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Nowialis P, Tobon J, Lopusna K, Opavska J, Badar A, Chen D, Abdelghany R, Pozas G, Fingeret J, Noel E, Riva A, Fujiwara H, Opavsky R. Genome-wide methylation profiling of Peripheral T-cell lymphomas identifies TRIP13 as a critical driver of tumor proliferation and survival. Res Sq 2024:rs.3.rs-3971059. [PMID: 38464090 PMCID: PMC10925438 DOI: 10.21203/rs.3.rs-3971059/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Cytosine methylation of genomic DNA contributes to the regulation of gene expression and is involved in normal development including hematopoiesis in mammals. It is catalyzed by the family of DNA methyltransferases (DNMTs) that include DNMT1, DNMT3A, and DNMT3B. Peripheral T-cell lymphomas (PTCLs) represent a diverse group of aggressive mature T-cell malignancies accounting for approximately 10-15% of non-Hodgkin lymphoma cases in the US. PTCLs exhibit a broad spectrum of clinical, histological, and immunophenotypic features with poor prognosis and inadequately understood molecular pathobiology. To better understand the molecular landscape and identify candidate genes involved in disease maintenance, we used high-resolution Whole Genome Bisulfite Sequencing (WGBS) and RNA-seq to profile DNA methylation and gene expression of PTCLs and normal T-cells. We found that the methylation patterns in PTCLs are deregulated and heterogeneous but share 767 hypo- and 567 hypermethylated differentially methylated regions (DMRs) along with 231 genes up- and 91 genes downregulated in all samples suggesting a potential association with tumor development. We further identified 39 hypomethylated promoters associated with increased gene expression in the majority of PTCLs. This putative oncogenic signature included the TRIP13 (thyroid hormone receptor interactor 13) gene whose both genetic and pharmacologic inactivation, inhibited cellular growth of PTCL cell lines by inducing G2-M arrest accompanied by apoptosis suggesting that such an approach might be beneficial in human lymphoma treatment. Altogether we show that human PTCLs are characterized by a large number of recurrent methylation alterations, and demonstrated that TRIP13 is critical for PTCL maintenance in vitro .
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Lopusna K, Nowialis P, Opavska J, Abraham A, Riva A, Opavsky R. Dnmt3b catalytic activity is critical for its tumour suppressor function in lymphomagenesis and is associated with c-Met oncogenic signalling. EBioMedicine 2021; 63:103191. [PMID: 33418509 PMCID: PMC7804970 DOI: 10.1016/j.ebiom.2020.103191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND DNA methylation regulates gene transcription in many physiological processes in mammals including development and haematopoiesis. It is catalysed by several DNA methyltransferases, including Dnmt3b that mediates both methylation-dependant and independent gene repression. Dnmt3b is critical for mouse embryogenesis and functions as a tumour suppressor in haematologic malignancies in mice. However, the extent to which Dnmt3b's catalytic activity (CA) is involved in development and cancer is unclear. METHODS We used a mouse model expressing catalytically inactive Dnmt3b (Dnmt3bCI) to study a role of Dnmt3b's CA in development and cancer. We utilized global approaches including Whole-genome Bisulfite sequencing and RNA-seq to analyse DNA methylation and gene expression to identify putative targets of Dnmt3b's CA. To analyse postnatal development and haematopoiesis, we used tissue staining, histological and FACS analysis. To determine potential involvement of selected genes in lymphomagenesis, we used overexpression and knock down approaches followed by in vitro growth assays. FINDINGS We show that mice expressing Dnmt3bCI only, survive postnatal development and develop ICF (the immunodeficiency-centromeric instability-facial anomalies) -like syndrome. The lack of Dnmt3b's CA promoted fibroblasts transformation in vitro, accelerated MLL-AF9 driven Acute Myeloid Leukaemia and MYC-induced T-cell lymphomagenesis in vivo. The elimination of Dnmt3b's CA resulted in decreased methylation of c-Met promoter and its upregulation, activated oncogenic Met signalling, Stat3 phosphorylation and up-regulation of Lin28b promoting lymphomagenesis. INTERPRETATION Our data demonstrates that Dnmt3b's CA is largely dispensable for mouse development but critical to prevent tumourigenesis by controlling events involved in cellular transformation. FUNDING This study was supported by Department of Anatomy and Cell Biology and Cancer Centre at the University of Florida start-up funds, NIH/NCI grant 1R01CA188561-01A1 (R.O.).
