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Mullen M, Kojic A, Alamana C, Canel G, Lai C, Knowles JW, Wu JC. Generation of two induced pluripotent stem cell lines from healthy patients of African American ancestry. Stem Cell Res 2024; 76:103322. [PMID: 38359472 DOI: 10.1016/j.scr.2024.103322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Stem cells are a resourceful tool for investigating cardiovascular disease in the context of race and gender. Once derived from blood or skin cells, the reprogrammed induced pluripotent stem cells (iPSCs) adopt an embryonic-like pluripotent state, enabling researchers to develop drug screening or disease modeling platforms. Here, we generated two iPSC lines from peripheral blood mononuclear cells (PBMCs) of two healthy African American patients. Both lines display the usual morphology of pluripotent stem cells, demonstrate elevated expression of pluripotent markers, show normal karyotype, and differentiate into all three germ layers in vitro.
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Affiliation(s)
- McKay Mullen
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ana Kojic
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Alamana
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gabriela Canel
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Celine Lai
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Greenstone Biosciences, Palo Alto, CA, 94304, USA
| | - Joshua W Knowles
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Sanderson DJ, Rodriguez KM, Bejan DS, Olafsen NE, Bohn ID, Kojic A, Sundalam S, Siordia IR, Duell AK, Deng N, Schultz C, Grant DM, Matthews J, Cohen MS. Structurally distinct PARP7 inhibitors provide new insights into the function of PARP7 in regulating nucleic acid-sensing and IFN-β signaling. Cell Chem Biol 2023; 30:43-54.e8. [PMID: 36529140 PMCID: PMC9868104 DOI: 10.1016/j.chembiol.2022.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 09/07/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
The mono-ADP-ribosyltransferase PARP7 has emerged as a key negative regulator of cytosolic NA-sensors of the innate immune system. We apply a rational design strategy for converting a pan-PARP inhibitor into a potent selective PARP7 inhibitor (KMR-206). Consistent with studies using the structurally distinct PARP7 inhibitor RBN-2397, co-treatment of mouse embryonic fibroblasts with KMR-206 and NA-sensor ligands synergistically induced the expression of the type I interferon, IFN-β. In mouse colon carcinoma (CT-26) cells, KMR-206 alone induced IFN-β. Both KMR-206 and RBN-2397 increased PARP7 protein levels in CT-26 cells, demonstrating that PARP7's catalytic activity regulates its own protein levels. Curiously, treatment with saturating doses of KMR-206 and RBN-2397 achieved different levels of PARP7 protein, which correlated with the magnitude of type I interferon gene expression. These latter results have important implications for the mechanism of action of PARP7 inhibitors and highlights the usefulness of having structurally distinct chemical probes for the same target.
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Affiliation(s)
- Daniel J Sanderson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Kelsie M Rodriguez
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Daniel S Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Ninni E Olafsen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo 0315, Norway
| | - Inga D Bohn
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo 0315, Norway
| | - Ana Kojic
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Sunil Sundalam
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Ivan R Siordia
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Anna K Duell
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Nancy Deng
- Computational Chemistry, ChemPartner, San Francisco, CA 94080, USA
| | - Carsten Schultz
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA
| | - Denis M Grant
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S, Canada
| | - Jason Matthews
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo 0315, Norway; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S, Canada
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Road, Portland, OR 97239, USA.
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Kojic A, Kim H, Guevara JV, Ravada S, Sallam K, Wu JC. Generation of two induced pluripotent stem cell lines from dilated cardiomyopathy patients carrying heterozygous FLNC mutations. Stem Cell Res 2022; 64:102928. [PMID: 36194907 PMCID: PMC10871033 DOI: 10.1016/j.scr.2022.102928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 10/14/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is a heterogeneous cardiac disorder characterized by left ventricular dilatation and dysfunction. Mutations in dozens of cardiac genes have been connected to the development of DCM including the filamin C gene (FLNC). We generated two induced pluripotent stem cell (iPSCs) lines from DCM patients carrying single missense heterozygote FLNC mutations (c.6689G > A and c.3745G > A). Both lines expressed high levels of pluripotency markers, differentiated into derivatives of the three germ layers and possessed normal karyotypes. The derived iPSC lines can serve as powerful tools to model DCM in vitro and as a platform for therapeutic development.
