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Wang Y, Wang Y. Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles. NPJ Syst Biol Appl 2024; 10:62. [PMID: 38816426 PMCID: PMC11139989 DOI: 10.1038/s41540-024-00388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Individual may response to drug treatment differently due to their genetic variants located in enhancers. These variants can alter transcription factor's (TF) binding strength, affect enhancer's chromatin activity or interaction, and eventually change expression level of downstream gene. Here, we propose a computational framework, PERD, to Predict the Enhancers Responsive to Drug. A machine learning model was trained to predict the genome-wide chromatin accessibility from transcriptome data using the paired expression and chromatin accessibility data collected from ENCODE and ROADMAP. Then the model was applied to the perturbed gene expression data from Connectivity Map (CMAP) and Cancer Drug-induced gene expression Signature DataBase (CDS-DB) and identify drug responsive enhancers with significantly altered chromatin accessibility. Furthermore, the drug responsive enhancers were related to the pharmacogenomics genome-wide association studies (PGx GWAS). Stepping on the traditional drug-associated gene signatures, PERD holds the promise to enhance the causality of drug perturbation by providing candidate regulatory element of those drug associated genes.
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Affiliation(s)
- Yongcui Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 330106, China.
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2
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Abrahams-October Z, Lloyd S, Pearce B, Johnson R, Benjeddou M. Promoter haplotype structure of solute carrier 22 member 2 (SLC22A2) in the Xhosa population of South Africa and their differential effect on gene expression. Gene X 2022; 820:146292. [PMID: 35143948 DOI: 10.1016/j.gene.2022.146292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 02/03/2022] [Indexed: 11/20/2022] Open
Abstract
SLC22A2 is abundantly expressed in the kidney and facilitates the transport of endogenous and exogenous cationic compounds. It plays a pivotal role in the transport of pharmacologically important compounds such as metformin, cisplatin, lamivudine and cimetidine. Polymorphisms within SLC22A2 could potentially contribute to the inter-individual variable response to drugs. The SLC22A2 gene is known to show polymorphism variability amongst populations of different ethnicities. The present study was undertaken to characterize the promoter haplotype structure of the SLC22A2 gene in the Xhosa population of South Africa. In addition to this, we also investigate the effects of the observed promoter haplotypes on gene expression levels in vitro. We identified six known single nucleotide polymorphisms in the promoter region, namely rs60249401 (G424A), rs113150889 (G289A), rs55920607 (C246T), rs59695691 (A195G), rs572296424 (G156A), rs150063153 (A95C/G) and one novel SNP at location 6:160258967 (A209T). While these polymorphisms appeared in other African and non-African populations, their minor allele frequencies differed considerably from the non-African populations and could be considered to be African specific. A total of nine promoter haplotypes were characterized and the functional significance of each haplotype on promoter activity was determined using a luciferase reporter assay system. Amongst the nine observed haplotypes, three haplotypes (i.e. haplotypes 7, 8 and 9) displayed a significant decrease in expression level when compared to the wild-type with p -values of: 0.0317, <0.0001 and 0.0013 respectively. The data presented here shows African specific promoter haplotypes to cause a decrease in SLC22A2 gene expression levels, which in turn may have an impact on the pharmacokinetic profiles of cationic drugs.
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Affiliation(s)
- Zainonesa Abrahams-October
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa.
| | - Sheridon Lloyd
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | - Brendon Pearce
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, 7505 Cape Town, South Africa; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Mongi Benjeddou
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
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3
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Pavlovic S, Kotur N, Stankovic B, Zukic B, Gasic V, Dokmanovic L. Pharmacogenomic and Pharmacotranscriptomic Profiling of Childhood Acute Lymphoblastic Leukemia: Paving the Way to Personalized Treatment. Genes (Basel) 2019; 10:E191. [PMID: 30832275 PMCID: PMC6471971 DOI: 10.3390/genes10030191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Personalized medicine is focused on research disciplines which contribute to the individualization of therapy, like pharmacogenomics and pharmacotranscriptomics. Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood. It is one of the pediatric malignancies with the highest cure rate, but still a lethal outcome due to therapy accounts for 1%⁻3% of deaths. Further improvement of treatment protocols is needed through the implementation of pharmacogenomics and pharmacotranscriptomics. Emerging high-throughput technologies, including microarrays and next-generation sequencing, have provided an enormous amount of molecular data with the potential to be implemented in childhood ALL treatment protocols. In the current review, we summarized the contribution of these novel technologies to the pharmacogenomics and pharmacotranscriptomics of childhood ALL. We have presented data on molecular markers responsible for the efficacy, side effects, and toxicity of the drugs commonly used for childhood ALL treatment, i.e., glucocorticoids, vincristine, asparaginase, anthracyclines, thiopurines, and methotrexate. Big data was generated using high-throughput technologies, but their implementation in clinical practice is poor. Research efforts should be focused on data analysis and designing prediction models using machine learning algorithms. Bioinformatics tools and the implementation of artificial i Lack of association of the CEP72 rs924607 TT genotype with intelligence are expected to open the door wide for personalized medicine in the clinical practice of childhood ALL.
