Li D, Prescott NJ, Lewis CM, Mathew CG, Parker MI. Association of a deletion of GSTT2B with an altered risk of oesophageal squamous cell carcinoma in a South African population: a case-control study. PLoS One 2011; 6:e29366. [PMID: 22216261 PMCID: PMC3246501 DOI: 10.1371/journal.pone.0029366] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 11/27/2011] [Indexed: 12/28/2022] Open
Abstract
Background Polymorphisms in the Glutathione S-transferase genes are associated with altered risks in many cancers, but their role in oesophageal cancer is unclear. Recently a 37-kb deletion polymorphism of GSTT2B that reduces expression of GSTT2 has been described. We evaluated the influence of the GSTT1 and GSTT2B deletion polymorphisms, and the GSTP1 Ile105Val polymorphism (rs1695) on susceptibility to oesophageal squamous cell carcinoma (OSCC) in the Black and Mixed Ancestry populations of South Africa. Methods and Results The GSTT1, GSTT2B and GSTP1 variants were genotyped in 562 OSCC cases and 907 controls, and tested for association with OSCC and for interaction with smoking and alcohol consumption. Linkage disequilibrium (LD) between the deletions at GSTT1 and GSTT2B was determined, and the haplotypes tested for association with OSCC. Neither the GSTT1 deletion nor the GSTP1 Ile105Val polymorphism was associated with OSCC risk in the Black or Mixed Ancestry populations. The GSTT2B deletion was not associated with OSCC risk in the Black population, but was associated with reduced risk of OSCC in the Mixed Ancestry population (OR = 0.71; 95% CI 0.57–0.90, p = 0.004). Case-only analysis showed no interaction between the GST polymorphisms and smoking or alcohol consumption. LD between the neighboring GSTT1 and GSTT2B deletions was low in both populations (r2Black = 0.04; r2MxA = 0.07), thus these deletions should be assessed independently for effects on disease risk. Conclusions Although there was no association between the GSTT1 deletion polymorphism or the GSTP1 Ile105Val polymorphism with OSCC, our results suggest that the presence of the recently described GSTT2B deletion may have a protective effect on the risk of OSCC in the Mixed Ancestry South African population. This is the first report of the contribution of the GSTT2B deletion to cancer risk.
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Affiliation(s)
- Marco Matejcic
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Observatory, Cape Town, South Africa
- Division of Medical Biochemistry and IIDMM, UCT Faculty of Health Sciences, Cape Town, South Africa
| | - DongPing Li
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Observatory, Cape Town, South Africa
- Division of Medical Biochemistry and IIDMM, UCT Faculty of Health Sciences, Cape Town, South Africa
| | - Natalie J. Prescott
- Department of Medical and Molecular Genetics, King's College London, King's Health Partners, Guy's Hospital, London, United Kingdom
| | - Cathryn M. Lewis
- Department of Medical and Molecular Genetics, King's College London, King's Health Partners, Guy's Hospital, London, United Kingdom
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Christopher G. Mathew
- Department of Medical and Molecular Genetics, King's College London, King's Health Partners, Guy's Hospital, London, United Kingdom
| | - M. Iqbal Parker
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Observatory, Cape Town, South Africa
- Division of Medical Biochemistry and IIDMM, UCT Faculty of Health Sciences, Cape Town, South Africa
- * E-mail:
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28
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Polimanti R, Piacentini S, Fuciarelli M. HapMap-based study of human soluble glutathione S-transferase enzymes. Pharmacogenet Genomics 2011; 21:665-72. [DOI: 10.1097/fpc.0b013e328349da4d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Hernando-Rodriguez M, Rey-Barja N, Marichalar-Mendia X, Rodriguez-Tojo MJ, Acha-Sagredo A, Aguirre-Urizar JM. Role of cytochrome P-450 genetic polymorphisms in oral carcinogenesis. J Oral Pathol Med 2011; 41:1-8. [DOI: 10.1111/j.1600-0714.2011.01067.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Josephy PD, Pan D, Ianni MD, Mannervik B. Functional studies of single-nucleotide polymorphic variants of human glutathione transferase T1-1 involving residues in the dimer interface. Arch Biochem Biophys 2011; 513:87-93. [PMID: 21781954 DOI: 10.1016/j.abb.2011.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 07/02/2011] [Accepted: 07/04/2011] [Indexed: 11/27/2022]
Abstract
Glutathione transferase T1-1 catalyses detoxication and bioactivation processes in which glutathione conjugates are formed from endogenous and xenobiotic substrates, including alkylating agents and halogenated alkanes. Although the common null polymorphism of the human GSTT1 gene has been studied extensively, little is known about the consequences of GSTT1 single-nucleotide polymorphisms (SNPs). Here, we have examined the effects of two SNPs that alter amino acid residues in the dimer interface of the GST T1-1 protein and one that causes a conservative substitution in the core of the subunit. Variant proteins were expressed in an Escherichia coli strain in which the metabolism of ethylene dibromide to a glutathione conjugate leads to lacZ reversion mutations. We measured the kinetic properties of the enzymes with the characteristic substrate 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP) and determined the specific activities with several other substrates. Circular dichroism spectroscopy was used to measure protein thermal denaturation profiles. Variant T104P, which has been reported as inactive, showed weak but detectable activity with each substrate. Variant R76S was expressed at lower levels and showed much-reduced thermal stability. The results are interpreted in the context of the three-dimensional structure of human GST T1-1.
