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Villani F, Guarracino A, Ward RR, Green T, Emms M, Pravenec M, Prins P, Garrison E, Williams RW, Chen H, Colonna V. Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575041. [PMID: 38260597 PMCID: PMC10802574 DOI: 10.1101/2024.01.10.575041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between Pirl1l1, chromogranin expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
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Affiliation(s)
- Flavia Villani
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Rachel R Ward
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Tomomi Green
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Madeleine Emms
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W. Williams
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Vincenza Colonna
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
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Doris PA. Genetics of hypertension: an assessment of progress in the spontaneously hypertensive rat. Physiol Genomics 2017; 49:601-617. [PMID: 28916635 DOI: 10.1152/physiolgenomics.00065.2017] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The application of gene mapping methods to uncover the genetic basis of hypertension in the inbred spontaneously hypertensive rat (SHR) began over 25 yr ago. This animal provides a useful model of genetic high blood pressure, and some of its features are described. In particular, it appears to be a polygenic model of disease, and polygenes participate in human hypertension genetic risk. The SHR hypertension alleles were fixed rapidly by selective breeding in just a few generations and so are presumably common genetic variants present in the outbred Wistar strain from which SHR was created. This review provides a background to the origins and genesis of this rat line. It considers its usefulness as a model organism for a common cardiovascular disease. The progress and obstacles facing mapping are considered in depth, as are the emergence and application of other genome-wide genetic discovery approaches that have been applied to investigate this model. Candidate genes, their identification, and the evidence to support their potential role in blood pressure elevation are considered. The review assesses the progress that has arisen from this work has been limited. Consideration is given to some of the factors that have impeded progress, and prospects for advancing understanding of the genetic basis of hypertension in this model are discussed.
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Affiliation(s)
- Peter A Doris
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
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Braun MC, Herring SM, Gokul N, Monita M, Bell R, Zhu Y, Gonzalez-Garay ML, Wenderfer SE, Doris PA. Hypertensive renal injury is associated with gene variation affecting immune signaling. ACTA ACUST UNITED AC 2014; 7:903-10. [PMID: 25366137 DOI: 10.1161/circgenetics.114.000533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND The spontaneously hypertensive rat (SHR) strain exists in lines that contrast strongly in susceptibility to renal injury in hypertension. These inbred lines share common ancestry, and only 13% of their genomes arise from different ancestors. METHODS AND RESULTS We used next gen sequencing to detect natural allelic variation in 5 genes of the immunoreceptor signaling pathway (IgH, Dok3, Src, Syk, and JunD) that arise from different ancestors in the injury-prone SHR-A3 and the resistant SHR-B2 lines. We created an intercross between these lines, and in the F2 progeny, we observed that the inheritance of haplotype blocks containing the SHR-A3 alleles of these 5 genes correlated with increased albuminuria and histological measures of renal injury. To test whether accumulated genetic variation in this pathway may create a therapeutic target in hypertensive renal injury, rats of both lines were treated with the immunosuppressant mycophenolate mofetil (MMF). MMF reduced proteinuria (albumin to creatinine ratio) from 6.6 to 1.2 mg/mg (P<0.001) in SHR-A3. Glomerular injury scores were reduced in MMF-treated SHR-A3 from 1.6 to 1.4 (P<0.002). Tubulo-interstitial injury was reduced in MMF-treated SHR-A3 from 2.62 to 2.0 (P=0.001). MMF treatment also reduced renal fibrosis in SHR-A3 (3.9 versus 2.0; P<0.001). CONCLUSIONS Polygenic susceptibility to renal injury in hypertension arises in association with genetic variation in genes that participate in immune responses and is dramatically improved by reduction of immune system activity.
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Affiliation(s)
- Michael C Braun
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Stacy M Herring
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Nisha Gokul
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Monique Monita
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Rebecca Bell
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Yaming Zhu
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Manuel L Gonzalez-Garay
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Scott E Wenderfer
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston
| | - Peter A Doris
- From the Department of Pediatrics, Baylor College of Medicine (M.C.B., S.E.W.), and Institute of Molecular Medicine (S.M.H., N.G., M.M., R.B., Y.Z., M.L.G.-G., P.A.D.), University of Texas Health Science Center at Houston.
