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Mouton S, Mougel A, Ustyantsev K, Dissous C, Melnyk O, Berezikov E, Vicogne J. Optimized protocols for RNA interference in Macrostomum lignano. G3 (Bethesda) 2024:jkae037. [PMID: 38421640 DOI: 10.1093/g3journal/jkae037] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
Macrostomum lignano, a marine free-living flatworm, has emerged as a potent invertebrate model in developmental biology for studying stem cells, germline, and regeneration processes. In recent years, many tools have been developed to manipulate this worm and to facilitate genetic modification. RNA interference is currently the most accessible and direct technique to investigate gene functions. It is obtained by soaking worms in artificial seawater containing dsRNA targeting the gene of interest. Although easy to perform, the original protocol calls for daily exchange of dsRNA solutions, usually until phenotypes are observed, which is both time- and cost-consuming. In this work, we have evaluated alternative dsRNA delivery techniques, such as electroporation and osmotic shock, to facilitate the experiments with improved time and cost efficiency. During our investigation to optimize RNAi, we demonstrated that, in the absence of diatoms, regular single soaking in artificial seawater containing dsRNA directly produced in bacteria or synthesized in vitro is, in most cases, sufficient to induce a potent gene knockdown for several days with a single soaking step. Therefore, this new and highly simplified method allows a very significant reduction of dsRNA consumption and lab work. In addition, it enables performing experiments on a larger number of worms at minimal cost.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Alexandra Mougel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Colette Dissous
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9700AD, The Netherlands
| | - Jérôme Vicogne
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
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2
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Thorne AM, Wolters JC, Lascaris B, Bodewes SB, Lantinga VA, van Leeuwen OB, de Jong IEM, Ustyantsev K, Berezikov E, Lisman T, Kuipers F, Porte RJ, de Meijer VE. Bile proteome reveals biliary regeneration during normothermic preservation of human donor livers. Nat Commun 2023; 14:7880. [PMID: 38036513 PMCID: PMC10689461 DOI: 10.1038/s41467-023-43368-y] [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] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023] Open
Abstract
Normothermic machine perfusion (NMP) after static cold storage is increasingly used for preservation and assessment of human donor livers prior to transplantation. Biliary viability assessment during NMP reduces the risk of post-transplant biliary complications. However, understanding of molecular changes in the biliary system during NMP remains incomplete. We performed an in-depth, unbiased proteomics analysis of bile collected during sequential hypothermic machine perfusion, rewarming and NMP of 55 human donor livers. Longitudinal analysis during NMP reveals proteins reflective of cellular damage at early stages, followed by upregulation of secretory and immune response processes. Livers with bile chemistry acceptable for transplantation reveal protein patterns implicated in regenerative processes, including cellular proliferation, compared to livers with inadequate bile chemistry. These findings are reinforced by detection of regenerative gene transcripts in liver tissue before machine perfusion. Our comprehensive bile proteomics and liver transcriptomics data sets provide the potential to further evaluate molecular mechanisms during NMP and refine viability assessment criteria.
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Affiliation(s)
- Adam M Thorne
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands
| | - Justina C Wolters
- Department of Pediatrics, University of Groningen, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Bianca Lascaris
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands
| | - Silke B Bodewes
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands
| | - Veerle A Lantinga
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands
| | - Otto B van Leeuwen
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands
| | - Iris E M de Jong
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ton Lisman
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Surgical Research Laboratory, Department of Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Robert J Porte
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Erasmus MC Transplant Institute, Department of Surgery, Division of HPB and Transplant Surgery, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Vincent E de Meijer
- Department of Liver Transplantation and HPB Surgery, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
- UMCG Comprehensive Transplant Center, Groningen, the Netherlands.
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3
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van Beijnum H, Koopmans T, Tomasso A, Disela V, Te Lindert S, Bakkers J, Alemany A, Berezikov E, Bartscherer K. Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse ( Acomys) ear. Genome Res 2023; 33:1424-1437. [PMID: 37726147 PMCID: PMC10547259 DOI: 10.1101/gr.277538.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/19/2023] [Indexed: 09/21/2023]
Abstract
In contrast to other mammals, the spiny mouse (Acomys) regenerates skin and ear tissue, which includes hair follicles, glands, and cartilage, in a scar-free manner. Ear punch regeneration is asymmetric with only the proximal wound side participating in regeneration. Here, we show that cues originating from the proximal side are required for normal regeneration and use spatially resolved transcriptomics (tomo-seq) to understand the molecular and cellular events underlying this process. Analyzing gene expression across the ear and comparing expression modules between proximal and distal wound sides, we identify asymmetric gene expression patterns and pinpoint regenerative processes in space and time. Moreover, using a comparative approach with nonregenerative rodents (Mus, Meriones), we strengthen a hypothesis in which particularities in the injury-induced immune response may be one of the crucial determinants for why spiny mice regenerate whereas their relatives do not. Our data are available in SpinyMine, an easy-to-use and expandable web-based tool for exploring Acomys regeneration-associated gene expression.
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Affiliation(s)
- Henriëtte van Beijnum
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Tim Koopmans
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Antonio Tomasso
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Vanessa Disela
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Severin Te Lindert
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Wageningen University, Wageningen, 6708WE, The Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Anna Alemany
- Department of Anatomy and Embryology, Leiden University Medical Center, and the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, 2300RC Leiden, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Kerstin Bartscherer
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands;
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
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Martinez P, Ustyantsev K, Biryukov M, Mouton S, Glasenburg L, Sprecher SG, Bailly X, Berezikov E. Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis. G3 (Bethesda) 2023; 13:jkac336. [PMID: 36542495 PMCID: PMC9911081 DOI: 10.1093/g3journal/jkac336] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found, mostly, lying in large pools on the surface of sand at low tide. As a member of the Acoela it has been thought as a proxy for ancestral bilaterian animals; however, its phylogenetic position remains still debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic species S. roscoffensis. The size of this genome was measured to be in the range of 910-940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate it. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.
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Affiliation(s)
- Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona 08193, Spain
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Mikhail Biryukov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Liza Glasenburg
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Chemin du Musee 10, 1700 Fribourg, Switzerland
| | - Xavier Bailly
- Station Biologique de Roscoff, Multicellular Marine Models (M3) team, FR2424, CNRS/Sorbonne Université—Place Georges Teissier, 29680 Roscoff, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
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Biryukov M, Dmitrieva A, Vavilova V, Ustyantsev K, Bazarova E, Sukhikh I, Berezikov E, Blinov A. Mlig-SKP1 Gene Is Required for Spermatogenesis in the Flatworm Macrostomum lignano. Int J Mol Sci 2022; 23:ijms232315110. [PMID: 36499445 PMCID: PMC9740662 DOI: 10.3390/ijms232315110] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
In a free-living flatworm, Macrostomum lignano, an S-phase kinase-associated protein 1 (SKP1) homologous gene was identified as enriched in proliferating cells, suggesting that it can function in the regulation of stem cells or germline cells since these are the only two types of proliferating cells in flatworms. SKP1 is a conserved protein that plays a role in ubiquitination processes as a part of the Skp1-Cullin 1-F-box (SCF) ubiquitin ligase complex. However, the exact role of Mlig-SKP1 in M. lignano was not established. Here, we demonstrate that Mlig-SKP1 is neither involved in stem cell regulation during homeostasis, nor in regeneration, but is required for spermatogenesis. Mlig-SKP1(RNAi) animals have increased testes size and decreased fertility as a result of the aberrant maturation of sperm cells. Our findings reinforce the role of ubiquitination pathways in germ cell regulation and demonstrate the conserved role of SKP1 in spermatogenesis.
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Affiliation(s)
- Mikhail Biryukov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Anastasia Dmitrieva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Valeriya Vavilova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9700AD Groningen, The Netherlands
| | - Erzhena Bazarova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Igor Sukhikh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9700AD Groningen, The Netherlands
| | - Alexandr Blinov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Science, 630090 Novosibirsk, Russia
- Correspondence:
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Wudarski J, Ustyantsev K, Reinoite F, Berezikov E. Random Integration Transgenesis in a Free-Living Regenerative Flatworm Macrostomum lignano. Methods Mol Biol 2022; 2450:493-508. [PMID: 35359325 PMCID: PMC9761508 DOI: 10.1007/978-1-0716-2172-1_26] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Regeneration-capable flatworms are highly informative research models to study the mechanisms of stem cell regulation, regeneration, and tissue patterning. Transgenesis is a powerful research tool for investigating gene function, but until recently, a transgenesis method was missing in flatworms, hampering their wider adoption in biomedical research. Here we describe a detailed protocol to create stable transgenic lines of the flatworm M. lignano using random integration of DNA constructs through microinjection into single-cell stage embryos.
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Affiliation(s)
- Jakub Wudarski
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Filipa Reinoite
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
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7
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Ustyantsev K, Wudarski J, Sukhikh I, Reinoite F, Mouton S, Berezikov E. Erratum to: Proof of principle for piggyBac-mediated transgenesis in the flatworm Macrostomum lignano. Genetics 2021; 220:6489456. [PMID: 35100380 PMCID: PMC9097247 DOI: 10.1093/genetics/iyab219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Bomer N, Pavez-Giani MG, Deiman FE, Linders AN, Hoes MF, Baierl CL, Oberdorf-Maass SU, de Boer RA, Silljé HH, Berezikov E, Simonides WS, Westenbrink BD, van der Meer P. Selenoprotein DIO2 Is a Regulator of Mitochondrial Function, Morphology and UPRmt in Human Cardiomyocytes. Int J Mol Sci 2021; 22:11906. [PMID: 34769334 PMCID: PMC8584701 DOI: 10.3390/ijms222111906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 09/28/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022] Open
Abstract
Members of the fetal-gene-program may act as regulatory components to impede deleterious events occurring with cardiac remodeling, and constitute potential novel therapeutic heart failure (HF) targets. Mitochondrial energy derangements occur both during early fetal development and in patients with HF. Here we aim to elucidate the role of DIO2, a member of the fetal-gene-program, in pluripotent stem cell (PSC)-derived human cardiomyocytes and on mitochondrial dynamics and energetics, specifically. RNA sequencing and pathway enrichment analysis was performed on mouse cardiac tissue at different time points during development, adult age, and ischemia-induced HF. To determine the function of DIO2 in cardiomyocytes, a stable human hPSC-line with a DIO2 knockdown was made using a short harpin sequence. Firstly, we showed the selenoprotein, type II deiodinase (DIO2): the enzyme responsible for the tissue-specific conversion of inactive (T4) into active thyroid hormone (T3), to be a member of the fetal-gene-program. Secondly, silencing DIO2 resulted in an increased reactive oxygen species, impaired activation of the mitochondrial unfolded protein response, severely impaired mitochondrial respiration and reduced cellular viability. Microscopical 3D reconstruction of the mitochondrial network displayed substantial mitochondrial fragmentation. Summarizing, we identified DIO2 to be a member of the fetal-gene-program and as a key regulator of mitochondrial performance in human cardiomyocytes. Our results suggest a key position of human DIO2 as a regulator of mitochondrial function in human cardiomyocytes.