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Affiliation(s)
- P David Josephy
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G2W1.
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Abstract
Cisplatin ototoxicity affects different individuals in a widely variable manner. These variations are likely to be explained by genetic differences among those affected. It would be highly advantageous to identify genetic variants that predispose to cisplatin ototoxicity in order to minimize the risk to susceptible subgroups. Although this area of research is very important, only a few studies have rigorously examined the genetic basis for cisplatin-induced susceptibility to hearing loss. This article addresses recent progress in clarifying the incidence of cisplatin ototoxicity and the risk factors and controversies regarding the identification of genetic variants associated with cisplatin-induced hearing loss.
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Affiliation(s)
- Debashree Mukherjea
- Department of Surgery, Division of Otolaryngology, Southern Illinois University, School of Medicine, Springfield, IL, USA.
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Pot L, Alizadeh B, Ahrenberg D, Coenraads PJ, Snieder H, Blömeke B. No major role for glutathione S-transferase gene polymorphisms in sensitization to para-phenylenediamine and other xenobiotics: a study of association and a meta-analysis. Br J Dermatol 2011; 164:890-2. [DOI: 10.1111/j.1365-2133.2010.10197.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Butler MW, Hackett NR, Salit J, Strulovici-Barel Y, Omberg L, Mezey J, Crystal RG. Glutathione S-transferase copy number variation alters lung gene expression. Eur Respir J 2011; 38:15-28. [PMID: 21349909 DOI: 10.1183/09031936.00029210] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The glutathione S-transferase (GST) enzymes catalyse the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNVs) modulate some GST gene expression levels, and that the small airway epithelium (SAE) and alveolar macrophages (AMs) are involved early in the pathogenesis of smoking-induced lung disease, we asked: do germline CNVs modulate GST expression levels in SAE and AMs? Microarrays were used to survey GST gene expression and determine CNVs genotypes in SAE and AMs obtained by bronchoscopy from current smokers and nonsmokers. 26% of subjects were null for both GSTM1 alleles, with reduced GSTM1 mRNA levels seen in both SAE and AMs. 30% of subjects had homozygous deletions of GSTT1, with reduced mRNA levels in both tissues. Interestingly, GSTT2B exhibited homozygous deletion in the blood of 27% of subjects and was not expressed in SAE in the remainder of subjects, but was expressed in AMs of heterozygotes and wild-type subjects, proportionate to genotype. These data show a germline CNV-mediated linear relationship of genotype with expression level, suggesting minimal compensation of gene expression levels in heterozygotes, consistent with GST polymorphisms playing a role in the risk of smoking-associated, xenobiotic-induced lung disease.