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Affiliation(s)
- Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Lidija Dokmanovic
- University Children's Hospital, 11000 Belgrade, Serbia.
- University of Belgrade, Faculty of Medicine, 11000 Belgrade, Serbia.
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4
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Lauschke VM, Ingelman-Sundberg M. Prediction of drug response and adverse drug reactions: From twin studies to Next Generation Sequencing. Eur J Pharm Sci 2019; 130:65-77. [PMID: 30684656 DOI: 10.1016/j.ejps.2019.01.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/12/2023]
Abstract
Understanding and predicting inter-individual differences related to the success of drug therapy is of tremendous importance, both during drug development and for clinical applications. Importantly, while seminal twin studies indicate that the majority of inter-individual differences in drug disposition are driven by hereditary factors, common genetic polymorphisms explain only less than half of this genetically encoded variability. Recent progress in Next Generation Sequencing (NGS) technologies has for the first time allowed to comprehensively map the genetic landscape of human pharmacogenes. Importantly, these projects have unveiled vast numbers of rare genetic variants, which are estimated to contribute substantially to the missing heritability of drug metabolism phenotypes. However, functional interpretation of these rare variants remains challenging and constitutes one of the important frontiers of contemporary pharmacogenomics. Furthermore, NGS technologies face challenges in the interrogation of genes residing in complex genomic regions, such as CYP2D6 and HLA genes. We here provide an update of the implementation of pharmacogenomic variations in the clinical setting and present emerging strategies that facilitate the translation of NGS data into clinically useful information. Importantly, we anticipate that these developments will soon result in a paradigm shift of pre-emptive genotyping away from the interrogation to candidate variants and towards the comprehensive profiling of an individuals genotype, thus allowing for a true individualization of patient drug treatment regimens.
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Affiliation(s)
- Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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5
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Eclov RJ, Kim MJ, Chhibber A, Smith RP, Ahituv N, Kroetz DL. ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression. Pharmacogenet Genomics 2018; 27:454-463. [PMID: 28930109 DOI: 10.1097/fpc.0000000000000312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The expression and activity of the breast cancer resistance protein (ABCG2) contributes toward the pharmacokinetics of endogenous and xenobiotic substrates. The effect of genetic variation on the activity of cis-regulatory elements and nuclear response elements in the ABCG2 locus and their contribution toward ABCG2 expression have not been investigated systematically. In this study, the effect of genetic variation on the in vitro and in vivo enhancer activity of six previously identified liver enhancers in the ABCG2 locus was examined. METHODS Reference and variant liver enhancers were tested for their ability to alter luciferase activity in vitro in HepG2 and HEK293T cell lines and in vivo using a hydrodynamic tail vein assay. Positive in vivo single-nucleotide polymorphisms (SNPs) were tested for association with gene expression and for altered protein binding in electrophoretic mobility shift assays. RESULTS Multiple SNPs were found to alter enhancer activity in vitro. Four of these variants (rs9999111, rs12508471, ABCG2RE1*2, and rs149713212) decreased and one (rs2725263) increased enhancer activity in vivo. In addition, rs9999111 and rs12508471 were associated with ABCG2 expression in lymphoblastoid cell lines, lymphocytes, and T cells, and showed increased HepG2 nuclear protein binding. CONCLUSION This study identifies SNPs within regulatory regions of the ABCG2 locus that alter enhancer activity in vitro and in vivo. Several of these SNPs correlate with tissue-specific ABCG2 expression and alter DNA/protein binding. These SNPs could contribute toward reported tissue-specific variability in ABCG2 expression and may influence the correlation between ABCG2 expression and disease risk or the pharmacokinetics and pharmacodynamics of breast cancer resistance protein substrates.