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Affiliation(s)
- Nils Bomer
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Mario G. Pavez-Giani
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Frederik E. Deiman
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Annet N. Linders
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Martijn F. Hoes
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Christiane L.J. Baierl
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Silke U. Oberdorf-Maass
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Rudolf A. de Boer
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Herman H.W. Silljé
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Centre Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands;
| | - Warner S. Simonides
- Department of Physiology, Amsterdam University Medical Centre, Vrije Unversiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - B. Daan Westenbrink
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
| | - Peter van der Meer
- Department of Cardiology, University Medical Centre Groningen, University of Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (M.G.P.-G.); (F.E.D.); (A.N.L.); (M.F.H.); (C.L.J.B.); (S.U.O.-M.); (R.A.d.B.); (H.H.W.S.); (B.D.W.); (P.v.d.M.)
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9
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben-Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2021; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long‐lived, lineage‐restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ‐restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ‐cell markers, but often lack germ‐line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole‐body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.,Institut Català de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
| | - Ildiko Somorjai
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Oshrat Ben-Hamo
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, University Embankment, 7/9, Saint-Petersburg, 199034, Russia.,Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon University, Jardin du Pharo, 58 Boulevard Charles Livon, Marseille, 13007, France.,Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Ulitsa Vavilova, 26, Moscow, 119334, Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, Paris, F-75006, France
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Bygg 19, Gaustad Sykehus, Sognsvannsveien 21, Oslo, 0188, Norway
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, Padova, 35121, Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological Research, National Institute of Oceanography, POB 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, 06107, France.,Université Côte d'Azur, Federative Research Institute - Marine Resources (IFR MARRES), 28 Avenue de Valrose, Nice, 06103, France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP), Università degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06234 Villefranche-sur-Mer, Villefranche sur Mer, Cedex, France
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Technikerstr, Innsbruck, 256020, Austria
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Ustyantsev K, Wudarski J, Sukhikh I, Reinoite F, Mouton S, Berezikov E. Proof of principle for piggyBac-mediated transgenesis in the flatworm Macrostomum lignano. Genetics 2021; 218:6276877. [PMID: 33999134 PMCID: PMC8717057 DOI: 10.1093/genetics/iyab076] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/06/2021] [Indexed: 12/03/2022] Open
Abstract
Regeneration-capable flatworms are informative research models to study the mechanisms of stem cell regulation, regeneration, and tissue patterning. The free-living flatworm Macrostomum lignano is currently the only flatworm where stable transgenesis is available, and as such it offers a powerful experimental platform to address questions that were previously difficult to answer. The published transgenesis approach relies on random integration of DNA constructs into the genome. Despite its efficiency, there is room and need for further improvement and diversification of transgenesis methods in M. lignano. Transposon-mediated transgenesis is an alternative approach, enabling easy mapping of the integration sites and the possibility of insertional mutagenesis studies. Here, we report for the first time that transposon-mediated transgenesis using piggyBac can be performed in M. lignano to create stable transgenic lines with single-copy transgene insertions.
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Affiliation(s)
- Kirill Ustyantsev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - Jakub Wudarski
- Laboratory of Biological Diversity, National Institute for Basic Biology, Okazaki 444-8585 Aichi, Japan
| | - Igor Sukhikh
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - Filipa Reinoite
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9700AD, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9700AD, The Netherlands
| | - Eugene Berezikov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9700AD, The Netherlands
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11
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Wudarski J, Egger B, Ramm SA, Schärer L, Ladurner P, Zadesenets KS, Rubtsov NB, Mouton S, Berezikov E. The free-living flatworm Macrostomum lignano. EvoDevo 2020; 11:5. [PMID: 32158530 PMCID: PMC7053086 DOI: 10.1186/s13227-020-00150-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/12/2020] [Indexed: 01/20/2023] Open
Abstract
Macrostomum lignano is a free-living flatworm that is emerging as an attractive experimental animal for research on a broad range of biological questions. One feature setting it apart from other flatworms is the successful establishment of transgenesis methods, facilitated by a steady supply of eggs in the form of single-cell zygotes that can be readily manipulated. This, in combination with the transparency of the animal and its small size, creates practical advantages for imaging and fluorescence-activated cell sorting in studies related to stem cell biology and regeneration. M. lignano can regenerate most of its body parts, including the germline, thanks to the neoblasts, which represent the flatworm stem cell system. Interestingly, neoblasts seem to have a high capacity of cellular maintenance, as M. lignano can survive up to 210 Gy of γ-irradiation, and partially offset the negative consequence of ageing. As a non-self-fertilizing simultaneous hermaphrodite that reproduces in a sexual manner, M. lignano is also used to study sexual selection and other evolutionary aspects of sexual reproduction. Work over the past several years has led to the development of molecular resources and tools, including high-quality genome and transcriptome assemblies, transcriptional profiling of the germline and somatic neoblasts, gene knockdown, and in situ hybridization. The increasingly detailed characterization of this animal has also resulted in novel research questions, such as bio-adhesion based on its adhesion-release glands and genome evolution due to its recent whole-genome duplication.![]()
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Affiliation(s)
- Jakub Wudarski
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Bernhard Egger
- 2Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Steven A Ramm
- 3Department of Evolutionary Biology, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Lukas Schärer
- 4Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter Ladurner
- 2Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Kira S Zadesenets
- 5The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
| | - Nikolay B Rubtsov
- 5The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
| | - Stijn Mouton
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Eugene Berezikov
- 1European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands.,5The Federal Research Center Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
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12
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Oliveira KMC, Barker JH, Berezikov E, Pindur L, Kynigopoulos S, Eischen-Loges M, Han Z, Bhavsar MB, Henrich D, Leppik L. Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model. Sci Rep 2019; 9:11433. [PMID: 31391536 PMCID: PMC6685943 DOI: 10.1038/s41598-019-47389-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/19/2022] Open
Abstract
Different species respond differently to severe injury, such as limb loss. In species that regenerate, limb loss is met with complete restoration of the limbs’ form and function, whereas in mammals the amputated limb’s stump heals and scars. In in vitro studies, electrical stimulation (EStim) has been shown to promote cell migration, and osteo- and chondrogenesis. In in vivo studies, after limb amputation, EStim causes significant new bone, cartilage and vessel growth. Here, in a rat model, the stumps of amputated rat limbs were exposed to EStim, and we measured extracellular matrix (ECM) deposition, macrophage distribution, cell proliferation and gene expression changes at early (3 and 7 days) and later stages (28 days). We found that EStim caused differences in ECM deposition, with less condensed collagen fibrils, and modified macrophage response by changing M1 to M2 macrophage ratio. The number of proliferating cells was increased in EStim treated stumps 7 days after amputation, and transcriptome data strongly supported our histological findings, with activated gene pathways known to play key roles in embryonic development and regeneration. In conclusion, our findings support the hypothesis that EStim shifts injury response from healing/scarring towards regeneration. A better understanding of if and how EStim controls these changes, could lead to strategies that replace scarring with regeneration.
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Affiliation(s)
- K M C Oliveira
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - J H Barker
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - L Pindur
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany.,Department of Plastic, Hand and Reconstructive Surgery, BG Trauma Center Frankfurt am Main gGmbH, Frankfurt am Main, Germany
| | - S Kynigopoulos
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - M Eischen-Loges
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - Z Han
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - M B Bhavsar
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - D Henrich
- Department of Trauma, Hand and Reconstructive Surgery, J.W. Goethe University, Frankfurt am Main, Germany
| | - L Leppik
- Frankfurt Initiative for Regenerative Medicine, Experimental Orthopedics & Trauma Surgery, J.W. Goethe University, Frankfurt am Main, Germany.
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13
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Ramm SA, Lengerer B, Arbore R, Pjeta R, Wunderer J, Giannakara A, Berezikov E, Ladurner P, Schärer L. Sex allocation plasticity on a transcriptome scale: Socially sensitive gene expression in a simultaneous hermaphrodite. Mol Ecol 2019; 28:2321-2341. [PMID: 30891857 DOI: 10.1111/mec.15077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 11/01/2017] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Phenotypic plasticity can enable organisms to produce optimal phenotypes in multiple environments. A crucial life history trait that is often highly plastic is sex allocation, which in simultaneous hermaphrodites describes the relative investment into the male versus female sex functions. Theory predicts-and morphological evidence supports-that greater investment into the male function is favoured with increasing group size, due to the increasing importance of sperm competition for male reproductive success. Here, we performed a genome-wide gene expression assay to test for such sex allocation plasticity in a model simultaneous hermaphrodite, the free-living flatworm Macrostomum lignano. Based on RNA-Seq data from 16 biological replicates spanning four different group size treatments, we demonstrate that at least 10% of the >75,000 investigated transcripts in M. lignano are differentially expressed according to the social environment, rising to >30% of putative gonad-specific transcripts (spermatogenesis and oogenesis candidates) and tail-specific transcripts (seminal fluid candidates). This transcriptional response closely corresponds to the expected shift away from female and towards male reproductive investment with increasing sperm competition level. Using whole-mount in situ hybridization, we then confirm that many plastic transcripts exhibit the expected organ-specific expression, and RNA interference of selected testis- and ovary-specific candidates establishes that these indeed function in gametogenesis pathways. We conclude that a large proportion of sex-specific transcripts in M. lignano are differentially expressed according to the prevailing ecological conditions and that these are functionally relevant to key reproductive phenotypes. Our study thus begins to bridge organismal and molecular perspectives on sex allocation plasticity.
