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Linhares ND, Pereira DA, Conceição IM, Franco GR, Eckalbar WL, Ahituv N, Luizon MR. Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15. Pharmacogenomics 2020; 21:509-520. [PMID: 32427048 DOI: 10.2217/pgs-2020-0010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: GDF15 levels are a biomarker for metformin use. We performed the functional annotation of noncoding genome-wide association study (GWAS) SNPs for GDF15 levels and the Genotype-Tissue Expression (GTEx)-expression quantitative trait loci (eQTLs) for GDF15 expression within metformin-activated enhancers around GDF15. Materials & methods: These enhancers were identified using chromatin immunoprecipitation followed by sequencing data for active (H3K27ac) and silenced (H3K27me3) histone marks on human hepatocytes treated with metformin, Encyclopedia of DNA Elements data and cis-regulatory elements assignment tools. Results: The GWAS lead SNP rs888663, the SNP rs62122429 associated with GDF15 levels in the Outcome Reduction with Initial Glargine Intervention trial, and the GTEx-expression quantitative trait locus rs4808791 for GDF15 expression in whole blood are located in a metformin-activated enhancer upstream of GDF15 and tightly linked in Europeans and East Asians. Conclusion: Noncoding variation within a metformin-activated enhancer may increase GDF15 expression and help to predict GDF15 levels.
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Affiliation(s)
- Natália D Linhares
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Daniela A Pereira
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela McA Conceição
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Glória R Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Walter L Eckalbar
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marcelo R Luizon
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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Kovacsics D, Brózik A, Tihanyi B, Matula Z, Borsy A, Mészáros N, Szabó E, Németh E, Fóthi Á, Zámbó B, Szüts D, Várady G, Orbán TI, Apáti Á, Sarkadi B. Precision-engineered reporter cell lines reveal ABCG2 regulation in live lung cancer cells. Biochem Pharmacol 2020; 175:113865. [PMID: 32142727 DOI: 10.1016/j.bcp.2020.113865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/18/2020] [Indexed: 12/19/2022]
Abstract
Expression of the ABCG2 multidrug transporter is a marker of cancer stem cells and a predictor of recurrent malignant disease. Understanding how human ABCG2 expression is modulated by pharmacotherapy is crucial in guiding therapeutic recommendations and may aid rational drug development. Genome edited reporter cells are useful in investigating gene regulation and visualizing protein activity in live cells but require precise targeting to preserve native regulatory regions. Here, we describe a fluorescent reporter assay that allows the noninvasive assessment of ABCG2 regulation in human lung adenocarcinoma cells. Using CRISPR-Cas9 gene editing coupled with homology-directed repair, we targeted an EGFP coding sequence to the translational start site of ABCG2, generating ABCG2 knock-out and in situ tagged ABCG2 reporter cells. Using the engineered cell lines, we show that ABCG2 is upregulated by a number of anti-cancer medications, HDAC inhibitors, hypoxia-mimicking agents and glucocorticoids, supporting a model in which ABCG2 is under the control of a general stress response. To our knowledge, this is the first description of a fluorescent reporter assay system designed to follow the endogenous regulation of a human ABC transporter in live cells. The information gained may guide therapy recommendations and aid rational drug design.
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Affiliation(s)
- Daniella Kovacsics
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Anna Brózik
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Borbála Tihanyi
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Zsolt Matula
- South-Pest Hospital Centre, National Institute of Hematology and Infectious Diseases, Laboratory of Molecular and Cytogenetics, Budapest, Hungary
| | - Adrienn Borsy
- South-Pest Hospital Centre, National Institute of Hematology and Infectious Diseases, Laboratory of Molecular and Cytogenetics, Budapest, Hungary
| | - Nikolett Mészáros
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Edit Szabó
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Eszter Németh
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Ábel Fóthi
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Boglárka Zámbó
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Dávid Szüts
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - György Várady
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Tamás I Orbán
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Ágota Apáti
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Balázs Sarkadi
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary.
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Eclov RJ, Kim MJ, Smith R, Ahituv N, Kroetz DL. Rare Variants in the ABCG2 Promoter Modulate In Vivo Activity. Drug Metab Dispos 2018; 46:636-642. [PMID: 29467213 PMCID: PMC5896364 DOI: 10.1124/dmd.117.079541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/15/2018] [Indexed: 11/22/2022] Open
Abstract
ABCG2 encodes the breast cancer resistance protein (BCRP), an efflux membrane transporter important in the detoxification of xenobiotics. In the present study, the basal activity of the ABCG2 promoter in liver, kidney, intestine, and breast cell lines was examined using luciferase reporter assays. The promoter activities of reference and variant ABCG2 sequences were compared in human hepatocellular carcinoma cell (HepG2), human embryonic kidney cell (HEK293T), human colorectal carcinoma cell (HCT116), and human breast adenocarcinoma cell (MCF-7) lines. The ABCG2 promoter activity was strongest in the kidney and intestine cell lines. Four variants in the basal ABCG2 promoter (rs76656413, rs66664036, rs139256004, and rs59370292) decreased the promoter activity by 25%-50% in at least three of the four cell lines. The activity of these four variants was also examined in vivo using the hydrodynamic tail vein assay, and two single nucleotide polymorphisms (rs76656413 and rs59370292) significantly decreased in vivo liver promoter activity by 50%-80%. Electrophoretic mobility shift assays confirmed a reduction in nuclear protein binding to the rs59370292 variant probe, whereas the rs76656413 probe had a shift in transcription factor binding specificity. Although both rs59370292 and rs76656413 are rare variants in all populations, they could contribute to patient-level variation in ABCG2 expression in the kidney, liver, and intestine.
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Affiliation(s)
- Rachel J Eclov
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Mee J Kim
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Robin Smith
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
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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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