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Affiliation(s)
- Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, P.O. Box 103622. Gainesville, FL 32610, United States
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States.
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Lopusna K, Nowialis P, Opavska J, Abraham A, Riva A, Haney SL, Opavsky R. Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice. J Biol Chem 2021; 296:100285. [PMID: 33450231 PMCID: PMC7949038 DOI: 10.1016/j.jbc.2021.100285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
DNA methylation regulates gene transcription and is involved in various physiological processes in mammals, including development and hematopoiesis. It is catalyzed by DNA methyltransferases including Dnmt1, Dnmt3a, and Dnmt3b. For Dnmt3b, its effects on transcription can result from its own DNA methylase activity, the recruitment of other Dnmts to mediate methylation, or transcription repression in a methylation-independent manner. Low-frequency mutations in human DNMT3B are found in hematologic malignancies including cutaneous T-cell lymphomas, hairy cell leukemia, and diffuse large B-cell lymphomas. Moreover, Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. However, it is poorly understood how the different Dnmt3b activities contribute to these outcomes. We modulated Dnmt3b activity in vivo by generating Dnmt3b+/- mice expressing one wild-type allele as well as Dnmt3b+/CI and Dnmt3bCI/CI mice where one or both alleles express catalytically inactive Dnmt3bCI. We show that 43% of Dnmt3b+/- mice developed T-cell lymphomas, chronic lymphocytic leukemia, and myeloproliferation over 18 months, thus resembling phenotypes previously observed in Dnmt3a+/- mice, possibly through regulation of shared target genes. Interestingly, Dnmt3b+/CI and Dnmt3bCI/CI mice survived postnatal development and were affected by B-cell rather than T-cell malignancies with decreased penetrance. Genome-wide hypomethylation, increased expression of oncogenes such as Jdp2, STAT1, and Trip13, and p53 downregulation were major events contributing to Dnmt3b+/- lymphoma development. We conclude that Dnmt3b catalytic activity is critical to prevent B-cell transformation in vivo, whereas accessory and methylation-independent repressive functions are important to prevent T-cell transformation.
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MESH Headings
- ATPases Associated with Diverse Cellular Activities/genetics
- ATPases Associated with Diverse Cellular Activities/metabolism
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- DNA (Cytosine-5-)-Methyltransferases/deficiency
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Heterozygote
- Homozygote
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/enzymology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, B-Cell/enzymology
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, T-Cell/enzymology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Mice, Knockout
- Myeloproliferative Disorders/enzymology
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/pathology
- Neoplasms, Experimental/enzymology
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/pathology
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- STAT1 Transcription Factor/genetics
- STAT1 Transcription Factor/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- DNA Methyltransferase 3B
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Affiliation(s)
- Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, Gainesville, Florida, USA
| | - Staci L Haney
- Department of Internal Medicine, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA.