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Affiliation(s)
- Steven A Ramm
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany.,Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Birgit Lengerer
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | - Roberto Arbore
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Robert Pjeta
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | - Julia Wunderer
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | | | - Eugene Berezikov
- ERIBA, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Ladurner
- Institute of Zoology & CMBI, University of Innsbruck, Innsbruck, Austria
| | - Lukas Schärer
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
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14
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Mouton S, Wudarski J, Grudniewska M, Berezikov E. The regenerative flatworm Macrostomum lignano, a model organism with high experimental potential. Int J Dev Biol 2019; 62:551-558. [PMID: 29938766 DOI: 10.1387/ijdb.180077eb] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Understanding the process of regeneration has been one of the longstanding scientific aims, from a fundamental biological perspective, as well as within the applied context of regenerative medicine. Because regeneration competence varies greatly between organisms, it is essential to investigate different experimental animals. The free-living marine flatworm Macrostomum lignano is a rising model organism for this type of research, and its power stems from a unique set of biological properties combined with amenability to experimental manipulation. The biological properties of interest include production of single-cell fertilized eggs, a transparent body, small size, short generation time, ease of culture, the presence of a pluripotent stem cell population, and a large regeneration competence. These features sparked the development of molecular tools and resources for this animal, including high-quality genome and transcriptome assemblies, gene knockdown, in situ hybridization, and transgenesis. Importantly, M. lignano is currently the only flatworm species for which transgenesis methods are established. This review summarizes biological features of M. lignano and recent technological advances towards experimentation with this animal. In addition, we discuss the experimental potential of this model organism for different research questions related to regeneration and stem cell biology.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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15
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Wudarski J, Ustyantsev K, Glazenburg L, Berezikov E. Influence of temperature on development, reproduction and regeneration in the flatworm model organism, Macrostomum lignano. Zoological Lett 2019; 5:7. [PMID: 30805201 PMCID: PMC6371448 DOI: 10.1186/s40851-019-0122-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The free-living marine flatworm Macrostomum lignano is a powerful model organism for use in studying mechanisms of regeneration and stem cell regulation due to its combination of biological and experimental properties, including the availability of transgenesis methods, which is unique among flatworm models. However, due to its relatively recent introduction in research, many aspects of this animal's biology remain unknown. One such question is the influence of culture temperature on Macrostomum biology. RESULTS We systematically investigated how different culture temperatures affect development time, reproduction rate, regeneration, heat shock response, and gene knockdown efficiency by RNA interference (RNAi) in M. lignano. We used marker transgenic lines to accurately measure the regeneration endpoint, and to establish the stress response threshold for temperature shock. We found that compared to the culture temperature of 20 °C commonly used for M. lignano, temperatures of 25 °C-30 °C substantially increase the speed of development and regeneration, lead to faster manifestation of RNAi phenotypes, and increase reproduction rate without detectable negative consequences for the animal, while temperatures above 30 °C elicit a heat shock response. CONCLUSIONS We show that altering temperature conditions can be used to reduce the time required to establish M. lignano cultures, perform RNAi experiments, store important lines, and optimize microinjection procedures for transgenesis. These findings will help to optimize the design of experiments in M. lignano, and thus facilitate future research using this model organism.
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Affiliation(s)
- Jakub Wudarski
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Kirill Ustyantsev
- Institute of Cytology and Genetics, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Lisa Glazenburg
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
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16
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Ebbing A, Vértesy Á, Betist MC, Spanjaard B, Junker JP, Berezikov E, van Oudenaarden A, Korswagen HC. Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns. Dev Cell 2018; 47:801-813.e6. [DOI: 10.1016/j.devcel.2018.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/31/2018] [Accepted: 10/12/2018] [Indexed: 12/15/2022]
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Mouton S, Grudniewska M, Glazenburg L, Guryev V, Berezikov E. Resilience to aging in the regeneration-capable flatworm Macrostomum lignano. Aging Cell 2018; 17:e12739. [PMID: 29488325 PMCID: PMC5946080 DOI: 10.1111/acel.12739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/15/2022] Open
Abstract
Animals show a large variability of lifespan, ranging from short-lived as Caenorhabditis elegans to immortal as Hydra. A fascinating case is flatworms, in which reversal of aging by regeneration is proposed, yet conclusive evidence for this rejuvenation-by-regeneration hypothesis is lacking. We tested this hypothesis by inducing regeneration in the sexual free-living flatworm Macrostomum lignano. We studied survival, fertility, morphology, and gene expression as a function of age. Here, we report that after regeneration, genes expressed in the germline are upregulated at all ages, but no signs of rejuvenation are observed. Instead, the animal appears to be substantially longer lived than previously appreciated, and genes expressed in stem cells are upregulated with age, while germline genes are downregulated. Remarkably, several genes with known beneficial effects on lifespan when overexpressed in mice and C. elegans are naturally upregulated with age in M. lignano, suggesting that molecular mechanism for offsetting negative consequences of aging has evolved in this animal. We therefore propose that M. lignano represents a novel powerful model for molecular studies of aging attenuation, and the identified aging gene expression patterns provide a valuable resource for further exploration of anti-aging strategies.
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Affiliation(s)
- Stijn Mouton
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Magda Grudniewska
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Lisa Glazenburg
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
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18
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Grudniewska M, Mouton S, Grelling M, Wolters AHG, Kuipers J, Giepmans BNG, Berezikov E. A novel flatworm-specific gene implicated in reproduction in Macrostomum lignano. Sci Rep 2018; 8:3192. [PMID: 29453392 PMCID: PMC5816591 DOI: 10.1038/s41598-018-21107-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
Abstract
Free-living flatworms, such as the planarian Schmidtea mediterranea, are extensively used as model organisms to study stem cells and regeneration. The majority of flatworm studies so far focused on broadly conserved genes. However, investigating what makes these animals different is equally informative for understanding its biology and might have biomedical value. We re-analyzed the neoblast and germline transcriptional signatures of the flatworm M. lignano using an improved transcriptome assembly and show that germline-enriched genes have a high fraction of flatworm-specific genes. We further identified the Mlig-sperm1 gene as a member of a novel gene family conserved only in free-living flatworms and essential for producing healthy spermatozoa. In addition, we established a whole-animal electron microscopy atlas (nanotomy) to visualize the ultrastructure of the testes in wild type worms, but also as a reference platform for different ultrastructural studies in M. lignano. This work demonstrates that investigation of flatworm-specific genes is crucial for understanding flatworm biology and establishes a basis for such future research in M. lignano.
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Affiliation(s)
- Magda Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Margriet Grelling
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands.
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Ovchinnikova E, Hoes M, Ustyantsev K, Bomer N, de Jong TV, van der Mei H, Berezikov E, van der Meer P. Modeling Human Cardiac Hypertrophy in Stem Cell-Derived Cardiomyocytes. Stem Cell Reports 2018; 10:794-807. [PMID: 29456183 PMCID: PMC5918264 DOI: 10.1016/j.stemcr.2018.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 12/17/2022] Open
Abstract
Cardiac hypertrophy accompanies many forms of cardiovascular diseases. The mechanisms behind the development and regulation of cardiac hypertrophy in the human setting are poorly understood, which can be partially attributed to the lack of a human cardiomyocyte-based preclinical test system recapitulating features of diseased myocardium. The objective of our study is to determine whether human embryonic stem cell-derived cardiomyocytes (hESC-CMs) subjected to mechanical stretch can be used as an adequate in vitro model for studying molecular mechanisms of cardiac hypertrophy. We show that hESC-CMs subjected to cyclic stretch, which mimics mechanical overload, exhibit essential features of a hypertrophic state on structural, functional, and gene expression levels. The presented hESC-CM stretch approach provides insight into molecular mechanisms behind mechanotransduction and cardiac hypertrophy and lays groundwork for the development of pharmacological approaches as well as for discovering potential circulating biomarkers of cardiac dysfunction.
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Affiliation(s)
- Ekaterina Ovchinnikova
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, the Netherlands; European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan, 1, PO Box 196, Groningen, the Netherlands
| | - Martijn Hoes
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, the Netherlands
| | - Kirill Ustyantsev
- Laboratory of Molecular Genetic Systems, Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Nils Bomer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, the Netherlands
| | - Tristan V de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan, 1, PO Box 196, Groningen, the Netherlands
| | - Henny van der Mei
- University of Groningen, University Medical Center Groningen, Biomedical Engineering Department, Groningen, 9713AV, the Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan, 1, PO Box 196, Groningen, the Netherlands.
| | - Peter van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, PO Box 30.001, Groningen, the Netherlands.
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20
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Kenny NJ, de Goeij JM, de Bakker DM, Whalen CG, Berezikov E, Riesgo A. Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea. Mar Genomics 2018; 37:135-147. [DOI: 10.1016/j.margen.2017.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 02/07/2023]
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21
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van der Pol A, Gil A, Silljé HHW, Tromp J, Ovchinnikova ES, Vreeswijk-Baudoin I, Hoes M, Domian IJ, van de Sluis B, van Deursen JM, Voors AA, van Veldhuisen DJ, van Gilst WH, Berezikov E, van der Harst P, de Boer RA, Bischoff R, van der Meer P. Accumulation of 5-oxoproline in myocardial dysfunction and the protective effects of OPLAH. Sci Transl Med 2017; 9:eaam8574. [PMID: 29118264 DOI: 10.1126/scitranslmed.aam8574] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/01/2017] [Accepted: 10/03/2017] [Indexed: 12/28/2022]
Abstract
In response to heart failure (HF), the heart reacts by repressing adult genes and expressing fetal genes, thereby returning to a more fetal-like gene profile. To identify genes involved in this process, we carried out transcriptional analysis on murine hearts at different stages of development and on hearts from adult mice with HF. Our screen identified Oplah, encoding for 5-oxoprolinase, a member of the γ-glutamyl cycle that functions by scavenging 5-oxoproline. OPLAH depletion occurred as a result of cardiac injury, leading to elevated 5-oxoproline and oxidative stress, whereas OPLAH overexpression improved cardiac function after ischemic injury. In HF patients, we observed elevated plasma 5-oxoproline, which was associated with a worse clinical outcome. Understanding and modulating fetal-like genes in the failing heart may lead to potential diagnostic, prognostic, and therapeutic options in HF.
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Affiliation(s)
- Atze van der Pol
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Andres Gil
- Department of Pharmacy, Analytical Biochemistry, University of Groningen, 9713 AV Groningen, Netherlands
| | - Herman H W Silljé
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Jasper Tromp
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
- National Heart Centre Singapore, 169609 Singapore, Singapore
| | - Ekaterina S Ovchinnikova
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
- European Research Institute for the Biology of Aging, Laboratory of Stem Cell Regulation and Mechanisms of Regeneration, University of Groningen, 9713 AV Groningen, Netherlands
| | - Inge Vreeswijk-Baudoin
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Martijn Hoes
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Ibrahim J Domian
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bart van de Sluis
- Molecular Genetics Section, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | | | - Adriaan A Voors
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Dirk J van Veldhuisen
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Wiek H van Gilst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Aging, Laboratory of Stem Cell Regulation and Mechanisms of Regeneration, University of Groningen, 9713 AV Groningen, Netherlands
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Rudolf A de Boer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands
| | - Rainer Bischoff
- Department of Pharmacy, Analytical Biochemistry, University of Groningen, 9713 AV Groningen, Netherlands
| | - Peter van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands.