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Affiliation(s)
- Ana Kojic
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hobin Kim
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julio V Guevara
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sai Ravada
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karim Sallam
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Müller R, Kojic A, Citir M, Schultz C. Synthesis and Cellular Labeling of Multifunctional Phosphatidylinositol Bis- and Trisphosphate Derivatives. Angew Chem Int Ed Engl 2021; 60:19759-19765. [PMID: 34075669 PMCID: PMC8390440 DOI: 10.1002/anie.202103599] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/12/2021] [Revised: 05/07/2021] [Indexed: 12/15/2022]
Abstract
We synthesized the first multifunctionalized phosphoinositide polyphosphate derivatives featuring a photo-removable protecting group ("cage"), a photo-crosslinkable diazirine group, and a terminal alkyne group useful for click chemistry. We demonstrate that the lipid derivatives readily enter cells. After photo-crosslinking, cell fixation and fluorescent tagging via click chemistry, we determined the intracellular location of the lipid derivatives before and after uncaging of the lipids. We find that there is rapid trafficking of PI(3,4)P2 and PI(3,4,5)P3 derivatives to the plasma membrane, opening the intriguing possibility that there is active transport of these lipids involved. We employed the photo-crosslinking and click chemistry functions to analyze the proteome of PI(3,4,5)P3 -binding proteins. From the latter, we validated by RNAi that the putative lipid binding proteins ATP11A and MPP6 are involved in the transport of PI(3,4,5)P3 to the plasma membrane.
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Affiliation(s)
- Rainer Müller
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
| | - Ana Kojic
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint Ph.D. Degree between EMBL and Heidelberg University69117HeidelbergGermany
- Oregon Health & Science UniversityDepartment of Chemical Physiology and Biochemistry3181 SW Sam Jackson Park RdPortlandOR97239-3098USA
| | - Mevlut Citir
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint Ph.D. Degree between EMBL and Heidelberg University69117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL)Cell Biology & Biophysics UnitMeyerhofstr. 169117HeidelbergGermany
- Oregon Health & Science UniversityDepartment of Chemical Physiology and Biochemistry3181 SW Sam Jackson Park RdPortlandOR97239-3098USA
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Müller R, Kojic A, Citir M, Schultz C. Synthesis and Cellular Labeling of Multifunctional Phosphatidylinositol Bis‐ and Trisphosphate Derivatives. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Rainer Müller
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
| | - Ana Kojic
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
- Faculty of Biosciences Collaboration for Joint Ph.D. Degree between EMBL and Heidelberg University 69117 Heidelberg Germany
- Oregon Health & Science University Department of Chemical Physiology and Biochemistry 3181 SW Sam Jackson Park Rd Portland OR 97239-3098 USA
| | - Mevlut Citir
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
- Faculty of Biosciences Collaboration for Joint Ph.D. Degree between EMBL and Heidelberg University 69117 Heidelberg Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL) Cell Biology & Biophysics Unit Meyerhofstr. 1 69117 Heidelberg Germany
- Oregon Health & Science University Department of Chemical Physiology and Biochemistry 3181 SW Sam Jackson Park Rd Portland OR 97239-3098 USA
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Echalier C, Rutkowska A, Kojic A, Thomson DW, Edwards LJ, McKay BSJ, Mülbaier M, Schultz C, Bergamini G. amTCO, a new trans-cyclooctene derivative to study drug-target interactions in cells. Chem Commun (Camb) 2021; 57:1814-1817. [PMID: 33480895 DOI: 10.1039/d0cc06709a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Click chemistry probes have improved the study of drug interactions in live cells and relevant disease models. Proper design of the probes, including the choice of the click moiety coupled to the drug, is crucial to ensure good performance and broad application. A new trans-cyclooctene derivative, amTCO, was synthesised via a novel route using a phthalimide protecting group as a built-in photosensitiser for the cyclooctene isomerization. amTCO improved the physical chemical properties of click chemistry probes compared to standard TCO moieties. An amTCO probe targeting indoleamine 2,3-dioxygenase (IDO1) was a superior tool for visualizing IDO1 and measuring the binding affinities of small molecule inhibitors to IDO1 in cells.