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Nowialis P, Lopusna K, Opavska J, Haney SL, Abraham A, Sheng P, Riva A, Natarajan A, Guryanova O, Simpson M, Hlady R, Xie M, Opavsky R. Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions. Nat Commun 2019; 10:4374. [PMID: 31558711 PMCID: PMC6763448 DOI: 10.1038/s41467-019-12355-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/04/2019] [Indexed: 01/19/2023] Open
Abstract
DNA methylation regulates gene expression in a variety of processes, including mouse embryonic development. Four catalytically active enzymes function in mice as DNA methyltransferases (Dnmts) and as transcriptional regulators. Inactivation of Dnmt3b results in mouse embryonic lethality, but which activities are involved is unclear. Here we show that catalytically inactive Dnmt3b restores a majority of methylation and expression changes deregulated in the absence of Dnmt3b, and as a result, mice survive embryonic development. Thus, Dnmt3b functions as an accessory cofactor supporting catalytic activities performed by other Dnmts. We further demonstrate that Dnmt3b is linked to a control of major developmental pathways, including Wnt and hedgehog signaling. Dnmt3b directly represses Wnt9b whose aberrant up-regulation contributes to embryonic lethality of Dnmt3b knockout embryos. Our results highlight that Dnmt3b is a multifaceted protein that serves as an enzyme, an accessory factor for other methyltransferases, and as a transcriptional repressor in mouse embryogenesis.
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Affiliation(s)
- Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Staci L Haney
- Department of Internal Medicine, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 263, Gainesville, FL, 32610, USA
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, P.O. Box 103622, Gainesville, FL, 32610, USA
| | - Amarnath Natarajan
- University of Nebraska Medical Center, The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, 986805 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Olga Guryanova
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 260, Gainesville, FL, 32610, USA
| | - Melanie Simpson
- Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27695, USA
| | - Ryan Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55901, USA
| | - Mingyi Xie
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 263, Gainesville, FL, 32610, USA
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
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Lopusna K, Nowialis P, Haney SL, Abraham A, Opavska J, Opavsky R. Abstract 4339: Critical role of Dnmt3b catalytic activity in prevention of oncogene-induced leukemias and lymphomas. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cytosine methylation is involved in a variety of biological processes, including development, X-chromosome inactivation, imprinting, and suppressing unwanted transcription. DNA methylation in mammalian cells is catalyzed by several DNA methyltransferases, including DNMT1, DNMT3A and DNMT3B. In addition to DNA methylation catalysis, these enzymes interact with a number of repressive proteins including HDACs, thereby repressing transcription in methylation-independent manner. The extent to which methylation-dependent and independent activities play roles in biological processes remains poorly understood. Here we examined the role of methyltransferase (MT) activity of Dnmt3b in normal mouse embryogenesis and in prevention of hematologic malignancies. Loss of Dnmt3b in mice is embryonically lethal between 10.5-12.5 dpc. Dnmt3b was also identified as tumor suppressor in murine models of lymphoid and myeloid malignancies. To address whether Dnmt3b’s catalytic activity is important for mouse embryogenesis and prevention of hematologic malignancies, we generated mice bearing a conventional Dnmt3bCI allele using CRISPR/Cas9 system. This catalytically inactive allele of Dnmt3b (Dnmt3bCI) was generated by a double amino acid substitution in enzyme active center (P656V and C657D) abolishing its ability to perform transfer of methyl group onto cytosine. Surprisingly, Dnmt3bCI/CI mice were born at similar ratios as wild-type littermates and lived over 12 months suggesting that Dnmt3b is dispensable for both pre- and post-natal development. Importantly, MYC-induced T-cell lymphomagenesis was accelerated in the absence of Dnmt3b’s methyltransferase activity in MYC;Dnmt3bCI/CI mice. Global gene expression and methylation profiling revealed a number of deregulated events specific for MYC;Dnmt3bCI/CI, resulting in activation of Pak, Fgfr and Igf2 signaling and downregulation of tumor suppressors (e.g. Lrp12, Dusp6 and Marcks). The lack of Dnmt3b catalytic activity also accelerated a development of acute myeloid leukemia induced by MLL-AF9 overexpression in mice. Altogether, our data suggest that Dnmt3b’s MT activity is dispensable for mouse development but critical to prevent hematologic malignancies.