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22
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Zadesenets KS, Ershov NI, Berezikov E, Rubtsov NB. Chromosome Evolution in the Free-Living Flatworms: First Evidence of Intrachromosomal Rearrangements in Karyotype Evolution of Macrostomum lignano (Platyhelminthes, Macrostomida). Genes (Basel) 2017; 8:E298. [PMID: 29084138 PMCID: PMC5704211 DOI: 10.3390/genes8110298] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/16/2017] [Accepted: 10/26/2017] [Indexed: 12/15/2022] Open
Abstract
The free-living flatworm Macrostomum lignano is a hidden tetraploid. Its genome was formed by a recent whole genome duplication followed by chromosome fusions. Its karyotype (2n = 8) consists of a pair of large chromosomes (MLI1), which contain regions of all other chromosomes, and three pairs of small metacentric chromosomes. Comparison of MLI1 with metacentrics was performed by painting with microdissected DNA probes and fluorescent in situ hybridization of unique DNA fragments. Regions of MLI1 homologous to small metacentrics appeared to be contiguous. Besides the loss of DNA repeat clusters (pericentromeric and telomeric repeats and the 5S rDNA cluster) from MLI1, the difference between small metacentrics MLI2 and MLI4 and regions homologous to them in MLI1 were revealed. Abnormal karyotypes found in the inbred DV1/10 subline were analyzed, and structurally rearranged chromosomes were described with the painting technique, suggesting the mechanism of their origin. The revealed chromosomal rearrangements generate additional diversity, opening the way toward massive loss of duplicated genes from a duplicated genome. Our findings suggest that the karyotype of M. lignano is in the early stage of genome diploidization after whole genome duplication, and further studies on M. lignano and closely related species can address many questions about karyotype evolution in animals.
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Affiliation(s)
- Kira S. Zadesenets
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk 630090, Russia; (N.I.E.); (N.B.R.)
| | - Nikita I. Ershov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk 630090, Russia; (N.I.E.); (N.B.R.)
| | - Eugene Berezikov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk 630090, Russia; (N.I.E.); (N.B.R.)
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713AV, Groningen, The Netherlands;
| | - Nikolay B. Rubtsov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Lavrentiev ave., 10, Novosibirsk 630090, Russia; (N.I.E.); (N.B.R.)
- Novosibirsk State University, Pirogova str., 2, Novosibirsk 630090, Russia
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23
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Lengerer B, Wunderer J, Pjeta R, Carta G, Kao D, Aboobaker A, Beisel C, Berezikov E, Salvenmoser W, Ladurner P. Organ specific gene expression in the regenerating tail of Macrostomum lignano. Dev Biol 2017; 433:448-460. [PMID: 28757111 DOI: 10.1016/j.ydbio.2017.07.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 04/28/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 11/25/2022]
Abstract
Temporal and spatial characterization of gene expression is a prerequisite for the understanding of cell-, tissue-, and organ-differentiation. In a multifaceted approach to investigate gene expression in the tail plate of the free-living marine flatworm Macrostomum lignano, we performed a posterior-region-specific in situ hybridization screen, RNA sequencing (RNA-seq) of regenerating animals, and functional analyses of selected tail-specific genes. The in situ screen revealed transcripts expressed in the antrum, cement glands, adhesive organs, prostate glands, rhabdite glands, and other tissues. Next we used RNA-seq to characterize temporal expression in the regenerating tail plate revealing a time restricted onset of both adhesive organs and copulatory apparatus regeneration. In addition, we identified three novel previously unannotated genes solely expressed in the regenerating stylet. RNA interference showed that these genes are required for the formation of not only the stylet but the whole male copulatory apparatus. RNAi treated animals lacked the stylet, vesicula granulorum, seminal vesicle, false seminal vesicle, and prostate glands, while the other tissues of the tail plate, such as adhesive organs regenerated normally. In summary, our findings provide a large resource of expression data during homeostasis and regeneration of the morphologically complex tail regeneration and pave the way for a better understanding of organogenesis in M. lignano.
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Affiliation(s)
- Birgit Lengerer
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Julia Wunderer
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Giada Carta
- Division of Physiology, Medical University of Innsbruck, Schöpfstraße 41/EG, A-6020 Innsbruck, Austria.
| | - Damian Kao
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
| | - Aziz Aboobaker
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.
| | - Willi Salvenmoser
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria.
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24
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Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM. Guanine quadruplex structures localize to heterochromatin. Nucleic Acids Res 2017; 45:6253. [PMID: 28449026 PMCID: PMC5449592 DOI: 10.1093/nar/gkx301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Roland F Hoffmann
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Nicola A Grzeschik
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ruby D Kalicharan
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Kazuki Nishida
- Faculty of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Aleksander V Romashchenko
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jan Postberg
- Helios Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, Germany
| | - Hans Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research, Witten/Herdecke University, Witten, Germany
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ody C M Sibon
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands.,Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medicine, University of British Columbia Vancouver, BC, V5Z 1L3, Canada
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25
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Vegter EL, Ovchinnikova ES, van Veldhuisen DJ, Jaarsma T, Berezikov E, van der Meer P, Voors AA. Low circulating microRNA levels in heart failure patients are associated with atherosclerotic disease and cardiovascular-related rehospitalizations. Clin Res Cardiol 2017; 106:598-609. [PMID: 28293796 PMCID: PMC5529487 DOI: 10.1007/s00392-017-1096-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Circulating microRNAs (miRNAs) have been implicated in both heart failure and atherosclerotic disease. The aim of this study was to examine associations between heart failure specific circulating miRNAs, atherosclerotic disease and cardiovascular-related outcome in patients with heart failure. METHODS The levels of 11 heart failure-specific circulating miRNAs were compared in plasma of 114 heart failure patients with and without different manifestations of atherosclerotic disease. We then studied these miRNAs in relation to biomarkers associated to atherosclerosis and to cardiovascular-related rehospitalizations during 18 months of follow-up. RESULTS At least one manifestation of atherosclerotic disease was found in 70 (61%) of the heart failure patients. A consistent trend was found between an increasing number of manifestations of atherosclerosis (peripheral arterial disease in specific), and lower levels of miR-18a-5p, miR-27a-3p, miR-199a-3p, miR-223-3p and miR-652-3p (all P < 0.05). Target prediction and network analyses identified several interactions between miRNA targets and biomarkers related to inflammation, angiogenesis and endothelial dysfunction. Lower miRNA levels were associated with higher levels of these atherosclerosis-related biomarkers. In addition, lower miRNA levels were significantly associated with rehospitalizations due to cardiovascular causes within 18 months, with let-7i-5p as strongest predictor [HR 2.06 (95% CI 1.29-3.28), C-index 0.70, P = 0.002]. CONCLUSIONS A consistent pattern of lower levels of circulating miRNAs was found in heart failure patients with atherosclerotic disease, in particular peripheral arterial disease. In addition, lower levels of miRNAs were associated with higher levels of biomarkers involved in atherosclerosis and an increased risk of a cardiovascular-related rehospitalization.
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Affiliation(s)
- Eline L Vegter
- Department of Cardiology, AB31, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Ekaterina S Ovchinnikova
- Department of Cardiology, AB31, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.,European Research Institute for the Biology of Ageing, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Dirk J van Veldhuisen
- Department of Cardiology, AB31, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Tiny Jaarsma
- Faculty of Medical and Health Sciences, University of Linkoping, 581 83, Linköping, Sweden
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter van der Meer
- Department of Cardiology, AB31, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Adriaan A Voors
- Department of Cardiology, AB31, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
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26
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Grudniewska M, Mouton S, Simanov D, Beltman F, Grelling M, de Mulder K, Arindrarto W, Weissert PM, van der Elst S, Berezikov E. Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano. eLife 2016; 5. [PMID: 27997336 PMCID: PMC5173321 DOI: 10.7554/elife.20607] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022] Open
Abstract
The regeneration-capable flatworm Macrostomum lignano is a powerful model organism to study the biology of stem cells in vivo. As a flatworm amenable to transgenesis, it complements the historically used planarian flatworm models, such as Schmidtea mediterranea. However, information on the transcriptome and markers of stem cells in M. lignano is limited. We generated a de novo transcriptome assembly and performed the first comprehensive characterization of gene expression in the proliferating cells of M. lignano, represented by somatic stem cells, called neoblasts, and germline cells. Knockdown of a selected set of neoblast genes, including Mlig-ddx39, Mlig-rrm1, Mlig-rpa3, Mlig-cdk1, and Mlig-h2a, confirmed their crucial role for the functionality of somatic neoblasts during homeostasis and regeneration. The generated M. lignano transcriptome assembly and gene expression signatures of somatic neoblasts and germline cells will be a valuable resource for future molecular studies in M. lignano. DOI:http://dx.doi.org/10.7554/eLife.20607.001
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Affiliation(s)
- Magda Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Daniil Simanov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Frank Beltman
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Margriet Grelling
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katrien de Mulder
- Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wibowo Arindrarto
- Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Philipp M Weissert
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan van der Elst
- Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Hubrecht Institute-KNAW, Utrecht, The Netherlands.,University Medical Centre Utrecht, Utrecht, The Netherlands
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27
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Isik M, Blackwell TK, Berezikov E. MicroRNA mir-34 provides robustness to environmental stress response via the DAF-16 network in C. elegans. Sci Rep 2016; 6:36766. [PMID: 27905558 PMCID: PMC5131338 DOI: 10.1038/srep36766] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/20/2016] [Indexed: 12/16/2022] Open
Abstract
Diverse stresses and aging alter expression levels of microRNAs, suggesting a role for these posttranscriptional regulators of gene expression in stress modulation and longevity. Earlier studies demonstrated a central role for the miR-34 family in promoting cell cycle arrest and cell death following stress in human cells. However, the biological significance of this response was unclear. Here we show that in C. elegans mir-34 upregulation is necessary for developmental arrest, correct morphogenesis, and adaptation to a lower metabolic state to protect animals against stress-related damage. Either deletion or overexpression of mir-34 lead to an impaired stress response, which can largely be explained by perturbations in DAF-16/FOXO target gene expression. We demonstrate that mir-34 expression is regulated by the insulin signaling pathway via a negative feedback loop between miR-34 and DAF-16/FOXO. We propose that mir-34 provides robustness to stress response programs by controlling noise in the DAF-16/FOXO-regulated gene network.