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Affiliation(s)
- Rachel J Eclov
- aDepartment of Bioengineering and Therapeutic Sciences bInstitute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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6
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Han N, Song YK, Burckart GJ, Ji E, Kim IW, Oh JM. Regulation of Pharmacogene Expression by microRNA in The Cancer Genome Atlas (TCGA) Research Network. Biomol Ther (Seoul) 2017; 25:482-489. [PMID: 28835003 PMCID: PMC5590791 DOI: 10.4062/biomolther.2017.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 01/19/2017] [Accepted: 06/26/2017] [Indexed: 11/16/2022] Open
Abstract
Individual differences in drug responses are associated with genetic and epigenetic variability of pharmacogene expression. We aimed to identify the relevant miRNAs which regulate pharmacogenes associated with drug responses. The miRNA and mRNA expression profiles derived from data for normal and solid tumor tissues in The Cancer Genome Atlas (TCGA) Research Network. Predicted miRNAs targeted to pharmacogenes were identified using publicly available databases. A total of 95 pharmacogenes were selected from cholangiocarcinoma and colon adenocarcinoma, as well as kidney renal clear cell, liver hepatocellular, and lung squamous cell carcinomas. Through the integration analyses of miRNA and mRNA, 35 miRNAs were found to negatively correlate with mRNA expression levels of 16 pharmacogenes in normal bile duct, liver, colon, and lung tissues (p<0.05). Additionally, 36 miRNAs were related to differential expression of 32 pharmacogene mRNAs in those normal and tumorigenic tissues (p<0.05). These results indicate that changes in expression levels of miRNAs targeted to pharmacogenes in normal and tumor tissues may play a role in determining individual variations in drug response.
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Affiliation(s)
- Nayoung Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826,
Republic of Korea
| | - Yun-Kyoung Song
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826,
Republic of Korea
| | - Gilbert J. Burckart
- Office of Clinical Pharmacology, Office of Translational Sciences, Food and Drug Administration, Silver Spring, Maryland 20993,
USA
| | - Eunhee Ji
- College of Pharmacy, Gacheon University, Incheon 13120,
Republic of Korea
| | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826,
Republic of Korea
| | - Jung Mi Oh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826,
Republic of Korea
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7
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LIU LIJUN, CHANG YU, DU SHULI, SHI XUGANG, YANG HUA, KANG LONGLI, JIN TIANBO, YUAN DONGYA, HE YONGJUN. Genetic analysis of drug metabolizing phase-I enzymes CYP3A4 in Tibetan populations. J Genet 2017; 96:219-225. [DOI: 10.1007/s12041-017-0757-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Dalvie S, Koen N, McGregor N, O'Connell K, Warnich L, Ramesar R, Nievergelt CM, Stein DJ. Toward a Global Roadmap for Precision Medicine in Psychiatry: Challenges and Opportunities. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:557-564. [PMID: 27636104 DOI: 10.1089/omi.2016.0110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mental disorders represent a major public health burden worldwide. This is likely to rise in the next decade, with the highest increases predicted to occur in low- and middle-income countries. Current psychotropic medication treatment guidelines focus on uniform approaches to the treatment of heterogeneous disorders and achieve only partial therapeutic success. Developing a global precision medicine approach in psychiatry appears attractive, given the value of this approach in other fields of medicine, such as oncology and infectious diseases. In this horizon scanning analysis, we review the salient opportunities and challenges for precision medicine in psychiatry over the next decade. Variants within numerous genes involved in a range of pathways have been implicated in psychotropic drug response and might ultimately be used to guide choice of pharmacotherapy. Multipronged approaches such as multi-omics (genomics, proteomics, metabolomics) analyses and systems diagnostics together with high-throughput sequencing and genotyping technologies hold promise for identifying precise and targeted treatments in mental disorders. To date, however, the vast majority of pharmacogenomics work has been undertaken in high-income countries on a relatively small proportion of the global population, and many other challenges face the field. Opportunities and challenges for establishing a global roadmap for precision medicine in psychiatry are discussed in this article.