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Abstract
BACKGROUND Spontaneously hypertensive rat (SHR) lines differ in their susceptibility to hypertensive end-organ disease and may provide an informative model of genetic risk of disease. Lines derived from the original SHR-B and SHR-C clades are highly resistant to hypertensive end-organ disease, whereas lines derived from the SHR-A clade were selected for stroke susceptibility and experience hypertensive renal disease. METHOD Here we characterize the temporal development of progressive renal injury in SHR-A3 animals consuming 0.3% sodium in the diet and drinking water. SHR-A3 rats demonstrate albuminuria, glomerular damage, tubulointerstitial injury, and renal fibrosis that emerge at 18 weeks of age and progress. RESULTS AND CONCLUSION Mortality of SHR-A3 animals was 50% at 40 weeks of age, and animals surviving to this age had reduced renal function. In contrast SHR-B2, which are 87% genetically identical to SHR-A3, are substantially protected from renal injury and demonstrate only moderate changes in albuminuria and renal histological injury over this time period. At 40 weeks of age, electron microscopy of the renal glomerulus revealed severe podocyte effacement in SHR-A3, but slit diaphragm architecture in SHR-B2 at this age was well preserved. Renal injury traits in the F1 and F2 progeny of an intercross between SHR-A3 and SHR-B2 were measured to determine heritability of renal injury in this model. Heritability of albuminuria, glomerular injury, and tubulointerstitial injury were estimated at 48.9, 66.5 and 58.6%, respectively. We assessed the relationship between blood pressure and renal injury measures in the F2 animals and found some correlation between these variables that explain up to 26% of the trait variation. Quantitative trait locus (QTL) mapping was performed using over 200 single nucleotide polymorphism markers distributed across the 13% of the genome that differs between these two closely related lines. Mapping of albuminuria, tubulointerstitial injury, and renal fibrosis failed to identify loci linked with disease susceptibility, suggesting a complex inheritance of disease risk. We detected a single QTL conferring susceptibility to glomerular injury that was confined to a small haplotype block at chromosome 14:70-76Mb.
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Haloui M, Tremblay J, Seda O, Koltsova SV, Maksimov GV, Orlov SN, Hamet P. Increased Renal Epithelial Na Channel Expression and Activity Correlate With Elevation of Blood Pressure in Spontaneously Hypertensive Rats. Hypertension 2013; 62:731-7. [PMID: 23959560 DOI: 10.1161/hypertensionaha.113.01295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mounsif Haloui
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
| | - Johanne Tremblay
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
| | - Ondrej Seda
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
| | - Svetlana V. Koltsova
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
| | - Georgy V. Maksimov
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
| | - Sergei N. Orlov
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
| | - Pavel Hamet
- From the Centre de Recherche, Centre Hospitalier de l’Université de Montréal (CRCHUM) – Technopôle Angus, QC, Canada (M.H., J.T., O.S., S.V.K., S.N.O.); and the Faculty of Biology, M.V. Lomonosov Moscow State University, Russia (G.V.M., S.N.O.)
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Gaur U, Li K, Mei S, Liu G. Research progress in allele-specific expression and its regulatory mechanisms. J Appl Genet 2013; 54:271-83. [PMID: 23609142 DOI: 10.1007/s13353-013-0148-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/22/2013] [Accepted: 04/03/2013] [Indexed: 12/12/2022]
Abstract
Although the majority of genes are expressed equally from both alleles, some genes are differentially expressed. Organisms possess characteristics to preferentially express a particular allele under regulatory factors, which is termed allele-specific expression (ASE). It is one of the important genetic factors that lead to phenotypic variation and can be used to identify the variance of gene regulation factors. ASE indicates mechanisms such as DNA methylation, histone modifications, and non-coding RNAs function. Here, we review a broad survey of progress in ASE studies, and what this simple yet very effective approach can offer in functional genomics, and possible implications toward our better understanding of the underlying mechanisms of complex traits.
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Affiliation(s)
- Uma Gaur
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, People's Republic of China
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Shen HC, Hammock BD. Discovery of inhibitors of soluble epoxide hydrolase: a target with multiple potential therapeutic indications. J Med Chem 2012; 55:1789-808. [PMID: 22168898 PMCID: PMC3420824 DOI: 10.1021/jm201468j] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hong C. Shen
- RY800-C114, Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, NJ07065, 609-716-9647
| | - Bruce D. Hammock
- Department of Entomology &Cancer Center, University of California, Davis, CA 95616 USA, 530-752-7519
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Nabika T, Ohara H, Kato N, Isomura M. The stroke-prone spontaneously hypertensive rat: still a useful model for post-GWAS genetic studies? Hypertens Res 2012; 35:477-84. [PMID: 22399095 DOI: 10.1038/hr.2012.30] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The stroke-prone spontaneously hypertensive rat (SHRSP) is a unique genetic model of severe hypertension and cerebral stroke. SHRSP, as well as the spontaneously hypertensive rat, the parental strain of SHRSP, has made a tremendous contribution to cardiovascular research. However, the genetic mechanisms underlying hypertension and stroke in these rats have not yet been clarified. Recent studies using whole-genome sequencing and comprehensive gene expression analyses combined with classical quantitative trait loci analyses provided several candidate genes, such as Ephx2, Gstm1 and Slc34a1, which still need further evidence to define their pathological roles. Currently, genome-wide association studies can directly identify candidate genes for hypertension in the human genome. Thus, genetic studies in SHRSP and other rat models must be focused on the pathogenetic roles of 'networks of interacting genes' in hypertension, instead of searching for individual candidate genes.