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Affiliation(s)
- Meltem Isik
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.,Joslin Diabetes Center, Harvard Stem Cell Institute and Harvard Medical School Department of Genetics, Boston, Massachusetts, United States of America
| | - T Keith Blackwell
- Joslin Diabetes Center, Harvard Stem Cell Institute and Harvard Medical School Department of Genetics, Boston, Massachusetts, United States of America
| | - Eugene Berezikov
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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28
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Zadesenets KS, Vizoso DB, Schlatter A, Konopatskaia ID, Berezikov E, Schärer L, Rubtsov NB. Evidence for Karyotype Polymorphism in the Free-Living Flatworm, Macrostomum lignano, a Model Organism for Evolutionary and Developmental Biology. PLoS One 2016; 11:e0164915. [PMID: 27755577 PMCID: PMC5068713 DOI: 10.1371/journal.pone.0164915] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 07/07/2016] [Accepted: 10/03/2016] [Indexed: 11/19/2022] Open
Abstract
Over the past decade, the free-living flatworm Macrostomum lignano has been successfully used in many areas of biology, including embryology, stem cells, sexual selection, bioadhesion and aging. The increased use of this powerful laboratory model, including the establishment of genomic resources and tools, makes it essential to have a detailed description of the chromosome organization of this species, previously suggested to have a karyotype with 2n = 8 and one pair of large and three pairs of small metacentric chromosomes. We performed cytogenetic analyses for chromosomes of one commonly used inbred line of M. lignano (called DV1) and uncovered unexpected chromosome number variation in the form of aneuploidies of the largest chromosomes. These results prompted us to perform karyotypic studies in individual specimens of this and other lines of M. lignano reared under laboratory conditions, as well as in freshly field-collected specimens from different natural populations. Our analyses revealed a high frequency of aneuploids and in some cases other numerical and structural chromosome abnormalities in laboratory-reared lines of M. lignano, and some cases of aneuploidy were also found in freshly field-collected specimens. Moreover, karyological analyses were performed in specimens of three further species: Macrostomum sp. 8 (a close relative of M. lignano), M. spirale and M. hystrix. Macrostomum sp. 8 showed a karyotype that was similar to that of M. lignano, with tetrasomy for its largest chromosome being the most common karyotype, while the other two species showed a simpler karyotype that is more typical of the genus Macrostomum. These findings suggest that M. lignano and Macrostomum sp. 8 can be used as new models for studying processes of partial genome duplication in genome evolution.
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Affiliation(s)
- Kira S. Zadesenets
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- * E-mail:
| | - Dita B. Vizoso
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Aline Schlatter
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Eugene Berezikov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| | - Nikolay B. Rubtsov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
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Rodrigues M, Ostermann T, Kremeser L, Lindner H, Beisel C, Berezikov E, Hobmayer B, Ladurner P. Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics. Biofouling 2016; 32:1115-1129. [PMID: 27661452 PMCID: PMC5080974 DOI: 10.1080/08927014.2016.1233325] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
The differentiated ectodermal basal disc cells of the freshwater cnidarian Hydra secrete proteinaceous glue to temporarily attach themselves to underwater surfaces. Using transcriptome sequencing and a basal disc-specific RNA-seq combined with in situ hybridisation a highly specific set of candidate adhesive genes was identified. A de novo transcriptome assembly of 55,849 transcripts (>200 bp) was generated using paired-end and single reads from Illumina libraries constructed from different polyp conditions. Differential transcriptomics and spatial gene expression analysis by in situ hybridisation allowed the identification of 40 transcripts exclusively expressed in the ectodermal basal disc cells. Comparisons after mass spectrometry analysis of the adhesive secretion showed a total of 21 transcripts to be basal disc specific and eventually secreted through basal disc cells. This is the first study to survey adhesion-related genes in Hydra. The candidate list presented in this study provides a platform for unravelling the molecular mechanism of underwater adhesion of Hydra.
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Affiliation(s)
- Marcelo Rodrigues
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Thomas Ostermann
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremeser
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | | | - Eugene Berezikov
- ERIBA, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Peter Ladurner
- Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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Vegter EL, Schmitter D, Hagemeijer Y, Ovchinnikova ES, van der Harst P, Teerlink JR, O'Connor CM, Metra M, Davison BA, Bloomfield D, Cotter G, Cleland JG, Givertz MM, Ponikowski P, van Veldhuisen DJ, van der Meer P, Berezikov E, Voors AA, Khan MAF. Use of biomarkers to establish potential role and function of circulating microRNAs in acute heart failure. Int J Cardiol 2016; 224:231-239. [PMID: 27661412 DOI: 10.1016/j.ijcard.2016.09.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 09/02/2016] [Accepted: 09/08/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Circulating microRNAs (miRNAs) emerge as potential heart failure biomarkers. We aimed to identify associations between acute heart failure (AHF)-specific circulating miRNAs and well-known heart failure biomarkers. METHODS Associations between 16 biomarkers predictive for 180day mortality and the levels of 12 AHF-specific miRNAs were determined in 100 hospitalized AHF patients, at baseline and 48hours. Patients were divided in 4 pre-defined groups, based on clinical parameters during hospitalization. Correlation analyses between miRNAs and biomarkers were performed and complemented by miRNA target prediction and pathway analysis. RESULTS No significant correlations were found at hospital admission. However, after 48hours, 7 miRNAs were significantly negatively correlated to biomarkers indicative for a worse clinical outcome in the patient group with the most unfavorable in-hospital course (n=21); miR-16-5p was correlated to C-reactive protein (R=-0.66, p-value=0.0027), miR-106a-5p to creatinine (R=-0.68, p-value=0.002), miR-223-3p to growth differentiation factor 15 (R=-0.69, p-value=0.0015), miR-652-3p to soluble ST-2 (R=-0.77, p-value<0.001), miR-199a-3p to procalcitonin (R=-0.72, p-value<0.001) and galectin-3 (R=-0.73, p-value<0.001) and miR-18a-5p to procalcitonin (R=-0.68, p-value=0.002). MiRNA target prediction and pathway analysis identified several pathways related to cardiac diseases, which could be linked to some of the miRNA-biomarker correlations. CONCLUSIONS The majority of correlations between circulating AHF-specific miRNAs were related to biomarkers predictive for a worse clinical outcome in a subgroup of worsening heart failure patients at 48hours of hospitalization. The selective findings suggest a time-dependent effect of circulating miRNAs and highlight the susceptibility to individual patient characteristics influencing potential relations between miRNAs and biomarkers.
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Affiliation(s)
- Eline L Vegter
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Daniela Schmitter
- Momentum Research, Inc., Hagmattstrasse 17, CH-4123 Allschwil, Switzerland
| | - Yanick Hagemeijer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Ekaterina S Ovchinnikova
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands; European Research Institute for the Biology of Ageing and University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - John R Teerlink
- University of California at San Francisco, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | | | - Marco Metra
- Cardiology, The Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy
| | | | | | | | - John G Cleland
- National Heart & Lung Institute, Royal Brompton & Harefield Hospitals, Imperial College, London, UK
| | - Michael M Givertz
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Dirk J van Veldhuisen
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Peter van der Meer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing and University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Adriaan A Voors
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Mohsin A F Khan
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
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31
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Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM. Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Res 2016; 44:1036-51. [PMID: 26429969 PMCID: PMC4756854 DOI: 10.1093/nar/gkv978] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [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: 06/18/2015] [Revised: 08/27/2015] [Accepted: 09/16/2015] [Indexed: 01/09/2023] Open
Abstract
Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.
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Affiliation(s)
- Răzvan V Chereji
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tsung-Wai Kan
- Department of Biochemistry, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Magda K Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | | | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | - Alexandre V Morozov
- Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk 630090, Russia
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32
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Wu CC, Kruse F, Vasudevarao MD, Junker JP, Zebrowski DC, Fischer K, Noël ES, Grün D, Berezikov E, Engel FB, van Oudenaarden A, Weidinger G, Bakkers J. Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration. Dev Cell 2015; 36:36-49. [PMID: 26748692 DOI: 10.1016/j.devcel.2015.12.010] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/14/2015] [Accepted: 11/20/2015] [Indexed: 12/21/2022]
Abstract
In contrast to mammals, zebrafish regenerate heart injuries via proliferation of cardiomyocytes located near the wound border. To identify regulators of cardiomyocyte proliferation, we used spatially resolved RNA sequencing (tomo-seq) and generated a high-resolution genome-wide atlas of gene expression in the regenerating zebrafish heart. Interestingly, we identified two wound border zones with distinct expression profiles, including the re-expression of embryonic cardiac genes and targets of bone morphogenetic protein (BMP) signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast, we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation, ultimately compromising myocardial regeneration, while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non-regenerative hearts.
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Affiliation(s)
- Chi-Chung Wu
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Fabian Kruse
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | | | - Jan Philipp Junker
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - David C Zebrowski
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Krankenhausstr 8-10, 91054 Erlangen, Germany
| | - Kristin Fischer
- Institute of Clinical Genetics, Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | - Emily S Noël
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - Dominic Grün
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya Street 100, Skolkovo, Moscow Region 143025, Russia
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Krankenhausstr 8-10, 91054 Erlangen, Germany
| | - Alexander van Oudenaarden
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - Gilbert Weidinger
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Jeroen Bakkers
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands; Medical Physiology, University Medical Centre Utrecht, Yalelaan 50, 3584 CM Utrecht, the Netherlands.