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Affiliation(s)
- Shareefa Dalvie
- 1 Department of Psychiatry and Mental Health, University of Cape Town , Cape Town, South Africa .,2 MRC/UCT Human Genetics Research Unit, Division of Human Genetics, University of Cape Town , Cape Town, South Africa
| | - Nastassja Koen
- 1 Department of Psychiatry and Mental Health, University of Cape Town , Cape Town, South Africa .,3 Medical Research Council (MRC) Unit on Anxiety and Stress Disorders , Cape Town, South Africa
| | - Nathaniel McGregor
- 4 Department of Genetics, Stellenbosch University , Tygerberg, South Africa .,5 Department of Psychiatry, Stellenbosch University , Tygerberg, South Africa
| | - Kevin O'Connell
- 4 Department of Genetics, Stellenbosch University , Tygerberg, South Africa
| | - Louise Warnich
- 4 Department of Genetics, Stellenbosch University , Tygerberg, South Africa
| | - Raj Ramesar
- 2 MRC/UCT Human Genetics Research Unit, Division of Human Genetics, University of Cape Town , Cape Town, South Africa
| | - Caroline M Nievergelt
- 6 Department of Psychiatry, University of California San Diego , San Diego, California.,7 Veteran Affairs (VA) San Diego Center of Excellence for Stress and Mental Health , San Diego, California
| | - Dan J Stein
- 1 Department of Psychiatry and Mental Health, University of Cape Town , Cape Town, South Africa .,3 Medical Research Council (MRC) Unit on Anxiety and Stress Disorders , Cape Town, South Africa
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9
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Abstract
Nucleotide changes in gene regulatory elements can have a major effect on interindividual differences in drug response. For example, by reviewing all published pharmacogenomic genome-wide association studies, we show here that 96.4% of the associated single nucleotide polymorphisms reside in noncoding regions. We discuss how sequencing technologies are improving our ability to identify drug response-associated regulatory elements genome-wide and to annotate nucleotide variants within them. We highlight specific examples of how nucleotide changes in these elements can affect drug response and illustrate the techniques used to find them and functionally characterize them. Finally, we also discuss challenges in the field of drug-responsive regulatory elements that need to be considered in order to translate these findings into the clinic.
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Affiliation(s)
- Marcelo R Luizon
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
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10
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Tafrali C, Paizi A, Borg J, Radmilovic M, Bartsakoulia M, Giannopoulou E, Giannakopoulou O, Stojiljkovic-Petrovic M, Zukic B, Poulas K, Stavrou EF, Lambropoulou P, Kourakli A, Felice AE, Papachatzopoulou A, Philipsen S, Pavlovic S, Georgitsi M, Patrinos GP. Genomic variation in the MAP3K5 gene is associated with β-thalassemia disease severity and hydroxyurea treatment efficacy. Pharmacogenomics 2013; 14:469-83. [PMID: 23556445 DOI: 10.2217/pgs.13.31] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM In this study we explored the association between genetic variations in MAP3K5 and PDE7B genes, residing on chromosome 6q23, and disease severity in β-hemoglobinopathy patients, as well as the association between these variants with response to hydroxyurea (HU) treatment. Furthermore, we examined MAP3K5 expression in the context of high fetal hemoglobin (HbF) and upon HU treatment in erythroid progenitor cells from healthy and KLF1 haploinsufficient individuals. MATERIALS & METHODS For this purpose, we genotyped β-thalassemia intermedia and major patients and healthy controls, as well as a cohort of compound heterozygous sickle cell disease/β-thalassemia patients receiving HU as HbF augmentation treatment. Furthermore, we examined MAP3K5 expression in the context of high HbF and upon HU treatment in erythroid progenitor cells from healthy and KLF1 haploinsufficient individuals. RESULTS A short tandem repeat in the MAP3K5 promoter and two intronic MAP3K5 gene variants, as well as a PDE7B variant, are associated with low HbF levels and a severe disease phenotype. Moreover, MAP3K5 mRNA expression levels are altered in the context of high HbF and are affected by the presence of HU. Lastly, the abovementioned MAP3K5 variants are associated with HU treatment efficacy. CONCLUSION Our data suggest that these MAP3K5 variants are indicative of β-thalassemia disease severity and response to HU treatment.
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Affiliation(s)
- Christina Tafrali
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
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11
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Drögemöller B, Plummer M, Korkie L, Agenbag G, Dunaiski A, Niehaus D, Koen L, Gebhardt S, Schneider N, Olckers A, Wright G, Warnich L. Characterization of the genetic variation present in CYP3A4 in three South African populations. Front Genet 2013; 4:17. [PMID: 23423246 PMCID: PMC3574981 DOI: 10.3389/fgene.2013.00017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/01/2013] [Indexed: 12/26/2022] Open
Abstract
The CYP3A4 enzyme is the most abundant human cytochrome P450 (CYP) and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry (MA) individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of ~600 bp of the 5′-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4*12, CYP3A4*15, and the reportedly functional CYP3A4*1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.