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Affiliation(s)
- Cécile Echalier
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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Kirby IT, Kojic A, Arnold MR, Thorsell AG, Karlberg T, Vermehren-Schmaedick A, Sreenivasan R, Schultz C, Schüler H, Cohen MS. A Potent and Selective PARP11 Inhibitor Suggests Coupling between Cellular Localization and Catalytic Activity. Cell Chem Biol 2018; 25:1547-1553.e12. [PMID: 30344052 DOI: 10.1016/j.chembiol.2018.09.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 06/13/2017] [Revised: 06/08/2018] [Accepted: 09/24/2018] [Indexed: 12/15/2022]
Abstract
Poly-ADP-ribose polymerases (PARPs1-16) play pivotal roles in diverse cellular processes. PARPs that catalyze poly-ADP-ribosylation (PARylation) are the best characterized PARP family members because of the availability of potent and selective inhibitors for these PARPs. There has been comparatively little success in developing selective small-molecule inhibitors of PARPs that catalyze mono-ADP-ribosylation (MARylation), limiting our understanding of the cellular role of MARylation. Here we describe the structure-guided design of inhibitors of PARPs that catalyze MARylation. The most selective analog, ITK7, potently inhibits the MARylation activity of PARP11, a nuclear envelope-localized PARP. ITK7 is greater than 200-fold selective over other PARP family members. Using live-cell imaging, we show that ITK7 causes PARP11 to dissociate from the nuclear envelope. These results suggest that the cellular localization of PARP11 is regulated by its catalytic activity.
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Affiliation(s)
- Ilsa T Kirby
- Program in Chemical Biology, Oregon Health & Science University, Portland, OR 97210, USA; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97210, United States
| | - Ana Kojic
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; EMBL, Heidelberg University, Heidelberg, Germany
| | - Moriah R Arnold
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97210, United States
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157, Huddinge, Sweden
| | - Tobias Karlberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157, Huddinge, Sweden
| | - Anke Vermehren-Schmaedick
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97210, United States
| | - Raashi Sreenivasan
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97210, United States
| | - Carsten Schultz
- Program in Chemical Biology, Oregon Health & Science University, Portland, OR 97210, USA; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97210, United States; European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157, Huddinge, Sweden
| | - Michael S Cohen
- Program in Chemical Biology, Oregon Health & Science University, Portland, OR 97210, USA; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97210, United States.
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Boskovic S, Marín-Juez R, Jasnic J, Reischauer S, El Sammak H, Kojic A, Faulkner G, Radojkovic D, Stainier DYR, Kojic S. Characterization of zebrafish (Danio rerio) muscle ankyrin repeat proteins reveals their conserved response to endurance exercise. PLoS One 2018; 13:e0204312. [PMID: 30252882 PMCID: PMC6155536 DOI: 10.1371/journal.pone.0204312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/05/2018] [Indexed: 12/30/2022] Open
Abstract
Muscle proteins with ankyrin repeats (MARPs) ANKRD1 and ANKRD2 are titin-associated proteins with a putative role as transcriptional co-regulators in striated muscle, involved in the cellular response to mechanical, oxidative and metabolic stress. Since many aspects of the biology of MARPs, particularly exact mechanisms of their action, in striated muscle are still elusive, research in this field will benefit from novel animal model system. Here we investigated the MARPs found in zebrafish for protein structure, evolutionary conservation, spatiotemporal expression profiles and response to increased muscle activity. Ankrd1 and Ankrd2 show overall moderate conservation at the protein level, more pronounced in the region of ankyrin repeats, motifs indispensable for their function. The two zebrafish genes, ankrd1a and ankrd1b, counterparts of mammalian ANKRD1/Ankrd1, have different expression profiles during first seven days of development. Mild increase of ankrd1a transcript levels was detected at 72 hpf (1.74±0.24 fold increase relative to 24 hpf time point), while ankrd1b expression was markedly upregulated from 24 hpf onward and peaked at 72 hpf (92.18±36.95 fold increase relative to 24 hpf time point). Spatially, they exhibited non-overlapping expression patterns during skeletal muscle development in trunk (ankrd1a) and tail (ankrd1b) somites. Expression of ankrd2 was barely detectable. Zebrafish MARPs, expressed at a relatively low level in adult striated muscle, were found to be responsive to endurance exercise training consisting of two bouts of 3 hours of forced swimming daily, for five consecutive days. Three hours after the last exercise bout, ankrd1a expression increased in cardiac muscle (6.19±5.05 fold change), while ankrd1b and ankrd2 were upregulated in skeletal muscle (1.97±1.05 and 1.84±0.58 fold change, respectively). This study provides the foundation to establish zebrafish as a novel in vivo model for further investigation of MARPs function in striated muscle.
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Affiliation(s)
- Srdjan Boskovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Rubén Marín-Juez
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jovana Jasnic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sven Reischauer
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hadil El Sammak
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ana Kojic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Dragica Radojkovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Snezana Kojic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- * E-mail:
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