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Bruno N, ter Maaten JM, Ovchinnikova ES, Vegter EL, Valente MAE, van der Meer P, de Boer RA, van der Harst P, Schmitter D, Metra M, O'Connor CM, Ponikowski P, Teerlink JR, Cotter G, Davison B, Cleland JG, Givertz MM, Bloomfield DM, Dittrich HC, Pinto YM, van Veldhuisen DJ, Hillege HL, Berezikov E, Voors AA. MicroRNAs relate to early worsening of renal function in patients with acute heart failure. Int J Cardiol 2015; 203:564-9. [PMID: 26569364 DOI: 10.1016/j.ijcard.2015.10.217] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 10/09/2015] [Accepted: 10/27/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND Deregulation of microRNAs (miRNAs) may be involved in the pathogenesis of heart failure (HF) and renal disease. Our aim is to describe miRNA levels related to early worsening renal function in acute HF patients. METHOD AND RESULTS We studied the association between 12 circulating miRNAs and Worsening Renal Function (WRF; defined as an increase in the serum creatinine level of 0.3mg per deciliter or more from admission to day 3), absolute change in creatinine and Neutrophil Gelatinase Associated Lipocalin (NGAL) from admission to day 3 in 98 patients hospitalized for acute HF. At baseline, circulating levels of all miRNAs were lower in patients with WRF, with statistically significant decreased levels of miR-199a-3p, miR-423-3p, and miR-let-7i-5p (p-value<0.05). The increase in creatinine during the first 3 days of hospitalization was significantly associated with lower levels of miR-199a-3p, miR-27a-3p, miR-652-3p, miR-423-5p, and miR-let-7i-5p, while the increase in NGAL was significantly associated with lower levels of miR-18a-5p, miR-106a-5p, miR-223-3p, miR-199a-3p and miR-423-3p. MiR-199a-3p was the strongest predictor of WRF, with an Odds Ratio of 1.48 (1.061-2.065; p-value=0.021) and a C-index of 0.701. CONCLUSIONS Our results show that the levels of circulating miRNAs at hospital admission for acute HF were consistently lower in patients who developed worsening of renal function. MiR-199a-3p was the best predictor of WRF in these patients.
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Affiliation(s)
- Noemi Bruno
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Jozine M ter Maaten
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Ekaterina S Ovchinnikova
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eline L Vegter
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Mattia A E Valente
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter van der Meer
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rudolf A de Boer
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim van der Harst
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Marco Metra
- Department of Cardiology, University of Brescia, Brescia, Italy
| | | | | | - John R Teerlink
- University of California at San Francisco, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | | | | | - John G Cleland
- National Heart & Lung Institute, Royal Brompton & Harefield Hospitals, Imperial College, London, UK
| | - Michael M Givertz
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Howard C Dittrich
- University of Iowa Carver College of Medicine Cardiovascular Research Center, Iowa City, IA, USA
| | | | - Dirk J van Veldhuisen
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Hans L Hillege
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Adriaan A Voors
- University of Groningen, Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands.
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34
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Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH. miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. Trends Genet 2015; 31:613-626. [PMID: 26453491 DOI: 10.1016/j.tig.2015.09.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [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: 05/20/2015] [Revised: 08/10/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
High-throughput sequencing of miRNAs has revealed the diversity and variability of mature and functional short noncoding RNAs, including their genomic origins, biogenesis pathways, sequence variability, and newly identified products such as miRNA-offset RNAs (moRs). Here we review known cases of alternative mature miRNA-like RNA fragments and propose a revised definition of miRNAs to encompass this diversity. We then review nomenclature guidelines for miRNAs and propose to extend nomenclature conventions to align with those for protein-coding genes established by international consortia. Finally, we suggest a system to encompass the full complexity of sequence variations (i.e., isomiRs) in the analysis of small RNA sequencing experiments.
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Affiliation(s)
- T Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - P Batzel
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - E Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - K Eilbeck
- Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA
| | - J T Eppig
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - M S McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - A Singer
- ZFIN, 5291 University of Oregon, Eugene, OR 97403-5291, USA
| | - J H Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
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35
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Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM. Guanine quadruplex structures localize to heterochromatin. Nucleic Acids Res 2015; 44:152-63. [PMID: 26384414 PMCID: PMC4705689 DOI: 10.1093/nar/gkv900] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/21/2015] [Indexed: 12/27/2022] Open
Abstract
Increasing amounts of data support a role for guanine quadruplex (G4) DNA and RNA structures in various cellular processes. We stained different organisms with monoclonal antibody 1H6 specific for G4 DNA. Strikingly, immuno-electron microscopy showed exquisite specificity for heterochromatin. Polytene chromosomes from Drosophila salivary glands showed bands that co-localized with heterochromatin proteins HP1 and the SNF2 domain-containing protein SUUR. Staining was retained in SUUR knock-out mutants but lost upon overexpression of SUUR. Somatic cells in Macrostomum lignano were strongly labeled, but pluripotent stem cells labeled weakly. Similarly, germline stem cells in Drosophila ovaries were weakly labeled compared to most other cells. The unexpected presence of G4 structures in heterochromatin and the difference in G4 staining between somatic cells and stem cells with germline DNA in ciliates, flatworms, flies and mammals point to a conserved role for G4 structures in nuclear organization and cellular differentiation.
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Affiliation(s)
- Roland F Hoffmann
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Nicola A Grzeschik
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ruby D Kalicharan
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Kazuki Nishida
- Faculty of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Aleksander V Romashchenko
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jan Postberg
- Helios Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, Germany
| | - Hans Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research, Witten/Herdecke University, Witten, Germany
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ody C M Sibon
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medicine, University of British Columbia Vancouver, BC, V5Z 1L3, Canada
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Ovchinnikova ES, Schmitter D, Vegter EL, ter Maaten JM, Valente MA, Liu LC, van der Harst P, Pinto YM, de Boer RA, Meyer S, Teerlink JR, O'Connor CM, Metra M, Davison BA, Bloomfield DM, Cotter G, Cleland JG, Mebazaa A, Laribi S, Givertz MM, Ponikowski P, van der Meer P, van Veldhuisen DJ, Voors AA, Berezikov E. Signature of circulating microRNAs in patients with acute heart failure. Eur J Heart Fail 2015; 18:414-23. [DOI: 10.1002/ejhf.332] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/11/2015] [Accepted: 06/11/2015] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ekaterina S. Ovchinnikova
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
- European Research Institute for the Biology of Ageing and University Medical Center Groningen, University of Groningen; Groningen The Netherlands
| | | | - Eline L. Vegter
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Jozine M. ter Maaten
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Mattia A.E. Valente
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Licette C.Y. Liu
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Pim van der Harst
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | | | - Rudolf A. de Boer
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Sven Meyer
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - John R. Teerlink
- University of California at San Francisco and San Francisco Veterans Affairs Medical Center; San Francisco CA USA
| | | | - Marco Metra
- Cardiology, The Department of Medical and Surgical Specialties; Radiological Sciences, and Public Health; University of Brescia; Brescia Italy
| | | | | | | | - John G. Cleland
- National Heart & Lung Institute, Royal Brompton & Harefield Hospitals; Imperial College; London UK
| | - Alexandre Mebazaa
- University Paris Diderot, U942 INSERM, AP-HP, St Louis-Lariboisière University Hospitals; Department of Anesthesiology and Critical Care and Burn Unit; Paris France
| | - Said Laribi
- U942 INSERM, AP-HP, St Louis-Lariboisière University Hospitals; Department of Emergency Medicine; Paris France
| | | | | | - Peter van der Meer
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Dirk J. van Veldhuisen
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Adriaan A. Voors
- Department of Cardiology; University Medical Center Groningen; Groningen The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing and University Medical Center Groningen, University of Groningen; Groningen The Netherlands
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Arbore R, Sekii K, Beisel C, Ladurner P, Berezikov E, Schärer L. Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits. Front Zool 2015; 12:14. [PMID: 26146508 PMCID: PMC4490696 DOI: 10.1186/s12983-015-0106-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/15/2015] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION RNA interference (RNAi) of trait-specific genes permits the manipulation of specific phenotypic traits ("phenotypic engineering") and thus represents a powerful tool to test trait function in evolutionary studies. The identification of suitable candidate genes, however, often relies on existing functional gene annotation, which is usually limited in emerging model organisms, especially when they are only distantly related to traditional genetic model organisms. A case in point is the free-living flatworm Macrostomum lignano (Lophotrochozoa: Platyhelminthes: Rhabditophora), an increasingly powerful model organism for evolutionary studies of sex in simultaneous hermaphrodites. To overcome the limitation of sparse functional annotation, we have performed a positional RNA-Seq analysis on different body fragments in order to identify organ-specific candidate transcripts. We then performed gene expression (in situ hybridization) and gene function (RNAi) analyses on 23 candidate transcripts, both to evaluate the predictive potential of this approach and to obtain preliminary functional characterizations of these candidate genes. RESULTS We identified over 4000 transcripts that could be expected to show specific expression in different reproductive organs (including testis, ovary and the male and female genital systems). The predictive potential of the method could then be verified by confirming organ-specific expression for several candidate transcripts, some of which yielded interesting trait-specific knock-down phenotypes that can now be followed up in future phenotypic engineering studies. CONCLUSIONS Our positional RNA-Seq analysis represents a highly useful resource for the identification of candidate transcripts for functional and phenotypic engineering studies in M. lignano, and it has already been used successfully in several studies. Moreover, this approach can overcome some inherent limitations of homology-based candidate selection and thus should be applicable to a broad range of emerging model organisms.
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Affiliation(s)
- Roberto Arbore
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Kiyono Sekii
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | | | - Peter Ladurner
- Institute of Zoology and CMBI, University of Innsbruck, Innsbruck, Austria
| | - Eugene Berezikov
- ERIBA, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
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Babae N, Bourajjaj M, Liu Y, Van Beijnum JR, Cerisoli F, Scaria PV, Verheul M, Van Berkel MP, Pieters EHE, Van Haastert RJ, Yousefi A, Mastrobattista E, Storm G, Berezikov E, Cuppen E, Woodle M, Schaapveld RQJ, Prevost GP, Griffioen AW, Van Noort PI, Schiffelers RM. Systemic miRNA-7 delivery inhibits tumor angiogenesis and growth in murine xenograft glioblastoma. Oncotarget 2015; 5:6687-700. [PMID: 25149532 PMCID: PMC4196156 DOI: 10.18632/oncotarget.2235] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Tumor-angiogenesis is the multi-factorial process of sprouting of endothelial cells (EC) into micro-vessels to provide tumor cells with nutrients and oxygen. To explore miRNAs as therapeutic angiogenesis-inhibitors, we performed a functional screen to identify miRNAs that are able to decrease EC viability. We identified miRNA-7 (miR-7) as a potent negative regulator of angiogenesis. Introduction of miR-7 in EC resulted in strongly reduced cell viability, tube formation, sprouting and migration. Application of miR-7 in the chick chorioallantoic membrane assay led to a profound reduction of vascularization, similar to anti-angiogenic drug sunitinib. Local administration of miR-7 in an in vivo murine neuroblastoma tumor model significantly inhibited angiogenesis and tumor growth. Finally, systemic administration of miR-7 using a novel integrin-targeted biodegradable polymeric nanoparticles that targets both EC and tumor cells, strongly reduced angiogenesis and tumor proliferation in mice with human glioblastoma xenografts. Transcriptome analysis of miR-7 transfected EC in combination with in silico target prediction resulted in the identification of OGT as novel target gene of miR-7. Our study provides a comprehensive validation of miR-7 as novel anti-angiogenic therapeutic miRNA that can be systemically delivered to both EC and tumor cells and offers promise for miR-7 as novel anti-tumor therapeutic.