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Affiliation(s)
- Britt Drögemöller
- Department of Genetics, Stellenbosch University Stellenbosch, South Africa
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12
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Georgitsi M, Patrinos GP. Genetic databases in pharmacogenomics: the Frequency of Inherited Disorders Database (FINDbase). Methods Mol Biol 2013; 1015:321-336. [PMID: 23824866 DOI: 10.1007/978-1-62703-435-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pharmacogenomics studies how the variations of the individuals' genetic makeup are correlated with a person's response to certain drugs in relation to the therapeutic efficiency, clinical outcome, or even survival, and how they affect drug metabolism, transport, or clearance. Yet, since the incidence of these polymorphisms, being either single-point variations or small insertions/deletions, varies among different populations, a systematic collection and documentation of these variations is warranted, in order to facilitate implementation of pharmacogenomics in different populations. Here we review the existing electronic databases related to pharmacogenomics and pay particular attention in the description of the pharmacogenomics module Frequency of Inherited Disorders database (FINDbase), which documents curated allelic frequency data pertaining to 144 pharmacogenomics markers across 14 genes, representing approximately 87,000 individuals from 150 populations and ethnic groups worldwide. Long-term sustainability of these resources aims to contribute to the design, development, and implementation of pharmacogenomics testing towards the application of personalized approaches in medical treatment.
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Affiliation(s)
- Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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13
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Smith RP, Lam ET, Markova S, Yee SW, Ahituv N. Pharmacogene regulatory elements: from discovery to applications. Genome Med 2012; 4:45. [PMID: 22630332 PMCID: PMC3506911 DOI: 10.1186/gm344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Regulatory elements play an important role in the variability of individual responses to drug treatment. This has been established through studies on three classes of elements that regulate RNA and protein abundance: promoters, enhancers and microRNAs. Each of these elements, and genetic variants within them, are being characterized at an exponential pace by next-generation sequencing (NGS) technologies. In this review, we outline examples of how each class of element affects drug response via regulation of drug targets, transporters and enzymes. We also discuss the impact of NGS technologies such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq), and the ramifications of new techniques such as high-throughput chromosome capture (Hi-C), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and massively parallel reporter assays (MPRA). NGS approaches are generating data faster than they can be analyzed, and new methods will be required to prioritize laboratory results before they are ready for the clinic. However, there is no doubt that these approaches will bring about a systems-level understanding of the interplay between genetic variants and drug response. An understanding of the importance of regulatory variants in pharmacogenomics will facilitate the identification of responders versus non-responders, the prevention of adverse effects and the optimization of therapies for individual patients.
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Affiliation(s)
- Robin P Smith
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ernest T Lam
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Svetlana Markova
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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14
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Kotur N, Stankovic B, Kassela K, Georgitsi M, Vicha A, Leontari I, Dokmanovic L, Janic D, Krstovski N, Klaassen K, Radmilovic M, Stojiljkovic M, Nikcevic G, Simeonidis A, Sivolapenko G, Pavlovic S, Patrinos GP, Zukic B. 6-mercaptopurine influences TPMT gene transcription in a TPMT gene promoter variable number of tandem repeats-dependent manner. Pharmacogenomics 2012; 13:283-95. [DOI: 10.2217/pgs.11.153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: TPMT activity is characterized by a trimodal distribution, namely low, intermediate and high methylator. TPMT gene promoter contains a variable number of GC-rich tandem repeats (VNTRs), namely A, B and C, ranging from three to nine repeats in length in an AnBmC architecture. We have previously shown that the VNTR architecture in the TPMT gene promoter affects TPMT gene transcription. Materials, methods & results: Here we demonstrate, using reporter assays, that 6-mercaptopurine (6-MP) treatment results in a VNTR architecture-dependent decrease of TPMT gene transcription, mediated by the binding of newly recruited protein complexes to the TPMT gene promoter, upon 6-MP treatment. We also show that acute lymphoblastic leukemia patients undergoing 6-MP treatment display a VNTR architecture-dependent response to 6-MP. Conclusion: These data suggest that the TPMT gene promoter VNTR architecture can be potentially used as a pharmacogenomic marker to predict toxicity due to 6-MP treatment in acute lymphoblastic leukemia patients. Original submitted 27 July 2011; Revision submitted 24 October 2011
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Affiliation(s)
- Nikola Kotur
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Biljana Stankovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Katerina Kassela
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Anna Vicha
- Hematology Division, School of Health Sciences, Faculty of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Iliana Leontari
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Lidija Dokmanovic
- University Children’s Hospital, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Dragana Janic
- University Children’s Hospital, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Nada Krstovski
- University Children’s Hospital, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Milena Radmilovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Gordana Nikcevic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Argiris Simeonidis
- Hematology Division, School of Health Sciences, Faculty of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Gregory Sivolapenko
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Sonja Pavlovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Branka Zukic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
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