Citation Format: Katarina Lopusna, Pawel Nowialis, Staci L. Haney, Ajay Abraham, Jana Opavska, Rene Opavsky. Critical role of Dnmt3b catalytic activity in prevention of oncogene-induced leukemias and lymphomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4339.
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Lencesova L, Szadvari I, Babula P, Kubickova J, Chovancova B, Lopusna K, Rezuchova I, Novakova Z, Krizanova O, Novakova M. Disruption of dopamine D1/D2 receptor complex is involved in the function of haloperidol in cardiac H9c2 cells. Life Sci 2017; 191:186-194. [PMID: 29054453 DOI: 10.1016/j.lfs.2017.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 01/11/2023]
Abstract
AIMS Haloperidol is an antipsychotic agent and acts as dopamine D2 receptor (D2R) antagonist, as a prototypical ligand of sigma1 receptors (Sig1R) and it increases expression of type 1 IP3 receptors (IP3R1). However, precise mechanism of haloperidol action on cardiomyocytes through dopaminergic signaling was not described yet. This study investigated a role of dopamine receptors in haloperidol-induced increase in IP3R1 and Sig1R, and compared physiological effect of melperone and haloperidol on basic heart parameters in rats. MATERIALS AND METHODS We used differentiated NG-108 cells and H9c2 cells. Gene expression, Western blot and immunofluorescence were used to evaluate haloperidol-induced differences; proximity ligation assay (PLA) and immunoprecipitation to determine interactions of D1/D2 receptors. To evaluate cardiac parameters, Wistar albino male rats were used. KEY FINDINGS We have shown that antagonism of D2R with either haloperidol or melperone results in upregulation of both, IP3R1 and Sig1R, which is associated with increased D2R, but reduced D1R expression. Immunofluorescence, immunoprecipitation and PLA support formation of heteromeric D1/D2 complexes in H9c2 cells. Treatment with haloperidol (but not melperone) caused decrease in systolic and diastolic blood pressure and significant increase in heart rate. SIGNIFICANCE Because D1R/D2R complexes can engage Gq-like signaling in other experimental systems, these results are consistent with the possibility that disruption of D1R/D2R complex in H9c2 cells might cause a decrease in IP3R1 activity, which in turn may account for the increase expression of IP3R and Sig1R. D2R is probably not responsible for changes in cardiac parameters, since melperone did not have any effect.
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Affiliation(s)
- L Lencesova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - I Szadvari
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - P Babula
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - J Kubickova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - B Chovancova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - K Lopusna
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - I Rezuchova
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Z Novakova
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - O Krizanova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
| | - M Novakova
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic.
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Lekes D, Szadvari I, Krizanova O, Lopusna K, Rezuchova I, Novakova M, Novakova Z, Parak T, Babula P. Nilotinib induces ER stress and cell death in H9c2 cells. Physiol Res 2017; 65:S505-S514. [PMID: 28006933 DOI: 10.33549/physiolres.933504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Tyrosine kinases inhibitors (TKi) represent a relatively novel class of anticancer drugs that target cellular pathways overexpressed in certain types of malignancies, such as chronic myeloid leukaemia (CML). Nilotinib, ponatinib and imatinib exhibit cardiotoxic and vascular effects. In this study, we focused on possible cardiotoxicity of nilotinib using H9c2 cells as a suitable cell model. We studied role of endoplasmic reticulum (ER) stress and apoptosis in nilotinib toxicity using a complex approach. Nilotinib impaired mitochondrial function and induced formation of ROS under clinically relevant concentrations. In addition, ability of nilotinib to induce ER stress has been shown. These events result in apoptotic cell death. All these mechanisms contribute to cytotoxic effect of the drug. In addition, involvement of ER stress in nilotinib toxicity may be important in co-treatment with pharmaceuticals affecting ER and ER stress, e.g. beta-blockers or sartans, and should be further investigated.
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Affiliation(s)
- D Lekes
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
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