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Affiliation(s)
- Negar Babae
- Utrecht Institute for Pharmaceutical Sciences, University Utrecht, Utrecht, the Netherlands. These authors contributed equally to this work
| | - Meriem Bourajjaj
- InteRNA Technologies B.V., Utrecht, the Netherlands. These authors contributed equally to this work
| | - Yijia Liu
- Aparna Biosciences Corporation, Rockville MD, USA. These authors contributed equally to this work
| | | | | | | | - Mark Verheul
- InteRNA Technologies B.V., Utrecht, the Netherlands
| | | | - Ebel H E Pieters
- Utrecht Institute for Pharmaceutical Sciences, University Utrecht, Utrecht, the Netherlands.
| | | | - Afrouz Yousefi
- Utrecht Institute for Pharmaceutical Sciences, University Utrecht, Utrecht, the Netherlands.
| | - Enrico Mastrobattista
- Utrecht Institute for Pharmaceutical Sciences, University Utrecht, Utrecht, the Netherlands.
| | - Gert Storm
- MIRA Institute for Biomedical Technology & Technical Medicine, Faculty of Science & Technology, University of Twente, AE Enschede, the Netherlands
| | - Eugene Berezikov
- Hubrecht Institute, Cancer Genomics Center and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Cancer Genomics Center and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | | | | | - Raymond M Schiffelers
- Laboratory Clinical Chemistry & Haematology, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
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Lengerer B, Pjeta R, Wunderer J, Rodrigues M, Arbore R, Schärer L, Berezikov E, Hess MW, Pfaller K, Egger B, Obwegeser S, Salvenmoser W, Ladurner P. Biological adhesion of the flatworm Macrostomum lignano relies on a duo-gland system and is mediated by a cell type-specific intermediate filament protein. Front Zool 2014; 11:12. [PMID: 24520881 PMCID: PMC4016567 DOI: 10.1186/1742-9994-11-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/20/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Free-living flatworms, in both marine and freshwater environments, are able to adhere to and release from a substrate several times within a second. This reversible adhesion relies on adhesive organs comprised of three cell types: an adhesive gland cell, a releasing gland cell, and an anchor cell, which is a modified epidermal cell responsible for structural support. However, nothing is currently known about the molecules that are involved in this adhesion process. RESULTS In this study we present the detailed morphology of the adhesive organs of the free-living marine flatworm Macrostomum lignano. About 130 adhesive organs are located in a horse-shoe-shaped arc along the ventral side of the tail plate. Each organ consists of exactly three cells, an adhesive gland cell, a releasing gland cell, and an anchor cell. The necks of the two gland cells penetrate the anchor cell through a common pore. Modified microvilli of the anchor cell form a collar surrounding the necks of the adhesive- and releasing glands, jointly forming the papilla, the outer visible part of the adhesive organs. Next, we identified an intermediate filament (IF) gene, macif1, which is expressed in the anchor cells. RNA interference mediated knock-down resulted in the first experimentally induced non-adhesion phenotype in any marine animal. Specifically, the absence of intermediate filaments in the anchor cells led to papillae with open tips, a reduction of the cytoskeleton network, a decline in hemidesmosomal connections, and to shortened microvilli containing less actin. CONCLUSION Our findings reveal an elaborate biological adhesion system in a free-living flatworm, which permits impressively rapid temporary adhesion-release performance in the marine environment. We demonstrate that the structural integrity of the supportive cell, the anchor cell, is essential for this adhesion process: the knock-down of the anchor cell-specific intermediate filament gene resulted in the inability of the animals to adhere. The RNAi mediated changes of the anchor cell morphology are comparable to situations observed in human gut epithelia. Therefore, our current findings and future investigations using this powerful flatworm model system might contribute to a better understanding of the function of intermediate filaments and their associated human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Technikerstr, 25, Innsbruck A-6020, Austria.
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Moreno-Mateos MA, Barragán V, Torres B, Rodríguez-Mateo C, Méndez-Vidal C, Berezikov E, Mudduluru G, Allgayer H, Pintor-Toro JA. Novel small RNA expression libraries uncover hsa-miR-30b and hsa-miR-30c as important factors in anoikis resistance. RNA 2013; 19:1711-1725. [PMID: 24129493 PMCID: PMC3884670 DOI: 10.1261/rna.039461.113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/30/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) have been widely studied in order to elucidate their biological functions. MicroRNA microarrays or miRNA overexpression libraries generated by synthesis and cloning of individual miRNAs have been used to study their different roles. In this work, we have developed a novel methodology to express mature miRNAs and other small RNAs from a double convergent RNA polymerase III promoter. We show that the generated miRNAs function similarly to those processed from primary transcripts or pri-miRNAs. This system allowed us to produce a lentiviral library expressing the whole population of small RNAs present in a metastatic cell line. A functional screening using this library led to the identification of hsa-miR-30b and hsa-miR-30c as negative regulators of cell death induced by loss of attachment (anoikis). Importantly, we demonstrated that the acquisition of anoikis resistance via these miRNAs is achieved through down-regulation of caspase 3 expression. Moreover, overexpression of these miRNAs resulted in a decrease of other types of caspase 3-dependent cell death and enhanced the survival of MCF10A acinar cells in morphogenesis assays, suggesting a putative role as oncomirs. In summary, this novel methodology provides a powerful and effective way for identifying novel small RNAs involved in a particular biological process.
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Affiliation(s)
- Miguel A. Moreno-Mateos
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER-CSIC, 41092 Sevilla, Spain
| | - Verónica Barragán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER-CSIC, 41092 Sevilla, Spain
| | - Belén Torres
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER-CSIC, 41092 Sevilla, Spain
| | - Cristina Rodríguez-Mateo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER-CSIC, 41092 Sevilla, Spain
| | - Cristina Méndez-Vidal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER-CSIC, 41092 Sevilla, Spain
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713AV Groningen, The Netherlands
| | - Giridhar Mudduluru
- Department of Experimental Surgery Mannheim/Molecular Oncology of Solid Tumors, DKFZ and University of Heidelberg, 68167 Heidelberg, Germany
| | - Heike Allgayer
- Department of Experimental Surgery Mannheim/Molecular Oncology of Solid Tumors, DKFZ and University of Heidelberg, 68167 Heidelberg, Germany
| | - José A. Pintor-Toro
- Centro Andaluz de Biología Molecular y Medicina Regenerativa, CABIMER-CSIC, 41092 Sevilla, Spain
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Janicke T, Marie-Orleach L, De Mulder K, Berezikov E, Ladurner P, Vizoso DB, Schärer L. Sex allocation adjustment to mating group size in a simultaneous hermaphrodite. Evolution 2013; 67:3233-42. [PMID: 24152005 DOI: 10.1111/evo.12189] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [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: 02/18/2013] [Accepted: 05/22/2013] [Indexed: 11/29/2022]
Abstract
Sex allocation theory is considered as a touchstone of evolutionary biology, providing some of the best supported examples for Darwinian adaptation. In particular, Hamilton's local mate competition theory has been shown to generate precise predictions for extraordinary sex ratios observed in many separate-sexed organisms. In analogy to local mate competition, Charnov's mating group size model predicts how sex allocation in simultaneous hermaphrodites is affected by the mating group size (i.e., the number of mating partners plus one). Until now, studies have not directly explored the relationship between mating group size and sex allocation, which we here achieve in the simultaneously hermaphroditic flatworm Macrostomum lignano. Using transgenic focal worms with ubiquitous expression of green-fluorescent protein (GFP), we assessed the number of wild-type mating partners carrying GFP+ sperm from these focal worms when raised in different social group sizes. This allowed us to test directly how mating group size was related to the sex allocation of focal worms. We find that the proportion of male investment initially increases with increasing mating group size, but then saturates as predicted by theory. To our knowledge, this is the first direct test of the mating group size model in a simultaneously hermaphroditic animal.
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Affiliation(s)
- Tim Janicke
- Zoological Institute, University of Basel, Switzerland; Centre d'Écologie Fonctionnelle et Évolutive, Montpellier, France.
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Demircan T, Berezikov E. The Hippo pathway regulates stem cells during homeostasis and regeneration of the flatworm Macrostomum lignano. Stem Cells Dev 2013; 22:2174-85. [PMID: 23495768 DOI: 10.1089/scd.2013.0006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The Hippo pathway orchestrates activity of stem cells during development and tissue regeneration and is crucial for controlling organ size. However, roles of the Hippo pathway in highly regenerative organisms, such as flatworms, are unknown. Here we show that knockdown of the Hippo pathway core genes in the flatworm Macrostomum lignano affects tissue homeostasis and causes formation of outgrowths through hyperproliferation of stem cells (neoblasts), and leads to disruption of allometric scaling during regeneration and increased size of regenerated parts. We further show that Yap, the downstream effector of the Hippo pathway, is a potential neoblast marker gene, as it is expressed in dividing cells in M. lignano and is essential for neoblast self-renewal. The phenotypes we observe in M. lignano upon knockdown of the Hippo pathway core genes and Yap are consistent with the known functions of the pathway in other model organisms and demonstrate that the Hippo pathway is functionally conserved between flatworms and mammals. This work establishes M. lignano as a productive model for investigation of the Hippo pathway.
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Affiliation(s)
- Turan Demircan
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Center Utrecht, Utrecht, The Netherlands
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Kaaij LJ, Hoogstrate SW, Berezikov E, Ketting RF. piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles. RNA 2013; 19:345-356. [PMID: 23335638 PMCID: PMC3677245 DOI: 10.1261/rna.036400.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/20/2012] [Indexed: 06/01/2023]
Abstract
Transposable elements (TEs) are mobile genetic elements that can have many deleterious effects on the fitness of their host. The germline-specific PIWI pathway guards the genome against TEs, deriving its specificity from sequence complementarity between PIWI-bound small RNAs (piRNAs) and the TEs. The piRNAs are derived from so-called piRNA clusters. Recent studies have demonstrated that the piRNA repertoire can be adjusted to accommodate recent TE invasions by capturing invading TEs in piRNA loci. Thus far, no information concerning piRNA divergence is available from vertebrates. We present piRNA analyses of two relatively divergent zebrafish strains. We find that significant differences in the piRNA populations have accumulated, most notably among active class I TEs. This divergence can be split into differences in piRNA abundance per element and differences in sense/antisense polarity ratios. In crosses between animals of the different strains, many of these differences are resolved in the progeny. However, some differences remain, often leaning to the maternally contributed piRNA population. These differences can be detected at least two generations later. Our data illustrate, for the first time, the fluidity of piRNA populations in vertebrates and how the established diversity is transmitted to future generations.