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Affiliation(s)
- M W Butler
- Dept of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USA
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Kogevinas M, Villanueva CM, Font-Ribera L, Liviac D, Bustamante M, Espinoza F, Nieuwenhuijsen MJ, Espinosa A, Fernandez P, DeMarini DM, Grimalt JO, Grummt T, Marcos R. Genotoxic effects in swimmers exposed to disinfection by-products in indoor swimming pools. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:1531-7. [PMID: 20833606 PMCID: PMC2974689 DOI: 10.1289/ehp.1001959] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 06/21/2010] [Accepted: 08/03/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Exposure to disinfection by-products (DBPs) in drinking water has been associated with cancer risk. A recent study (Villanueva et al. 2007; Am J Epidemiol 165:148-156) found an increased bladder cancer risk among subjects attending swimming pools relative to those not attending. OBJECTIVES We evaluated adults who swam in chlorinated pools to determine whether exposure to DBPs in pool water is associated with biomarkers of genotoxicity. METHODS We collected blood, urine, and exhaled air samples from 49 nonsmoking adult volunteers before and after they swam for 40 min in an indoor chlorinated pool. We estimated associations between the concentrations of four trihalomethanes (THMs) in exhaled breath and changes in micronuclei (MN) and DNA damage (comet assay) in peripheral blood lymphocytes before and 1 hr after swimming; urine mutagenicity (Ames assay) before and 2 hr after swimming; and MN in exfoliated urothelial cells before and 2 weeks after swimming. We also estimated associations and interactions with polymorphisms in genes related to DNA repair or to DBP metabolism. RESULTS After swimming, the total concentration of the four THMs in exhaled breath was seven times higher than before swimming. The change in the frequency of micronucleated lymphocytes after swimming increased in association with higher exhaled concentrations of the brominated THMs (p = 0.03 for bromodichloromethane, p = 0.05 for chlorodibromomethane, p = 0.01 for bromoform) but not chloroform. Swimming was not associated with DNA damage detectable by the comet assay. Urine mutagenicity increased significantly after swimming, in association with the higher concentration of exhaled bromoform (p = 0.004). We found no significant associations with changes in micronucleated urothelial cells. CONCLUSIONS Our findings support potential genotoxic effects of exposure to DBPs from swimming pools. The positive health effects gained by swimming could be increased by reducing the potential health risks of pool water.
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Affiliation(s)
- Manolis Kogevinas
- Centre for Research in Environmental Epidemiology, Barcelona, Spain.
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35
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Josephy PD. Genetic variations in human glutathione transferase enzymes: significance for pharmacology and toxicology. HUMAN GENOMICS AND PROTEOMICS : HGP 2010; 2010:876940. [PMID: 20981235 PMCID: PMC2958679 DOI: 10.4061/2010/876940] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 03/22/2010] [Indexed: 01/21/2023]
Abstract
Glutathione transferase enzymes (GSTs) catalyze reactions in which electrophiles are conjugated to the tripeptide thiol glutathione. While many GST-catalyzed transformations result in the detoxication of xenobiotics, a few substrates, such as dihaloalkanes, undergo bioactivation to reactive intermediates. Many molecular epidemiological studies have tested associations between polymorphisms (especially, deletions) of human GST genes and disease susceptibility or response to therapy. This review presents a discussion of the biochemistry of GSTs, the sources-both genetic and environmental-of interindividual variation in GST activities, and their implications for pharmaco- and toxicogenetics; particular attention is paid to the Theta class GSTs.
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Affiliation(s)
- P David Josephy
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
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36
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Current world literature. Curr Opin Lipidol 2010; 21:148-52. [PMID: 20616627 DOI: 10.1097/mol.0b013e3283390e49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Shokeer A, Mannervik B. Minor modifications of the C-terminal helix reschedule the favored chemical reactions catalyzed by theta class glutathione transferase T1-1. J Biol Chem 2009; 285:5639-45. [PMID: 20022951 DOI: 10.1074/jbc.m109.074757] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adaptive responses to novel toxic challenges provide selective advantages to organisms in evolution. Glutathione transferases (GSTs) play a pivotal role in the cellular defense because they are main contributors to the inactivation of genotoxic compounds of exogenous as well as of endogenous origins. GSTs are promiscuous enzymes catalyzing a variety of chemical reactions with numerous alternative substrates. Despite broad substrate acceptance, individual GSTs display pronounced selectivities such that only a limited number of substrates are transformed with high catalytic efficiency. The present study shows that minor structural changes in the C-terminal helix of mouse GST T1-1 induce major changes in the substrate-activity profile of the enzyme to favor novel chemical reactions and to suppress other reactions catalyzed by the parental enzyme.
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Affiliation(s)
- Abeer Shokeer
- Department of Biochemistry and Organic Chemistry, Uppsala University, Biomedical Center, Box 576, SE-75123 Uppsala, Sweden
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DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences. Proc Natl Acad Sci U S A 2009; 107:234-9. [PMID: 19966297 DOI: 10.1073/pnas.0907606106] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease.
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