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Affiliation(s)
- Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan.
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Mick E, McGough JJ, Middleton FA, Neale B, Faraone SV. Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder. Prog Neuropsychopharmacol Biol Psychiatry 2011; 35:466-72. [PMID: 21130132 DOI: 10.1016/j.pnpbp.2010.11.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 12/31/2022]
Abstract
OBJECTIVE We conducted a genome-wide association study of blood pressure in an open-label study of the methylphenidate transdermal system (MTS) for the treatment of attention-deficit/hyperactivity disorder (ADHD). METHOD Genotyping was conducted with the Affymetrix Genome-Wide Human SNP Array 6.0. Multivariate association analyses were conducted using the software package PLINK. After data cleaning and quality control we tested 316,934 SNPs in 140 children with ADHD. RESULTS We observed no genome-wide statistically significant findings, but a SNP in a K(+)-dependent Na(+)/Ca(2+) exchanger expressed in vascular smooth muscle (SLC24A3) was included in our top associations at p<1E-04. Genetic enrichment analyses of genes with ≥1 SNP significant at p<0.01, implicated several functional categories (FERM domain, p=5.0E-07; immunoglobulin domain, p=8.1E-06; the transmembrane region, p=4.4E-05; channel activity, p=2.0E-04; and type-III fibronectins, p=2.7E-05) harboring genes previously associated with related cardiovascular phenotypes. CONCLUSIONS The hypothesis generating results from this study suggests that polymorphisms in several genes consistently associated with cardiovascular diseases may impact changes in blood pressure observed with methylphenidate pharmacotherapy in children with ADHD.
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Affiliation(s)
- Eric Mick
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States.
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Bell R, Herring SM, Gokul N, Monita M, Grove ML, Boerwinkle E, Doris PA. High-resolution identity by descent mapping uncovers the genetic basis for blood pressure differences between spontaneously hypertensive rat lines. ACTA ACUST UNITED AC 2011; 4:223-31. [PMID: 21406686 DOI: 10.1161/circgenetics.110.958934] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The recent development of a large panel of genome-wide single nucleotide polymorphisms (SNPs) provides the opportunity to examine genetic relationships between distinct SHR lines that share hypertension but differ in their susceptibility to hypertensive end-organ disease. METHODS AND RESULTS We compared genotypes at nearly 10,000 SNPs obtained for the hypertension end-organ injury-susceptible spontaneously hypertensive rat (SHR)-A3 (SHRSP, SHR-stroke prone) line and the injury-resistant SHR-B2 line. This revealed that that the 2 lines were genetically identical by descent (IBD) across 86.6% of the genome. Areas of the genome that were not IBD were distributed across 19 of the 20 autosomes and the X chromosome. A block structure of non-IBD comprising a total of 121 haplotype blocks was formed by clustering of SNPs inherited from different ancestors. To test the null hypothesis that distinct SHR lines share a common set of hypertension susceptibility alleles, we compared blood pressure in adult SHR animals from both lines and their F1 and F2 progeny using telemetry. In 16- to 18-week-old animals fed a normal diet, systolic blood pressure (SBP, mm Hg) in SHR-A3 was 205.7 ± 3.86 (mean ± SEM, n = 26), whereas in similar SHR-B2 animals, SBP was 186.7 ± 2.53 (n = 20). In F1 and F2 animals, SBP was 188.2 ± 4.23 (n = 19) and 185.6 ± 1.1 (n = 211), respectively (P<10(-6), ANOVA). To identify non-IBD haplotype blocks contributing to blood pressure differences between these SHR lines, we developed a high-throughput SNP genotyping system to genotype SNPs marking non-IBD blocks. We mapped a single non-IBD block on chromosome 17 extending over <10 Mb, at which SHR-A3 alleles significantly elevate blood pressure compared with SHR-B2. CONCLUSIONS Thus hypertension in SHR-A3 and -B2 appears to arise from an overlapping set of susceptibility alleles, with SHR-A3 possessing an additional hypertension locus that contributes to further increase blood pressure.
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Affiliation(s)
- Rebecca Bell
- Institute of Molecular Medicine, University of Texas HSC at Houston, Houston, TX 77030, USA
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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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de Matsumoto JPP, de Ferrari MFR, Fior-Chadi DR. Adenosine receptor type 2a is differently modulated by nicotine in dorsal brainstem cells of Wistar Kyoto and spontaneously hypertensive rats. J Neural Transm (Vienna) 2010; 117:799-807. [DOI: 10.1007/s00702-010-0417-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 05/02/2010] [Indexed: 02/04/2023]
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