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Leptidis S, el Azzouzi H, Lok SI, de Weger R, Olieslagers S, Kisters N, Silva GJ, Heymans S, Cuppen E, Berezikov E, De Windt LJ, da Costa Martins P. A deep sequencing approach to uncover the miRNOME in the human heart. PLoS One 2013; 8:e57800. [PMID: 23460909 PMCID: PMC3583901 DOI: 10.1371/journal.pone.0057800] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 01/29/2013] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs of ∼22 nucleotides in length, and constitute a novel class of gene regulators by imperfect base-pairing to the 3′UTR of protein encoding messenger RNAs. Growing evidence indicates that miRNAs are implicated in several pathological processes in myocardial disease. The past years, we have witnessed several profiling attempts using high-density oligonucleotide array-based approaches to identify the complete miRNA content (miRNOME) in the healthy and diseased mammalian heart. These efforts have demonstrated that the failing heart displays differential expression of several dozens of miRNAs. While the total number of experimentally validated human miRNAs is roughly two thousand, the number of expressed miRNAs in the human myocardium remains elusive. Our objective was to perform an unbiased assay to identify the miRNOME of the human heart, both under physiological and pathophysiological conditions. We used deep sequencing and bioinformatics to annotate and quantify microRNA expression in healthy and diseased human heart (heart failure secondary to hypertrophic or dilated cardiomyopathy). Our results indicate that the human heart expresses >800 miRNAs, the majority of which not being annotated nor described so far and some of which being unique to primate species. Furthermore, >250 miRNAs show differential and etiology-dependent expression in human dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM). The human cardiac miRNOME still possesses a large number of miRNAs that remain virtually unexplored. The current study provides a starting point for a more comprehensive understanding of the role of miRNAs in regulating human heart disease.
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Affiliation(s)
- Stefanos Leptidis
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Hamid el Azzouzi
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Sjoukje I. Lok
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel de Weger
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Serv Olieslagers
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Natasja Kisters
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Gustavo J. Silva
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Stephane Heymans
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands
| | - Eugene Berezikov
- Hubrecht Institute, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands
| | - Leon J. De Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Paula da Costa Martins
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- * E-mail:
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Chiodin M, Børve A, Berezikov E, Ladurner P, Martinez P, Hejnol A. Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads. PLoS One 2013; 8:e55499. [PMID: 23405161 PMCID: PMC3566195 DOI: 10.1371/journal.pone.0055499] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 12/23/2012] [Indexed: 01/23/2023] Open
Abstract
Acoelomorphs are bilaterally symmetric small marine worms that lack a coelom and possess a digestive system with a single opening. Two alternative phylogenetic positions of this group within the animal tree are currently debated. In one view, Acoelomorpha is the sister group to all remaining Bilateria and as such, is a morphologically simple stepping stone in bilaterian evolution. In the other, the group is a lineage within the Deuterostomia, and therefore, has derived a simple morphology from a more complex ancestor. Acoels and the closely related Nemertodermatida and Xenoturbellida, which together form the Acoelomorpha, possess a very limited number of cell types. To further investigate the diversity and origin of mesodermal cell types we describe the expression pattern of 12 orthologs of bilaterian mesodermal markers including Six1/2, Twist, FoxC, GATA4/5/6, in the acoel Isodiametra pulchra. All the genes are expressed in stem cells (neoblasts), gonads, and at least subsets of the acoel musculature. Most are expressed in endomesodermal compartments of I. pulchra developing embryos similar to what has been described in cnidarians. Our molecular evidence indicates a very limited number of mesodermal cell types and suggests an endomesodermal origin of the gonads and the stem cell system. We discuss our results in light of the two prevailing phylogenetic positions of Acoelomorpha.
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Affiliation(s)
- Marta Chiodin
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
| | - Aina Børve
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Peter Ladurner
- Institute of Zoology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Pedro Martinez
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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Abstract
The ability to generate transgenic animals to study gene expression and function is a powerful and important part of the Caenorhabditis elegans genetic toolbox. Transgenic animals can be created by introducing exogenous DNA into the worm germline either by microinjection or by microparticle bombardment (biolistic transformation). In this chapter we describe a simple and robust protocol to generate transgenic C. elegans animals by biolistic transformation with gold particles using the Bio-Rad PDS-1000/He system with Hepta adapter and unc-119 selection marker. We also point out the steps that need special attention to achieve successful transformations.
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Affiliation(s)
- Meltem Isik
- Hubrecht Institute and University Medical Center Utrecht, Utrecht, The Netherlands
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Abstract
MicroRNAs (miRNAs) are ∼22 nucleotide single-stranded RNA molecules that originate from hairpin precursors and regulate gene expression at the posttranscriptional level by basepairing with target messenger RNA and blocking its translation or inducing its degradation. miRNAs play important roles in a variety of biological processes, including development, proliferation, differentiation, cell fate determination, apoptosis, signal transduction, host-viral interactions, and tumorigenesis. Methodological advances in miRNA studies allowed identification of biological roles for many miRNAs, and establishing the spatiotemporal expression patterns of miRNAs is one of the approaches to elucidate their biological functions. Expression pattern analysis of miRNAs helps to identify potential genetic interactors that exhibit similar expression patterns and this, combined with further supporting experiments, helps to identify the genetic pathways in which the specific miRNAs are involved. In this chapter, we describe a detailed protocol for the analysis of miRNA expression patterns in Caenorhabditis elegans.
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Affiliation(s)
- Meltem Isik
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
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48
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Luteijn MJ, van Bergeijk P, Kaaij LJT, Almeida MV, Roovers EF, Berezikov E, Ketting RF. Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans. EMBO J 2012; 31:3422-30. [PMID: 22850670 DOI: 10.1038/emboj.2012.213] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 07/12/2012] [Indexed: 11/09/2022] Open
Abstract
In recent years, the Piwi pathway has been shown to regulate the silencing of mobile genetic elements. However, we know little about how Piwi pathways impose silencing and even less about trans-generational stability of Piwi-induced silencing. We demonstrate that the Caenorhabditis elegans Piwi protein PRG-1 can initiate an extremely stable form of gene silencing on a transgenic, single-copy target. This type of silencing is faithfully maintained over tens of generations in the absence of a functional Piwi pathway. Interestingly, RNAi can also trigger permanent gene silencing of a single-copy transgene and the phenomenon will be collectively referred to as RNA-induced epigenetic silencing (RNAe). RNAe can act in trans and is dependent on endogenous RNAi factors. The involvement of factors known to act in nuclear RNAi and the fact that RNAe is accompanied by repressive chromatin marks indicate that RNAe includes a transcriptional silencing component. Our results demonstrate that, at least in C. elegans, the Piwi pathway can impose a state of gene silencing that borders on 'permanently silent'. Such a property may be more widely conserved among Piwi pathways in different animals.
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Affiliation(s)
- Maartje J Luteijn
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, Utrecht, The Netherlands
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49
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3'-untranslated region (3'-UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected.
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Affiliation(s)
- Anne Dueck
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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van Noort PI, Babae N, Poell JB, Bourajjaj M, Vidic S, van Beijnum JR, van Haastert RJ, Schultz I, de Gunt T, van Hooij O, Verhaegh GW, Gommans WM, Cerisoli F, Verheul M, Schiffelers RM, Griffioen AW, Schalken JA, Berezikov E, Cuppen E, Schaapveld RQJ, Prevost GP. Abstract 1112: Identification of microRNA-based therapeutic candidates using a unique lentiviral microRNA overexpression library. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-1112] [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
microRNA (miRNA) genes transcribed by RNA polymerase II generate small noncoding miRNAs of 18 to 24 nucleotides after maturation process. The mature miRNAs and their associated isomirs specifically bind to different mRNA transcripts, resulting in down regulation of multiple genes within the cell in a highly multiplexed way. miRNA expression profiles differ between human cell types suggesting cell-specific impacts of each miRNA on the regulation of different biological processes. Comparison of miRNA profiles of tumor samples and adjacent normal tissues showed that some miRNAs are up- or down- regulated and suggested their implication during tumor progression. However, such a miRNA profiling approach is not sufficient to identify the respective role of each miRNA gene during the tumorigenesis. Here, to assess the individual role of each miRNA gene and its different isomirs in a specific cell environment, we have constructed a lentiviral miRNA expression library containing more than 1100 human known and novel miRNA precursors. The arrayed layout of our library allowed high-throughput screens with a large spectrum of functional read-outs using either normal or tumor cells. To exemplify this approach, the results of three different screens will be presented; i.e. identification of miRNAs that inhibit the BRAF pathway, miRNAs that inhibit tumor angiogenesis and miRNAs that stimulate the mesenchymal to epithelial transition. In addition, beyond this hit identification step, we will present detailed characterization of the role of the identified miRNAs in tumor progression by means of molecular and cellular functional assays. Combining our unique miRNA expression library with a functional screening platform has allowed the identification and the further characterization of several miRNAs able to significantly impact on tumor behavior supporting the therapeutic interest of some candidates.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1112. doi:1538-7445.AM2012-1112
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Affiliation(s)
| | - Negar Babae
- 2Utrecht Institute for Pharmaceutical Sciences, Utrecht, Netherlands
| | - Jos B. Poell
- 3Hubrecth Institute, Cancer Genomics Center University Medical Center, Utrecht, Netherlands
| | | | | | | | | | | | | | - Onno van Hooij
- 5Deparment of Urology, Radbout University Medical Center, Centre for Molecular Life Sciences, Nijmegen, Netherlands
| | - Gerald W. Verhaegh
- 5Deparment of Urology, Radbout University Medical Center, Centre for Molecular Life Sciences, Nijmegen, Netherlands
| | | | | | | | | | | | - Jack A. Schalken
- 5Deparment of Urology, Radbout University Medical Center, Centre for Molecular Life Sciences, Nijmegen, Netherlands
| | - Eugene Berezikov
- 3Hubrecth Institute, Cancer Genomics Center University Medical Center, Utrecht, Netherlands
| | - Edwin Cuppen
- 3Hubrecth Institute, Cancer Genomics Center University Medical Center, Utrecht, Netherlands
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